Berlin, Germany
Berlin, Germany

The Freie Universität Berlin is a renowned research university located in Berlin and one of the most prominent universities in Germany. It is internationally known for its research in the humanities and social science, as well as in the field of natural and life science. Founded in West Berlin during the early Cold War period and born out of the increasingly Communist-controlled Humboldt University, its name refers to West Berlin's status as part of the free world, as opposed to the Soviet-occupied "unfree" areas surrounding the city.Freie Universität Berlin was one of nine German universities to win in the German Universities Excellence Initiative, a national competition for universities organized by the German federal government. Winning a distinction for five doctoral programs, three interdisciplinary research clusters and its overall institutional strategy as an "International Network University", Freie Universität Berlin is one of the most successful universities in the initiative. Wikipedia.


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Lehmann J.,Cornell University | Rillig M.C.,Free University of Berlin | Thies J.,Cornell University | Masiello C.A.,Rice University | And 2 more authors.
Soil Biology and Biochemistry | Year: 2011

Soil amendment with biochar is evaluated globally as a means to improve soil fertility and to mitigate climate change. However, the effects of biochar on soil biota have received much less attention than its effects on soil chemical properties. A review of the literature reveals a significant number of early studies on biochar-type materials as soil amendments either for managing pathogens, as inoculant carriers or for manipulative experiments to sorb signaling compounds or toxins. However, no studies exist in the soil biology literature that recognize the observed large variations of biochar physico-chemical properties. This shortcoming has hampered insight into mechanisms by which biochar influences soil microorganisms, fauna and plant roots. Additional factors limiting meaningful interpretation of many datasets are the clearly demonstrated sorption properties that interfere with standard extraction procedures for soil microbial biomass or enzyme assays, and the confounding effects of varying amounts of minerals. In most studies, microbial biomass has been found to increase as a result of biochar additions, with significant changes in microbial community composition and enzyme activities that may explain biogeochemical effects of biochar on element cycles, plant pathogens, and crop growth. Yet, very little is known about the mechanisms through which biochar affects microbial abundance and community composition. The effects of biochar on soil fauna are even less understood than its effects on microorganisms, apart from several notable studies on earthworms. It is clear, however, that sorption phenomena, pH and physical properties of biochars such as pore structure, surface area and mineral matter play important roles in determining how different biochars affect soil biota. Observations on microbial dynamics lead to the conclusion of a possible improved resource use due to co-location of various resources in and around biochars. Sorption and thereby inactivation of growth-inhibiting substances likely plays a role for increased abundance of soil biota. No evidence exists so far for direct negative effects of biochars on plant roots. Occasionally observed decreases in abundance of mycorrhizal fungi are likely caused by concomitant increases in nutrient availability, reducing the need for symbionts. In the short term, the release of a variety of organic molecules from fresh biochar may in some cases be responsible for increases or decreases in abundance and activity of soil biota. A road map for future biochar research must include a systematic appreciation of different biochar-types and basic manipulative experiments that unambiguously identify the interactions between biochar and soil biota. © 2011 Elsevier Ltd.


Hassan B.A.,Center for the Biology of Disease | Hiesinger P.R.,Free University of Berlin | Hiesinger P.R.,Charité - Medical University of Berlin
Cell | Year: 2015

Molecular codes, like postal zip codes, are generally considered a robust way to ensure the specificity of neuronal target selection. However, a code capable of unambiguously generating complex neural circuits is difficult to conceive. Here, we re-examine the notion of molecular codes in the light of developmental algorithms. We explore how molecules and mechanisms that have been considered part of a code may alternatively implement simple pattern formation rules sufficient to ensure wiring specificity in neural circuits. This analysis delineates a pattern-based framework for circuit construction that may contribute to our understanding of brain wiring. © 2015 Elsevier Inc.


John V.,Weierstrass Institute for Applied Analysis And Stochastics | John V.,Free University of Berlin | Rang J.,TU Braunschweig
Computer Methods in Applied Mechanics and Engineering | Year: 2010

Adaptive time stepping is an important tool in Computational Fluid Dynamics for controlling the accuracy of simulations and for enhancing their efficiency. This paper presents a systematic study of three classes of implicit and linearly implicit time stepping schemes with adaptive time step control applied to a 2D laminar flow around a cylinder: θ-schemes, diagonal-implicit Runge-Kutta (DIRK) methods and Rosenbrock-Wanner (ROW) methods. The time step is controlled using embedded methods. It is shown that several ROW methods clearly outperform the more standard θ-schemes and the DIRK methods. The results depend on a prescribed tolerance in the time step control algorithm, whose appropriate choice varies from scheme to scheme. © 2009 Elsevier B.V. All rights reserved.


Hass U.,Free University of Berlin | Massmann G.,Carl von Ossietzky University
Water Research | Year: 2012

The occurrence and distribution of six psychoactive compounds (primidone, phenobarbital, oxazepam, diazepam, meprobamate, and pyrithyldione) and a metabolite of primidone (phenylethylmalonamide) were investigated in wastewater treatment plant (WWTP) effluents, surface water, groundwater of a bank filtration site, raw and final drinking water, and in groundwater affected by former sewage irrigation.Primidone and its metabolite phenylethylmalonamide were found to be ubiquitous in environmental water samples in Berlin. Maximum concentrations of 0.87 and 0.42 μg/L, respectively, were encountered in WWTP effluents. Both compounds are apparently not removed when passaging through the different compartments of the water cycle and concentrations are only reduced by dilution. Phenobarbital was present at nearly every stage of the Berlin water cycle with the exception of raw and final drinking water. The highest concentrations of phenobarbital (up to 0.96 μg/L) were measured in groundwater influenced by former sewage irrigation. Oxazepam was only present in WWTP effluents and surface waters (up to 0.18 μg/L), while diazepam was not detected in any matrix. Due to their withdrawal from the German market years ago, the pharmaceuticals meprobamate and pyrithyldione were only found in sewage farm groundwater (up to 0.50 and 0.04 μg/L, respectively) and, in case of meprobamate, also in decade old bank filtrate (0.03 μg/L).Our results indicate a high persistence of some of the investigated compounds in the aquatic system. As a consequence, these pollutants may potentially reach drinking water resources via bank filtration if present in WWTP effluents and/or surface waters in partly closed water cycles such as Berlin's. © 2012 Elsevier Ltd.


Felderer M.,University of Innsbruck | Schieferdecker I.,Free University of Berlin
International Journal on Software Tools for Technology Transfer | Year: 2014

Software testing has often to be done under severe pressure due to limited resources and a challenging time schedule facing the demand to assure the fulfillment of the software requirements. In addition, testing should unveil those software defects that harm the mission-critical functions of the software. Risk-based testing uses risk (re-)assessments to steer all phases of the test process to optimize testing efforts and limit risks of the software-based system. Due to its importance and high practical relevance, several risk-based testing approaches were proposed in academia and industry. This paper presents a taxonomy of risk-based testing providing a framework to understand, categorize, assess, and compare risk-based testing approaches to support their selection and tailoring for specific purposes. The taxonomy is aligned with the consideration of risks in all phases of the test process and consists of the top-level classes risk drivers, risk assessment, and risk-based test process. The taxonomy of risk-based testing has been developed by analyzing the work presented in available publications on risk-based testing. Afterwards, it has been applied to the work on risk-based testing presented in this special section of the International Journal on Software Tools for Technology Transfer. © 2014 Springer-Verlag Berlin Heidelberg.


Briest F.,Medizinische Klinik 1 CBF | Briest F.,Free University of Berlin | Grabowski P.,Medizinische Klinik 1 CBF
Theranostics | Year: 2014

Gastroenteropancreatic neuroendocrine neoplasms are heterogeneous in their clinical behavior and require therapies specially tailored according to staging, grading, origin and expression of peptide receptors. Despite extensive scientific efforts, the therapy options are still not satisfactory. The main reasons are due to the lack of a broad mechanistic knowledge, an insufficient classification of specific diagnostic sub-groups, and predictive markers. GEP-NEN tumors evade early diagnosis because of slow asymptomatic growth behavior and are frequently not detected until metastasized. How signaling networks contribute to tumor progression and how these networks interact remains unclear in large parts. In this review we summarize the knowledge on the growth factor responsive non-angiogenetic pathways in sporadic GEP-NENs, highlight promising mechanistic research approaches, and describe important therapy targets. © Ivyspring International Publisher.


Schroer B.,Free University of Berlin | Schroer B.,Brazilian Center for Research in Physics (CBPF)
Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics | Year: 2015

Recent insights into the conceptual structure of localization in QFT (modular localization) led to clarifications of old unsolved problems. The oldest one is the Einstein-Jordan conundrum which led Jordan in 1925 to the discovery of quantum field theory. This comparison of fluctuations in subsystems of heat bath systems (Einstein) with those resulting from the restriction of the QFT vacuum state to an open subvolume (Jordan) leads to a perfect analogy; the globally pure vacuum state becomes upon local restriction a strongly impure KMS state. This phenomenon of localization-caused thermal behavior as well as the vacuum-polarization clouds at the causal boundary of the localization region places localization in QFT into a sharp contrast with quantum mechanics and justifies the attribute "holstic". In fact it positions the E-J Gedankenexperiment into the same conceptual category as the cosmological constant problem and the Unruh Gedankenexperiment. The holistic structure of QFT resulting from "modular localization" also leads to a revision of the conceptual origin of the crucial crossing property which entered particle theory at the time of the bootstrap S-matrix approach but suffered from incorrect use in the S-matrix settings of the dual model and string theory.The new holistic point of view, which strengthens the autonomous aspect of QFT, also comes with new messages for gauge theory by exposing the clash between Hilbert space structure and localization and presenting alternative solutions based on the use of stringlocal fields in Hilbert space. Among other things this leads to a reformulation of the Englert-Higgs symmetry breaking mechanism. © 2015.


Liu W.,Free University of Berlin | Gust R.,Free University of Berlin | Gust R.,University of Innsbruck
Chemical Society Reviews | Year: 2013

The discovery of cisplatin's antitumor activity in 1969 prompted the search for novel metal-containing complexes as potential anticancer drugs. Among these novel complexes, metal N-heterocyclic carbene (NHC) complexes have recently gained considerable attention because they perfectly fit prerequisites for efficient drug design and fast optimization. Moreover, most of them have shown higher cytotoxicity than cisplatin. This review describes the advances that have been achieved in using transition metal (Ag, Au, Pt, Pd, Cu, Ni, and Ru) complexes containing NHC ligands as antitumor agents. Their modes of action at the cellular lever are further discussed. All these initial achievements clearly demonstrate the great potential of metal-NHC complexes as antitumor agents. © The Royal Society of Chemistry 2013.


John V.,Weierstrass Institute for Applied Analysis And Stochastics | John V.,Free University of Berlin | Novo J.,Autonomous University of Madrid
Journal of Computational Physics | Year: 2012

Finite element and finite difference discretizations for evolutionary convection-diffusion-reaction equations in two and three dimensions are studied which give solutions without or with small under- and overshoots. The studied methods include a linear and a nonlinear FEM-FCT scheme, simple upwinding, an ENO scheme of order 3, and a fifth order WENO scheme. Both finite element methods are combined with the Crank-Nicolson scheme and the finite difference discretizations are coupled with explicit total variation diminishing Runge-Kutta methods. An assessment of the methods with respect to accuracy, size of under- and overshoots, and efficiency is presented, in the situation of a domain which is a tensor product of intervals and of uniform grids in time and space. Some comments to the aspects of adaptivity and more complicated domains are given. The obtained results lead to recommendations concerning the use of the methods. © 2011 Elsevier Inc.


Reimann T.,Free University of Berlin | Reimann T.,Leibniz Institute for Applied Geophysics | Tsukamoto S.,Leibniz Institute for Applied Geophysics
Quaternary Geochronology | Year: 2012

The applicability of the post-IR IRSL single-aliquot regenerative-dose protocol (termed pIRIR protocol) has been tested on K-rich feldspar from recent coastal sediment samples (<500 a) from the southern North Sea coast and southern Baltic Sea coast. The most suitable post-IR IRSL (pIRIR) stimulation temperature is found to be 150 °C by using a preheat temperature of 180 °C. For this pIRIR stimulation temperature, a detectable pIRIR signal is obtained and the residual dose is minimized. Furthermore, anomalous fading is found to be negligible in the pIRIR 150 signal for our young samples whereas the fading rates for the conventional IRSL signal measured at 50 °C (IRSL 50) is between 5 and 7%/decade. However, the pIRIR 150 signal bleaches significantly slower compared to the IRSL 50, according to bleaching experiments using daylight, solar simulator and IR diodes, although the residual doses of both signals are similar. The laboratory residual doses in perfectly bleached aliquots are variable from sample to sample and vary between 300 ± 170 and 800 ± 460 mGy for the pIRIR 150. The precision of the residual dose determination is generally poor and causes large uncertainties on the residual subtracted ages. The laboratory residual doses alone cannot account for the observed overestimation in our two youngest samples (<70 a), indicating that the feldspar signals in these samples were presumably not fully bleached prior to aeolian or beach deposition. However, even if the age uncertainties are large we obtained pIRIR 150 ages in agreement with independent age estimates for the two older samples, which are 70 and 390 years old. © 2012 Elsevier B.V..


Liu Z.,CAS Institute of Physics | Liu Z.,Beijing Computational Science Research Center | Bergholtz E.J.,Free University of Berlin | Fan H.,CAS Institute of Physics | Lauchli A.M.,University of Innsbruck
Physical Review Letters | Year: 2012

Lattice models forming bands with higher Chern number offer an intriguing possibility for new phases of matter with no analogue in continuum Landau levels. Here, we establish the existence of a number of new bulk insulating states at fractional filling in flat bands with a Chern number C=N>1, forming in a recently proposed pyrochlore model with strong spin-orbit coupling. In particular, we find compelling evidence for a series of stable states at ν=1/(2N+1) for fermions as well as bosonic states at ν=1/(N+1). By examining the topological ground state degeneracies and the excitation structure as well as the entanglement spectrum, we conclude that these states are Abelian. We also explicitly demonstrate that these states are nevertheless qualitatively different from conventional quantum Hall (multilayer) states due to the novel properties of the underlying band structure. © 2012 American Physical Society.


Knoll N.,Free University of Berlin
Gerontology | Year: 2015

The study of health behaviors and fostering health-behavior change is an important endeavor even in old age. The aim of this viewpoint article is threefold. First, we use a broad perspective for the definition of health behaviors to capture all relevant aspects of health-behavior change in older adults. Particularly, we suggest a distinction between proximal (e.g., physical activity) and distal health behaviors (e.g., social participation). Second, we recommend a stronger orientation towards processes in order to study health behaviors and the design of health-behavior change interventions. Third, we review the advantages of a developmental perspective in health psychology. Future directions in the study of health behavior among older adults are discussed. © 2015 S. Karger AG, Basel.


Grant
Agency: Cordis | Branch: H2020 | Program: CSA | Phase: INT-02-2014 | Award Amount: 999.75K | Year: 2015

The MERID project (Middle East Research and Innovation Dialogue) proposes a comprehensive action to intensify and encourage research and innovation cooperation between the EU and the Middle East region, directly involving partners from Egypt, Iran, Iraq, Jordan, Lebanon and Palestine, directly involving partners from Egypt, Iran, Iraq, Jordan, Lebanon and Palestine. The project intends to build upon the experience carried out in countries of the region that have already participated in the previous framework programmes, and therefore are at a relatively advanced stage of research cooperation with Europe, like Egypt and Jordan. Attention is paid to calibrating in the most appropriate way the intervention logic of the project, adapting actions to the specific needs of the target countries and their research constituencies. The needs of Iran and Iraq will for sure prove different from those of countries where cooperation with the EU has a proven track record behind. The project is the first attempt to systematise support to the policy dialogue and involvement of research communities of Iran and Iraq in the H2020 programme, as well as an initiative that seeks to give continuity to collaboration frameworks already established between the EU and Middle East countries. The project has high potential to deliver long-lasting impact and structuring effects on cooperation between the EU and the Middle East region. It focuses on enhancing direct cooperation among researchers and on laying or consolidating preconditions, in the region, fostering joint research projects and initiatives with the EU, establishing optimal framework conditions for international cooperation and increasing coordination between policies and programmes. These objectives will be achieved through series of different on-line and in-person activities, among which are meetings of researchers, brokerage events, info-days, training and coaching, webinars and other tools, relevant for this project proposals.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2010.2.3.3-2 | Award Amount: 21.90M | Year: 2010

RNA virus infections kill millions of humans annually, largely due to the lack of suitable vaccines and drugs to control them. This problem is addressed in this FP7 call and in response a consortium of Europes and Asias leading molecular virologists, structural biologists, medicinal chemists and bioinformaticians has been brought together to generate a state-of-the-art drug discovery and design programme. The project aims to identify Small molecule Inhibitor Leads Versus Emerging and neglected RNA viruses (SILVER). It will focus its activities on selected medically important RNA viruses for which the development of drugs is considered essential (Dengue-, entero- and paramyxoviruses), whereas other relatively neglected and/or emerging RNA viruses will be explored to identify the most promising viral protein targets and antiviral compounds. A pipeline strategy has been developed to enable the inclusion in SILVER of viruses at all levels of existing knowledge. Targets for potential drugs include infectious virus, structurally characterised viral enzymes and other proteins. Leads for currently available antiviral drugs have been identified by screening compound libraries in virus-infected cell culture systems and in vitro assays using purified viral enzymes. Selective inhibitors of viral replication have also been (and are being) derived using detailed structural knowledge of viral proteins and structure-based drug design. Hits will be assayed using individual viral protein targets and replicative proteins in complex with viral RNA. The potential protective activity of the most potent inhibitors, that have a favourable (in vitro) ADME-tox profile, will be assessed in relevant infection models in animals. Licenses on promising compounds or compound classes will be presented to the interested pharmaceutical industry. The SILVER consortium will be well placed to play a major role in contributing to the international effort to develop strategies to improve world health.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2009.8.0 | Award Amount: 3.16M | Year: 2010

High dimensional geometric data are ubiquitous in science and engineering, and thus processing and analyzing them is a core task in these disciplines. The Computational Geometric Learning project (CG Learning) aims at extending the success story of geometric algorithms with guarantees, as achieved in the CGAL library and the related EU funded research projects, to spaces of high dimensions. This is not a straightforward task. For many problems, no efficient algorithms exist that compute the exact solution in high dimensions. This behavior is commonly called the curse of dimensionality. We plan to address the curse of dimensionality by focusing on inherent structure in the data like sparsity or low intrinsic dimension, and by resorting to fast approximation algorithms. The following two kinds of approximation guarantee are particularly desirable: first, the solution approximates an objective better if more time and memory resources are employed (algorithmic guarantee), and second, the approximation gets better when the data become more dense and/or more accurate (learning theoretic guarantee). To lay the foundation of a new field---computational geometric learning---we will follow an approach integrating both theoretical and practical developments, the latter in the form of the construction of a high quality software library and application software.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: FCT-10-2014 | Award Amount: 3.93M | Year: 2015

The main objective of the City.Risks project is to increase the perception of security of citizens in cities by activating in a more transparent and sustainable way their participation in communities, through which information and interventions can be provided both to proactively protect citizens from falling victims to criminal activities as well as to reactively provide more timely and effective response and assistance. In order to do so, the City.Risks project will leverage a set of innovative technologies, city infrastructures, and available data sources, but more importantly will aim at making the citizens smart phones the modern tool for increasing their personal and collective sense of security. The project will design and develop an innovative ecosystem of mobile services that will transform the smart phone or the tablet of the citizen into a tool that will collect, visualise and share safety-critical information with the appropriate authorities and communities. The project will rely on a wide spectrum of available technologies to design and implement an interactive framework among authorities and citizens through mobile applications that will allow in a collaboratively way to prevent or mitigate the impact of crime incidents or other security threats. Thus, it will contribute to an increase of the citizens perception of security, which will be measured and validated in real-life scenarios and conditions through the deployment and operation of pilot trials at several selected cities by the project partners. Moreover, to further found its sustainability, the project will devise business models and replication plans of its results that will contribute in the next generation innovative security solutions for the future smart cities.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2007.2.1.4.2. | Award Amount: 4.20M | Year: 2009

Tropical forests harbour thousands of useful plants which are harvested and used in subsistence economies or traded in local, regional or international markets. The effect on the ecosystem is little known, and the forests resilience is badly understod. Palms are the most useful group of plants in tropical American forests and we will study the effect of extraction and trade of palms on forest in the western Amazon, the Andes and the Pacific lowlands. We will determine the size of the resource by making palm community studies in the different forest formations and determine the number of species and individuals of all palm species. The genetic structure of useful palm species will be studied to determine how much harvesting of the species contributes to genetic erosion of its populations, and whether extraction can be made without harm. We then determine how much palms are used for subsistence purposes by carrying out quantitative, ethnobotanical research in different forest types and then we study trade patterns for palm products from local markets to markets which involve export to other countries and continents. Palm populations are managed in various ways from sustainable ones to destructive harvesting; we will study different ways in which palms are managed and propose sustainable methods to local farmers, local governments, NGOs and other interested parties. Finally we will study national level mechanism that governs extraction, trade and commercialization of palm products, to identify positive and negative policies in relation to resilience of ecosystems and use this to propose sustainable policies to the governments. The results will be diseminated in a variety of ways, depending on need and stake holders, from popular leaflets and videos for farmers, reports for policy makers to scientific publication for the research community. The team behind the proposal represents 10 universities and research institutions in Europe and northwestern South America.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: EINFRA-5-2015 | Award Amount: 4.84M | Year: 2015

E-CAM will create, develop and sustain a European infrastructure for computational science applied to simulation and modelling of materials and of biological processes of industrial and societal importance. Building on the already significant network of 15 CECAM centres across Europe and the PRACE initiative, it will create a distributed, sustainable centre for simulation and modelling at and across the atomic, molecular and continuum scales. The ambitious goals of E-CAM will be achieved through three complementary instruments: 1. development, testing, maintenance, and dissemination of robust software modules targeted at end-user needs; 2. advanced training of current and future academic and industrial researchers able to exploit these capabilities; 3. multidisciplinary, coordinated, top-level applied consultancy to industrial end-users (both large multinationals and SMEs). The creation and development of this infrastructure will also impact academic research by creating a training opportunity for over 300 researchers in computational science as applied to their domain expertise. It will also provide a structure for the optimisation and long-term maintenance of important codes and provide a route for their exploitation. Based on the requests from its industrial end-users, E-CAM will deliver new software in a broad field by creating over 200 new, robust software modules. The modules will be written to run with maximum efficiency on hardware with different architectures, available at four PRACE centres and at the Hartree Centre for HPC in Industry. The modules will form the core of a software library (the E-CAM library) that will continue to grow and provide benefit well beyond the funding period of the project. E-CAM has a 60 month duration, involves 48 staff years of effort, has a total budget of 5,836,897 and is requesting funding from the EC of 4,836,897, commensurate with achieving its ambitious goals.


Grant
Agency: Cordis | Branch: H2020 | Program: CSA | Phase: ISSI-1-2015 | Award Amount: 3.44M | Year: 2016

Ensuring the availability of and access to sufficient safe and nutritious food is a key priority that impacts all EU citizens and Horizon 2020 has therefore identified food security as one of the major challenges to be addressed. BGCI, an international network organisation will work with botanic gardens, experienced informal science centres with research expertise in food and food plants, alongside other key organisations to implement the BigPicnic project. This project builds, through the co-creation approach and public debate, public understanding of food security issues and enables adults and young people across Europe and in Africa to debate and articulate their views on Responsible Research and Innovation (RRI) in this field to their peers, scientists and policy makers. The project involves the delivery of low-cost, co-created outreach exhibitions on food security, using the metaphor of a picnic basket; the exhibition will include information, activities and participatory events that engage a broad range of target audiences (adults, schoolchildren and families). Building on audience engagement and data captured from these initial, locally held, exhibitions, the project will run science cafs in publicly accessible and informal engagement areas as well as in botanic gardens, again capturing public views on RRI and food security. The final phase of the project will consolidate the findings of the public engagement to produce two key publications, a report articulating public opinion and recommendations for RRI on food security and a co-creation toolkit that will build capacity for engagement in further science institutions across the EU. A number of case studies on RRI will be provided to support the EU RRI toolkit currently under construction. It is expected that the project evaluation will show organisational learning and change amongst partner institutions. Partners will go on to disseminate training and promotion of RRI for future public engagement.


Grant
Agency: Cordis | Branch: FP7 | Program: BSG-SME | Phase: SME-2012-1 | Award Amount: 1.25M | Year: 2013

With the proliferation of the Internet as the primary medium for data publishing and information exchange, we have seen an explosion in the amount of online content available on the Web. In addition to professionally-produced material being offered free on the Internet, the public has also been allowed and encouraged to make its content available online to everyone. The increasing popularity of open online communities and social-networking sites, image and video sharing portals, discussion boards, and community wikis has meant a dramatic drop in the barrier-to-entry for casual computer users to generate and upload their content on the Web. The volumes of such User-Generated Content (UGC) are already staggering and constantly growing. In the geospatial context, GeoWeb 2.0 is the geographic embodiment of the Web 2.0 moniker for the next generation Web, i.e., the next generation of geographic information publishing, discovery and use. The objective of CROWDIES is nothing less than to provide means for the channeling of the GeoWeb phenomenon towards the specific needs of the SMEs involved in this project. Specifically, the focus of the project will be on (i) smart data mining and fusion mechanism for User-Generated Geocontent, i.e., to tap into the vast amounts of such content existing on the Web and derive meaningful datasets from it, (ii) tools that support the user in the authoring of such data, i.e., based on a specific SME needs, create Web-based geospatial content authoring tools that allow the inclusion of as many users as possible to create content, and (iii) a means to publish such content and provide related services on the Web as well as on mobile devices. The latter case will lead to the creation of live mobile guides, in which users will create the live content shared with a larger community. Overall, GEOSTREAM will provide the participating SMEs with the tools to be able to turn the oncoming geospatial data tsunami into a compelling business advantage.


Grant
Agency: Cordis | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2016 | Award Amount: 3.87M | Year: 2017

Is there a crisis in the legitimacy of the European Union? That research question is timely and important. Investigating it is also an ideal way of training research leaders of tomorrow to rethink our assumptions about the study of legitimate political order. Whilst, however, the financial crisis has raised new questions about the legitimacy of the EU, existing theories of legitimacy crises are largely based on single-state political systems. New theory is, therefore, needed to understand what would count as legitimacy crises in the case of a non-state political system such as the EU. PLATOs (The Post-Crisis Legitimacy of the EU) ESRs will work together as a team to build new theory from 15 investigations into different standards and actors with whom the EU may need to be legitimate. ESRs will go well beyond the state-of-the-art by building a theory of legitimacy crisis in the EU from a uniquely interdisciplinary understanding of how democracy, power, law, economies and societies all fit together with institutions within and beyond the state to affect the legitimacy of contemporary political order. By developing the analytical tools needed to understand a core predicament in which the EU may both need to develop legitimate forms of political power beyond the state and find those forms of power hard to achieve, PLATO will train ESRs with the conceptual clarity needed to define new research questions at the very frontiers of their disciplines and the methodological skills needed to research those questions. They will also be prepared for careers in the non-academic sector (policy-advice, consulting, civil society, European institutions and expert bodies). PLATOs ambitious cross-university, cross-country and cross-sectoral programme of research training, supervision and secondments will pool resources from a unique network of 9 research-intensive universities and 11 non-academic partners who are themselves key users of state-of-the-art social science research.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: SiS-2009-2.2.3.1 | Award Amount: 5.34M | Year: 2010

European authorities and the international scientific community acknowledge the importance of Inquiry-Based Science and Mathematics Education (IBSME) to develop an integrated strategy for scientific literacy and awareness from primary to secondary school, reinforcing scientific careers. Scienceduc and Pollen FP6 projects as well as SINUS-Transfer have successfully implemented IBSME in a large number of European cities. Europe is now facing the urgent need to disseminate such approaches and enable all member States to have access, understand and implement them in a way that fits their own specificities. To go beyond best practices sharing and to provide effective know-how transfer at European level requires a dissemination model based on a systematic approach of IBSME at grassroots level, ensured by intermediary structures with successful experience in local IBSME implementation. The FIBONACCI project defines a dissemination process from 12 Reference Centres to 24 Twin Centres, based on quality and global approach. This will be done through the pairing of the former, selected for their large school-coverage and capacities for transfer of IBSME, with 12 Twin Centres 1 and 12 Twin Centres 2. These will receive training and tutoring for 2 years in order to become in turn Reference Centres and start disseminating. Transversal work between partners is organised through 5 major topics which will be explored through European training sessions and will lead to European guidelines in order to structure a common approach at European level. An external evaluation will be done to check achievement and quality. FIBONACCI will thus lead to the blueprint of a transfer methodology, valid for further Reference centre building in Europe. The project will be coordinated for 36 months by the Superior Normal School (France), with a shared scientific coordination with Bayreuth University. The Consortium will include 24 members over 21 countries, with endorsement from major institutions.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: SC1-PM-21-2016 | Award Amount: 7.58M | Year: 2017

STRENGTHS aims to provide effective community-based health care implementation strategies to scale-up the delivery and uptake of effective mental health interventions in different country contexts. The current refugee crisis across Europe and the Middle East effects both individual refugees psychological well-being, as they face extreme stressors in their flight from their home country, but also has large effects on the healthcare systems of countries housing refugees. In reponse to this crisis, the STRENGTHS project aims to provide a framework for scaling-up the delivery and uptake of effective community-based mental health strategies to address the specific needs of refugees within and outside Europes borders. STRENGTHS will outline necessary steps needed to integrate evidence based low-intensity psychological interventions for common mental disorders into health systems in Syrias surrounding countries taking up the majority of refugees (Turkey, Lebanon and Jordan), a LMIC (Egypt) and European countries (Germany, Switzerland the Netherlands and Sweden). The consortium is a unique partnership between academics, non-governmental organisations (NGOs), international agencies and local partners with the responsibility to provide and scale-up evidence-based mental health and psychosocial support interventions for refugees. Key preparatory steps in the local political, regulatory and governance processes for uptake and scaling-up of the intervention and key contextual and system-related factors for integration will be validated for the real-life impact on the responsiveness of the system. The low-intensity interventions and training materials will be adapted and implemented in Syrian refugees within Syrias surrounding countries taking up the majority of refugees (Turkey, Lebanon and Jordan), a LMIC (Egypt) and European countries (Germany, Switzerland the Netherlands and Sweden). STRENGTHS will disseminate and promote buy-in of a validated framework for large-scale implementation of the low intensity interventions to providers of health and social services, policy makers and funding agencies.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: INT-05-2015 | Award Amount: 2.50M | Year: 2016

The EUNPACK project unpacks EU crisis response mechanisms, with the aim to increase their conflict sensitivity and efficiency. By combining bottomup perspectives with an institutional approach, EUNPACK will increase our understanding of how EU crisis responses function and are received on the ground in crisis areas. This entails exploring local agencies and perceptions in target countries without losing sight of the EUs institutions and their expectations and ambitions. It also entails examining the whole cycle of crisis, from pre-crisis, through crisis, and into post-crisis phase. EUNPACK analyses two gaps in EU crisis response. First, the intentionsimplementation gap, which relates to 1) the capacity to make decisions and respond with one voice and to deploy the necessary resources, 2) how these responses are implemented on the ground by various EU institutions and member states, and 3) how other actors local and international enhance or undermine the EUs activities. Second, the project addresses the gap between the implementation of EU policies and approaches, and how these policies and approaches are received and perceived in target countries, what we refer to as the implementationlocal reception/perceptions gap. Our main hypothesis is that the severity of the two gaps is a decisive factor for the EUs impacts on crisis management and thereby its ability to contribute more effectively to problem-solving on the ground. We analyse these gaps through cases that reflect the variation of EU crisis responses in three concentric areas surrounding the EU: the enlargement area (Kosovo, Serbia), the neighbourhood area (Ukraine, Libya), and the extended neighbourhood (Mali, Iraq, Afghanistan). The results of our research will enable us to present policy recommendations fine-tuned to making the EUs crisis response mechanisms more conflict and context sensitive, and thereby more efficient and sustainable.


Aolita L.,Free University of Berlin | De Melo F.,Brazilian Center for Research in Physics (CBPF) | Davidovich L.,Federal University of Rio de Janeiro
Reports on Progress in Physics | Year: 2015

One of the greatest challenges in the fields of quantum information processing and quantum technologies is the detailed coherent control over each and every constituent of quantum systems with an ever increasing number of particles. Within this endeavor, harnessing of many-body entanglement against the detrimental effects of the environment is a major pressing issue. Besides being an important concept from a fundamental standpoint, entanglement has been recognized as a crucial resource for quantum speed-ups or performance enhancements over classical methods. Understanding and controlling many-body entanglement in open systems may have strong implications in quantum computing, quantum simulations of many-body systems, secure quantum communication or cryptography, quantum metrology, our understanding of the quantum-to-classical transition, and other important questions of quantum foundations. In this paper we present an overview of recent theoretical and experimental efforts to underpin the dynamics of entanglement under the influence of noise. Entanglement is thus taken as a dynamic quantity on its own, and we survey how it evolves due to the unavoidable interaction of the entangled system with its surroundings. We analyze several scenarios, corresponding to different families of states and environments, which render a very rich diversity of dynamical behaviors. In contrast to single-particle quantities, like populations and coherences, which typically vanish only asymptotically in time, entanglement may disappear at a finite time. In addition, important classes of entanglement display an exponential decay with the number of particles when subject to local noise, which poses yet another threat to the already-challenging scaling of quantum technologies. Other classes, however, turn out to be extremely robust against local noise. Theoretical results and recent experiments regarding the difference between local and global decoherence are summarized. Control and robustness-enhancement techniques, scaling laws, statistical and geometrical aspects of multipartite-entanglement decay are also reviewed; all in order to give a broad picture of entanglement dynamics in open quantum systems addressed to both theorists and experimentalists inside and outside the field of quantum information. © 2015 IOP Publishing Ltd.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: ENV.2013.6.5-4 | Award Amount: 1.13M | Year: 2013

This coordinating action will focus on climate action, resource efficiency and raw materials issues and will aim to enhance collaboration between researchers in the EU and the ASEAN region . Addressing these issues in a coherent way is vital for sustainable development that leads to economic prosperity, social cohesion and environmental integrity. Both regions have developed innovative ideas to reduce greenhouse gas emissions, to adapt to climate change, improve resource efficiency and manage raw materials. SUSTAIN EU-ASEAN will draw primarily on EU funded projects focusing on these issues from various programmes, such as the FP7, SWITCH-Asia, International cooperation and others and will also feed in experiences from the ASEAN region and bilateral projects into the mutual learning process. The approach taken by project is driven primarily by the assumption that a wealth of knowledge has been generated by EU-funded projects and other initiatives relevant for the ASEAN region. However, the exploitation and uptake of these research results and potential joint innovations can still be improved and so can the collaboration between researchers from the EU and the ASEAN region. To facilitate this, but also to advance research initiated by Europe, SUSTAIN EU-ASEAN will: - Identify and cluster EU-funded projects on climate action, resource efficiency and raw materials issues relevant for the ASEAN region, analyse thematic gaps and funding and cooperation opportunities (WP1); - Provide a number of services, such as project twinning, access to mobility funds, showcasing and training to interested projects and institutions which aim to enhanced cooperation with ASEAN counterparts, initiate pilot Actions to enhance uptake and implementation as show cases for EU-ASEAN cooperation (WP2); - Facilitate vision building and the development of concrete proposals for more sustainable collaboration (WP3).


Grant
Agency: Cordis | Branch: FP7 | Program: CP-TP | Phase: KBBE.2011.1.3-04 | Award Amount: 3.91M | Year: 2012

Infections with parasitic worms (nematodes and trematodes) represent a significant economic and welfare burden to the European ruminant livestock industry. The increasing prevalence of anthelmintic resistance means that current control programmes are costly and unsustainable in the long term. Recent changes in the epidemiology, seasonality and geographic distribution of helminth infections have been attributed to climate change. However, other changes in environment (e.g. land use) and in livestock farming, such as intensification and altered management practices, will also have an impact on helminth infections. Sustainable control of helminth infections in a changing world requires detailed knowledge of these interactions. GLOWORM will devise new, sustainable strategies for the effective control of ruminant helminthoses in the face of global change. We will: (1) optimise diagnosis, by developing novel, high-throughput diagnostic tests for mixed helminth infections, sub-clinical infections and anthelmintic resistance, (2) map, monitor and predict the impact of global change on parasite epidemiology, leading to spatial risk maps and improved forecasting of disease, (3) produce predictive models to identify optimal future intervention strategies, (4) identify and mitigate the economic impacts of infections and (5) involve end-users in the production and dissemination of detailed advice for effective worm control. We will work together to develop a panel of innovative technologies and models to monitor and predict changing patterns of infection and disease, optimise the use of anthelmintics to limit the development and spread of drug resistance, and reduce the overall economic impact of helminth infections. GLOWORM will contribute to the continued productivity and profitability of European livestock farming by delivering new tools, strategies and recommendations for the monitoring, surveillance, and sustainable control of helminth infections in grazing livestock.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP-SICA | Phase: SiS-2009-2.2.3.2 | Award Amount: 1.23M | Year: 2009

KidsINNscience will identify and promote innovative approaches for teaching and learning science, adapt and test them for implementation in mainstream schools and develop innovation strategies in all participating countries. The consortium proposes a collaborative project (specific international cooperation action (SICA)) for experts who work with and on new methods for science education. The overall objective of the project is to develop adaptive strategies to facilitate the innovation of science education in formal and informal settings. Strategies for innovating curricula and strategies for teaching and learning in science and technology will be analysed and compared among 8 different countries in Europe and 2 in Latin America. The role of gender and cultural diversity will explicitly be taken into account in all phases of the project. KidsINNscience proposes to adopt an adaptive strategy that enables participating countries to learn from each other and develop feasible innovation plans that fit the specific conditions of each of the countries. The project will deliver a long list of innovations from all participating countries, carry out effective pilots to contribute to a solid evidence base and formulate a set of criteria for innovation of teaching and learning of science. KidsINNscience will also make use of non-European educational settings in Brazil and Mexico in order to find new methods and strategies for science education to be adapted and used in all participating countries. The KidsINNscience consortium unites experienced partners from: -Universities and research institutions, who have been working on new methods in science education for many years (LSBU, RM3, IJS, UFRJ) -Research partners who are specified on innovative didactic models and new learning arrangements (UZH, FUB, SLO, AIE, USC, CINVESTAV ) The consortium reflects all required competencies to perform the proposed parts of KidsINNscience with the desired quality and expertise.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2012-IRSES | Award Amount: 222.10K | Year: 2012

The exchange concerns the social, cultural, media-analytical and educational-psychological dimensions of digital media practices with a focus on the devices that are used for capturing, editing and circulating video data. DIGIT-M-ED applies inter-disciplinary perspectives and knowledge to analyse how the use of digital technologies is shaped by and shapes todays global youth. Solid research synergies between German and Indian traditions of anthropological and sociological youth research, British scholarship in media analysis, Greek and Brazilian educational and youth research and Russian learning theories will be constructed more fully and creatively. Moreover, the methodological contribution of the project is very important. DIGIT-M-ED aims to develop an innovative methodology for the interdisciplinary and comparative/cross-cultural study of emerging digital media and technological practices and constellations with special attention to the voices and perspectives of the young people involved in the research. Existing theoretical and methodological tools from 1) post-Vygotskian psychology and learning theory 2) multimodal analysis and 3) anthropological theoretical and research traditions will be tested and further developed. A small-scale inquiry with young people in the age of 16-21 years who live in marginalized urban milieus in Athens, New Delhi and So Paulo is planed with the aim of designing large-scale research in the near future. Further activities such as workshops, collaborative teaching and joint publications and presentations will expand and intensify existing research partnerships. DIGIT-M-ED will thus facilitate the development of a productive and sustainable international research network that will investigate how digital media and technologies transform the everyday lives and affect the development of young people in North and South Europe, Brazil, Russia and India in the years to come.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2012.2.4-05 | Award Amount: 1.21M | Year: 2012

While there are many European scientific activities for each of the items related to either animal health or the occurrence of GM ingredients in animal feed, the proposed MARLON project will be unique in bringing these widely different fields of scientific expertise together for the cross-disciplinary task of developing an epidemiological model for the case-specific monitoring of potential health impacts of GM animal feeds in livestock. More specifically, the proposed MARLON project will create an inventory of which epidemiological and monitoring initiatives exist, both within and outside the EU, which could provide useful data for the purpose of monitoring for health impacts of animal feeds, in particular those containing GM ingredients, on livestock animals. It will also collate, in a systematized manner, information on the factors that have to be considered when developing an epidemiological model specifically geared towards this purpose. These factors include 1) the possibility to determine the exposure of animals to GM feed ingredients, 2) the health indicators that have to be considered for particular cases of health impacts identified during pre-market risk assessment of the GMOs, 3) the characteristics of the animal feed and livestock production chains. The project also will develop an epidemiological model specifically geared towards establishing links between measured health effects in livestock and their intake of GM ingredients from animal feed. As previously stated, there are many activities in the EU focusing on the specific items that together constitute the cross-disciplinary research within the proposed MARLON project, but so far none of them has done this in its totality for the specific purpose of linking health impacts in livestock to GM feed consumption. The proposed MARLON project is to take stock of these initiatives and assess the applicability of the data collected and/or generated by them for the purpose of case-specific monitoring.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2009-1.2-5 | Award Amount: 6.87M | Year: 2009

LIVIMODE aims to develop specific tools for non invasive in vivo imaging of disease related molecular events. Such tools are of high relevance for disease detection, staging, developing animal models of human disease, and evaluating novel therapies. We propose to use optical imaging, which is optimally suited for this task as it provides excellent sensitivity and allows visualizing molecular events via a fluorescent signal. While optical imaging technology has rapidly evolved over the last years, the availability of SMART (activatable) imaging agents that change their fluorescence properties upon disease related events, remains a critical gap. The LIVIMODE project proposes to combine expertises in medicinal chemistry, pharmacology and imaging in a conceptually new approach in designing SMART agents. In particular, we will (i) translate established strategies in medicinal/pharmaceutical chemistry to design highly selective SMART probes and (ii) optimize the cell/tissue specificity of probes integrating concepts from polymer and protein based targeted drug delivery. We will generate a toolset of highly selective targeted SMART probes for at least 10 disease-relevant proteases. The selection of target proteases is based on their relevance in disease processes that cannot yet be monitored with non invasive technology. These include (i) the development of tumor microenvironment as a critical factor in oncogenesis, (ii) tumor hypoxia and angiogenesis, and (iii) inflammatory and degenerative processes in osteoarthritis. LIVIMODE has established animal models for these conditions and will use in vivo optical imaging to evaluate the novel SMART probes as tools for monitoring disease progression and drug efficacy. This will enhance our knowledge of disease mechanisms and our ability to rapidly characterize drug candidates for in vivo efficacy (proof-of-efficacy). Selected SMART probes will be optimized to assess their potential as clinical diagnostics.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: REV-INEQUAL-06-2016 | Award Amount: 5.00M | Year: 2017

ISOTIS addresses the nature, causes and impact of early emerging social and educational inequalities in the context of socioeconomic, cultural and institutional processes. The aim is to contribute to effective policy and practice development to combat inequalities. Quasi-panels and pooled longitudinal datasets will be used to examine the variation in early educational gaps and developmental trajectories across countries, systems and time. To disentangle the complex interactions between characteristics of systems and target groups, ISOTIS will study significant immigrant, indigenous ethnic-cultural and low-income native groups, associated with persistent educational disadvantages. ISOTIS will examine current resources, experiences, aspirations, needs and well-being of children and parents in these groups in the context of acculturation and integration, and in relation to local and national policies. ISOTIS aims to contribute to effective policy and practice development by generating recommendations and concrete tools for (1) supporting disadvantaged families and communities in using their own cultural and linguistic resources to create safe and stimulating home environments for their children; for (2) creating effective and inclusive pedagogies in early childhood education and care centres and primary schools; for (3) professionalization of staff, centres and schools to improve quality and inclusiveness; for (4) establishing inter-agency coordination of support services to children and families; and for (5) developing policies to combat educational inequalities. ISOTIS will develop inter-linked programmes for parents, classrooms and professionals using Virtual Learning Environments for working in linguistically diverse contexts. All this work together is expected to support the education practice and policy field in Europe in meeting the challenges of reducing social and educational inequalities.


Grant
Agency: Cordis | Branch: FP7 | Program: CPCSA | Phase: INFRA-2011-1.2.1. | Award Amount: 6.01M | Year: 2011

Biodiversity Virtual e-Laboratory (BioVeL) meets the needs of Europes Biodiversity Science research community with tools for pipelining data and analysis into efficient workflows, urgently needed to understand biodiversity in a rapidly changing environment. BioVeL customises, deploys and supports the Taverna / myExperiment / BioCatalogue family of software to achieve this.Close user involvement is crucial to successful design and implementation of virtual laboratories. Close support and guidance makes all the difference in uptake of tools and their continued success. BioVeL places particular emphasis on targeted networking activities with specific sub-communities and tailored service activities that deliver training, helpdesk and consultancy assistance to solve specific problems.Using agile processes, BioVeL defines and deploys (web) service sets and workflow packs catering for sub-communities within the domain. The project focuses on pilot topic areas:i) DNA sequence-based phylogeny and metagenomics services that help link knowledge of model organisms to a broad range of species, that provide a measure of genetic diversity used in conservation planning and that help to understand adaptation in relation to climate change;ii) Taxonomy services to provide the underpinning checklist of diversity in Europe, identification aids to native, invasive and economic species;iii) Niche and population modelling for species, to better understand the processes of conservation and invasive species management; and,iv) Ecosystem functionality and valuation services, to improve modelling capabilities to ecosystem services and CO2 sequestration.Through use of gateways, workflows composed in the BioVeL environment can be executed on a wide range of computing resources, including European e-Infrastructures (EGI, PRACE, etc.).Joint research activities will investigate improvements to ease of use of workflows by exploring new middleware approaches to easier user interfaces.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: KBBE-2009-2-1-02 | Award Amount: 3.80M | Year: 2010

FoodRisC will characterise key configurations of food risk/benefit relationships and the consequent implications for risk communicators, make recommendations about the unique potential of new social media (e.g. social networks and blogging) and provide a systematic understanding of how consumers deal with food risk/benefit information. The FoodRisC consortium is comprised of experts in key fields relevant to food risk/benefit communication from research institutes, consumer organisations and SMEs in ten Member States. This consortium is supported by an Advisory Board of representatives from seven organisations of world renown in food risk/benefit communication (including EFSA, WHO and Google).The project will identify the barriers to communicating to consumers across Europe and identify key socio-psychological and socio-demographic characteristics, including gender, that affect food risk/benefit perceptions and processes as well as consumer preferences for communication channels. These objectives will be achieved through a range of research approaches and methods and by extending the theoretical basis of how people acquire and use information in food domains. The impact of the project will be at a European level and will be facilitated through the development of the FoodRisC toolkit together with practical guidance to enable the effective communication of coherent messages across the Member States. Use of the toolkit and guides will assist policy makers, food authorities and other end users in developing common approaches to communicating coherent messages to consumers in Europe. The effective spread of food risk/benefit information will assist initiatives aimed at reducing the burden of food-related illness and disease, reducing the economic impact of food crises and ensuring that confidence in safe and nutritious food is fostered and maintained in Europe.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2010.2.6-01 | Award Amount: 1.17M | Year: 2011

The proposed Coordination and support actions (Coordinating, CSA) has the overall objective to disseminate state-of-the-art research results in food safety and quality topics through a series of symposia, expert working group meetings, an online platform with best practise examples and coordination of cooperation and a plan for the preparation of future activities. In addition to the aim of disseminating research results of finalised and current EC funded projects from FP6 and FP7 and other projects focusing on food safety, the consortium will develop strategies and recommendations for European policies (e.g.: food, consumers, research, health, agriculture). The secure handling of food has main impact onto the safety of food products and the European consumers. Furthermore, detailed plans and actions to foster food safety research in Europe are part of the workplan and objectives. The CSA action will pave the way for highly innovative research projects in the field of food safety. FOODSEG will connect research and policy actors in the enlarged European Union and the Candidate countries, in order to fill transitional gaps and achieve a broader network and deeper collaboration between them. The following map gives an overview of the FOODSEG consortium and the very broad network which covers nearly all regions of the enlarged European Union, Candidate countries and also third countries.


CosmoPHOS-nano is a multidisciplinary, translational and business-oriented project, aiming to accomplish the following objectives: 1) develop the CosmoPHOS system, which is a novel theranostic (diagnostic & therapeutic) nanotechnology-enabled portable combination system enabling endovascular in vivo near-infrared fluorescence molecular imaging, endovascular near-infrared targeted photodynamic therapy, real-time & follow-up therapy monitoring of atherosclerotic coronary artery disease (CAD), 2) nonclinically evaluate this system, 3) clinically validate the system after regulatory approval, & 4) reduce in the long-term CAD deaths and morbidity by up to 40%, resulting in a significant decrease of the European and global healthcare costs for CAD, increasing the income of the European healthcare industry from CAD market which is the global largest. The CosmoPHOS-nano consortium has a five year history of successful collaboration between the industrial and academic partners, and its funding would underpin a team devoted to delivering a novel powerful & affordable healthcare solution against the leading cause of death, without the need for heavy and expensive medical equipment. The CosmoPHOS system consists of two interacting components: a) targeted theranostic near-infrared photoactivatable biocompatible nanomedicines, and b) medical devices. After systemic administration, the nanomedicines targeted accumulate in coronary atherosclerotic plaques, followed by endocoronary photoactivation and detection by the medical devices, enabling molecular imaging, targeted therapy, real-time & follow-up therapy monitoring of CAD. Preliminary in vitro & in vivo successful experimental results, as well as parts of the CosmoPHOS system are already available from the prior five year collaboration. The project plan includes: A) nonclinical R&D (30 months); B) nonclinical validation & regulatory approval (18 months); C) first-in-man phase-I clinical trial in 20 CAD patients (12 months).


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENERGY-2007-3.5-01 | Award Amount: 5.53M | Year: 2008

SOLAR-H2 brings together 12 world-leading European laboratories to carry out integrated, basic research aimed at achieving renewable hydrogen (H2) production from environmentally safe resources. The vision is to develop novel routes for the production of a Solar-fuel, in our case H2, from the very abundant, effectively inexhaustible resources, solar energy and water. Our multidisciplinary expertise spans from molecular biology, biotechnology, via biochemistry and biophysics to organo-metallic and physical chemistry. The project integrates two frontline research topics: artificial photosynthesis in man-made biomimetic systems, and photobiological H2 production in living organisms. H2 production by these methods on a relevant scale is still distant but has a vast potential and is of utmost importance for the future European economy. The scientific risk is high - the research is very demanding. Thus, our overall objective now, is to explore, integrate and provide the basic science necessary to develop these novel routes and advance them toward new horizons. Along the first track, the knowledge gained from biochemical/biophysical studies of efficient enzymes will be exploited by organometallic chemists to design and synthesize bio-mimetic compounds for artificial photosynthesis. The design of these molecules is based on molecular knowledge about how natural photosynthesis works and how hydrogenase enzymes form H2. Along the second track, we perform research and development on the genetic level to increase our understanding of critical H2 forming reactions in photosynthetic alga and cyanobacteria. These studies are directly aimed at the improvement of the H2 producing capability of the organisms using novel genetic and metabolic engineering. The project also involves research aimed at demonstrating the concept of photobiological H2 production in photobioreactors.


The CREDITS4HEALTH projects main goal is to develop a person centric approach based on the credits for health concept to reduce sedentary behavior and enhance the level of physical activity and healthy dietary styles in people living in Euro-Mediterranean Countries. The concept of credits is simple and effective: this means that each participant will earn credits from his local, regional or national Health Authority on the basis of his/her participation and involvement in the achievement of an healthy life-style, and his/her attitude to sponsor this philosophy in his community. The CREDITS4HEALTH vision is therefore to have people directly acting for their health and well being, operating on three fundamental levers to enhance the quality of their lives, through the reduction of sedentary behavior, the active participation to the social life and the adoption of an healthier diet. The CREDITS4HEALTH approach is virtuous and straightforward: 1)First, we will define personalised algorithms containing dietary and physical activity prescriptions, taking into account the medical, psychological, social, and economic background of each person; 2) Once screened by the local Credits4Health Committee, the participant receives an electronic card, which enables him to track his compliance to the regime through a dedicated web based platform; 3)With his electronic card, the participant also gets access to a full range of suppliers which offer him goods for fulfilling his health-related objectives;4)Suppliers must be certified by the local authority, according to a specified set of requirements and they must certify the products they intend to commercialise for this initiative;5)Participants gain credits as far as they comply with their daily, weekly and monthly goals; they are also subject to a six monthly mandatory assessment performed by the Credits4Health Committee, in which the algorithm can be modified and fine-tuned to the needs of the participant.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: SiS-2010-2.2.1.1 | Award Amount: 3.84M | Year: 2010

The PROFILES project promotes IBSE through raising the self-efficacy of science teachers and in so doing aiding a better understanding of the changing purpose of teaching science in schools and the value of stakeholder networking. The proposal innovation is in utilizing science teaching materials to support teachers, through an inspired, longitudinal training programme reflecting stakeholder views and needs, while simultaneously promoting a reflective IBSE school-based, training related, intervention to promote learning through creative, scientific problem solving and/or socio-scientific decision making procedures. The measures of success are through a) determining the self efficacy of science teachers in teaching innovative science education approaches allowing student acquisition of life skill competencies and b) in the attitudes of students toward this more context-led, student centered, IBSE-emphasised learning. Dissemination of approaches, reactions, and reflections form a further key project target. Initially PROFILES involves the development of science teachers on four fronts (teacher as learner, as teacher, as reflective practitioner and as leader) consolidating their ownership of the context-led approach and incorporating use-inspired research, evaluative methods and stakeholder networking. The project enhances its dissemination approaches with lead teachers spearheading training of further teachers at pre- and in-service levels and initiating workshops for key stakeholders nationwide. The project focuses on the secondary level so that open inquiry approaches are a major teaching target. PROFILE pays much attention to student motivation for the learning of science both in terms of intrinsic motivation (relevance, meaningful, as considered by the students) and extrinsic motivation (teacher encouragement and reinforcement) and attempts to make school science teaching more meaningful by paying attention to cultural differences, esp. at the gender level


Grant
Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: KBBE.2012.3.5-04 | Award Amount: 7.76M | Year: 2012

The project GRACE will a) elaborate and sustainably implement a transparent framework for the review of GMOs or GM food and feed effects on environment, socio-economics and health and b) reconsider the design, execution and interpretation of results of animal feeding trials as well as in vitro studies for assessing the safety of GM food and feed. The framework will create high quality reviewing processes for different fields of GMO impact assessment and address the need for a well documented, transparent and sustainable representation of these reviewing processes. This will provide valuable and accessible information addressing the main issues associated with GMOs and enabling risk assessors, managers, scientists and the general public to reiterate and update their evaluations and conclusions on GMOs. It will adapt recently elaborated methodologies for (systematic) reviewing of the risk assessment information of GMOs and derived food and feed. The quality assessment for all reviewed papers and studies as well as the reviews conducted by the consortium, will be referenced by an open access database and one-stop-shop for data and information relevant to GMO risk assessment. Animal feeding trials and in vitro studies will clarify and compare the scientific added value of 90day feeding trials with whole foods with advanced state-of-the-art analytical, in vitro and in-silico tools. Suitable animal GMO-feeding models will be investigated, that are based on European (EFSA) and international guidance, and the project will provide guidance for relevant, alternative in vitro cell-based approaches for specific topics within the overall food and feed safety assessment. Available standard or scientifically approved protocols form the basis of the investigations also in the case of the analytical, in-vitro and second in-silico approaches. GRACE will provide guidance for the use and improvement of existing and suggested assessment tools in the field of food and feed safety.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ENV.2013.6.1-2 | Award Amount: 11.32M | Year: 2013

StratoClim will produce more reliable projections of climate change and stratospheric ozone by a better understanding and improved representation of key processes in the Upper Troposphere and Stratosphere (UTS). This will be achieved by an integrated approach bridging observations from dedicated field activities, process modelling on all scales, and global modelling with a suite of chemistry climate models (CCMs) and Earth system models (ESMs). At present, complex interactions and feedbacks are inadequately represented in global models with respect to natural and anthropogenic emissions of greenhouse gases, aerosol precursors and other important trace gases, the atmospheric dynamics affecting transport into and through the UTS, and chemical and microphysical processes governing the chemistry and the radiative properties of the UTS. StratoClim will (a) improve the understanding of the microphysical, chemical and dynamical processes that determine the composition of the UTS, such as the formation, loss and redistribution of aerosol, ozone and water vapour, and how these processes will be affected by climate change; (b) implement these processes and fully include the interactive feedback from UTS ozone and aerosol on surface climate in CCMs and ESMs. Through StratoClim new measurements will be obtained in key regions: (1) in a tropical campaign with a high altitude research aircraft carrying an innovative and comprehensive payload, (2) by a new tropical station for unprecedented ground and sonde measurements, and (3) through newly developed satellite data products. The improved climate models will be used to make more robust and accurate predictions of surface climate and stratospheric ozone, both with a view to the protection of life on Earth. Socioeconomic implications will be assessed and policy relevant information will be communicated to policy makers and the public through a dedicated office for communication, stakeholder contact and international co-operation.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA | Phase: INFRA-2007-3.0-03 | Award Amount: 4.06M | Year: 2008

PESI provides standardised and authoritative taxonomic information by integrating and securing Europes taxonomically authoritative species name registers and nomenclators (name databases) that underpin the management of biodiversity in Europe.\nPESI defines and coordinates strategies to enhance the quality and reliability of European biodiversity information by integrating the infrastructural components of four major community networks on taxonomic indexing into a joint work programme. This will result in functional knowledge networks of taxonomic experts and regional focal points, which will collaborate on the establishment of standardised and authoritative taxonomic (meta-) data. In addition PESI will coordinate the integration and synchronisation of the European taxonomic information systems into a joint e-infrastructure and the set up of a common user-interface disseminating the pan-European checklists and associated user-services results\nThe organisation of national and regional focal point networks as projected not only assures the efficient access to local expertise, but is also important for the synergistic promotion of taxonomic standards throughout Europe, for instance to liaison with national governmental bodies on the implementation of European biodiversity legislations. In addition PESI will start with the geographic expansion of the European expertise networks to eventually cover the entire Palaearctic biogeographic region.\nPESI supports international efforts on the development of a Global Names Architecture by building a common intelligent name-matching device in consultation with the principal initiatives (GBIF, TDWG, EoL, SpeciesBase). PESI contributes the development of a unified cross-reference system and provides of high quality taxonomic standards. PESI will further involve the Europe-based nomenclatural services and link the planned joint European taxonomic e-infrastructures middle-layer to the global e-gateway.


Grant
Agency: Cordis | Branch: FP7 | Program: CPCSA | Phase: INFRA-2010-1.2.3 | Award Amount: 6.26M | Year: 2010

Biodiversity science brings information science and technologies to bear on the data and information generated by the study of organisms, their genes, and their interactions. ViBRANT will help focus the collective output of biodiversity science, making it more transparent, accountable, and accessible. Mobilising these data will address global environmental challenges, contribute to sustainable development, and promote the conservation of biological diversity. Through a platform of web based informatics tools and services we have built a successful data-publishing framework (Scratchpads) that allows distributed groups of scientists to create their own virtual research communities supporting biodiversity science. The infrastructure is highly user-oriented, focusing on the needs of research networks through a flexible and scalable system architecture, offering adaptable user interfaces for the development of various services. In just 28 months the Scratchpads have been adopted by over 120 communities in more than 60 countries, embracing over 1,500 users. ViBRANT will distribute the management, hardware infrastructure and software development of this system and connect with the broader landscape of biodiversity initiatives including PESI, Biodiversity Heritage Library (Europe), GBIF and EoL. The system will also inform the design of the LifeWatch Service Centre and is aligned with the ELIXIR and EMBRC objectives, all part of the ESFRI roadmap. ViBRANT will extend the userbase, reaching out to new multidisciplinary communities including citizen scientists by offering an enhanced suite of services and functionality.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2011.9.9 | Award Amount: 11.78M | Year: 2013

The overarching goal of our project is to develop systems based on direct and deterministic interactions between individual quantum entities, which by involving large-scale entanglement can outperform classical systems in a series of relevant applications.\nWe plan to achieve that by improving technologies from atomic, molecular and optical physics as well as from solid-state physics, and by developing new ones, including combinations across those different domains. We will explore a wide range of experimental platforms as enabling technologies: from cold collisions or Rydberg blockade in neutral atoms to electrostatic or spin interactions in charged systems like trapped ions and quantum dots; from photon-phonon interactions in nano-mechanics to photon-photon interactions in cavity quantum electrodynamics and to spin-photon interactions in diamond color centers.\nWe will work on two deeply interconnected lines to build experimentally working implementations of quantum simulators and of quantum interfaces. This will enable us to conceive and realize applications exploiting those devices for simulating important problems in other fields of physics, as well as for carrying out protocols outperforming classical communication and measurement systems.


News Article | November 28, 2016
Site: www.eurekalert.org

Wouldn't it be great if we could tell the state of an ecosystem or the like - whether it's healthy or heading for a crisis - by keeping track of just a few key signals? Thanks to the theory of 'tipping points', that's not unthinkable. Now a team of researchers led by Alena Gsell of the Netherlands Institute of Ecology (NIOO-KNAW) has tested early warning signals: in lakes. In the Early Edition of PNAS online, they conclude that predicting works but not in all cases yet. The term 'tipping point' has become popular to describe sudden and fundamental changes that take place even though exterior conditions haven't changed as radically. Think of a financial crisis. Think of a wall that will fall down - like the Berlin Wall - or one that will end up being built somewhere else just as suddenly. And what's true for human society is also true for ecosystems: in shallow lakes, clear, limpid water may suddenly turn into smelly green soup. Once such a 'regime shift' has occurred, it's difficult or even impossible to get things back to the way they were. But that doesn't mean there are no alarm signals. There is in fact a whole range of statistical indicators that have been proposed as possible early warnings. An international team led by NIOO-researcher Alena Gsell - formerly of the Leibniz Institute of Freshwater Ecology and Inland Fisheries in Berlin - has now for the first time tested the potential of four of these indicators to be applied to a wide range of lakes. "We've looked at five lakes for which long-term monitoring data (16-34 years) is available", explains Alena Gsell. One of them is the Veluwemeer in the Netherlands, another Lake Washington in the United States. The good news is that in some cases, early-warning indicators were indeed detected up to several years ahead of the moment when a 'regime shift' would take place. "That leaves some time for water managers to step in and take appropriate measures." These indicators show that the resilience of lake ecosystems becomes less ahead of a regime shift. "It's something you can observe if you know an ecosystem well", says Gsell. Perturbations become bigger: water turns turbid temporarily, smaller zooplankton species are favoured and edible green algae lose ground to the less tasty bluegreens. But on the whole, the team's tests produced many negative results as well. According to Gsell, this mixed outcome shows that the early warning indicators do hold promise as a method, but are not yet as suitable for general application as had been hoped by many. For the early alarm signals to be more effective, argue the researchers, collecting long term data - an essential "window into the past" - isn't the only thing that's important. The methods for mining the data also need to become more advanced. More frequent data collection would help: per day or even hour, instead of per week or less. "If you look at the current state of the environment, investing in the adaptation of indicator methods would definitely be an effort well spent." The NIOO counts more than 300 staff members and students and is one of the largest research institutes of the Royal Netherlands Academy of Arts and Sciences (KNAW). The institute specialises in water and land ecology. Since 2011, the institute is located in an innovative and sustainable research building located in Wageningen, the Netherlands. The institute has an impressive research history stretching back 60 years and which spans the entire country and beyond its borders. Article: Evaluating early-warning indicators of critical transitions in natural aquatic ecosystems, Alena Sonia Gsell, Ulrike Scharfenberger, Deniz Özkundakci, Annika Walters, Lars-Anders Hansson, Annette B. G. Janssen, Peeter Nõges, Philip C. Reid, Daniel E. Schindler, Ellen van Donk, Vasilis Dakos & Rita Adrian, Proceedings of the National Academy of Sciences (PNAS), 23 november 2016 (Early Edition, alvast online voorafgaand aan officiële uitgave in tijdschrift), http://www. Institutions involved: Leibniz Institute of Freshwater Ecology and Inland Fisheries (Duitsland); Nederlands Instituut voor Ecologie (NIOO-KNAW); Free University of Berlin (Duitsland); Waikato Regional Council (Nieuw Zeeland); US Geological Survey (VS); Lund University (Zweden); Wageningen University; Estonian University of Life Sciences (Estland); Sir Alister Hardy Foundation for Ocean Science (VK); Plymouth University (VK); Marine Biological Association of the United Kingdom (VK); University of Washington (VS); ETH Zürich (Zwitserland)


News Article | November 28, 2016
Site: www.eurekalert.org

Topics range from medical imaging to analysis of authority and trust in US politics and society; €87 million in funding for an initial 4.5 years The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) is establishing 20 new Research Training Groups (RTGs) to further support early career researchers in Germany. They include three International Research Training Groups (IRTGs) with partners in the UK, New Zealand and Austria. This was decided by the responsible Grants Committee during its autumn session in Bonn. The Research Training Groups will receive funding of around 87 million euros for an initial period of four and a half years. In addition to the 20 new collaborations, the Grants Committee approved the extension of seven Research Training Groups for another four and a half years. This funding instrument enables doctoral researchers to complete their theses in a structured research and qualification programme at a high academic level. In total the DFG is currently funding 206 Research Training Groups, including 41 International Research Training Groups; the 20 new groups will commence their work in 2017. The new Research Training Groups in detail (in alphabetical order by their host universities, including the name of the applicant universities): Sketches, abstracts, notes, records, excerpts, essays, articles and glosses: all these 'small forms' of writing are an essential part of the practice of research, teaching, art and the media. The Research Training Group "The Literary and Epistemic History of Small Forms" intends to study their emergence and development, with which they are also involved in the success of prose, from antiquity to the present day. The group will also seek to understand how processes of understanding are controlled, reflected and channelled in specific media using these small forms. (Host university: Humboldt University of Berlin, Spokesperson: Professor Dr. Joseph Vogl) Imaging techniques such as ultrasound, X-rays and CT scans are well known. Medical findings are established on the basis of the image data produced in technically and mathematically complex processes. However, physicians' diagnoses are normally made on the basis of qualitative arguments, which do not make full use of the information content of image data and in particular the potential of imaging methods. The "BIOQIC - BIOphysical Quantitative Imaging Towards Clinical Diagnosis" Research Training Group will therefore study biophysical quantitative medical imaging to further develop these quantitative methods and apply them in clinical pilot studies to obtain more information from the imaging process. (Host universities: Humboldt University of Berlin and Free University of Berlin / Charité - University Hospital Berlin, Spokesperson: Professor Dr. Ingolf Sack) The Research Training Group "World Politics: The Emergence of Political Arenas and Modes of Observation in World Society" is concerned with the emergence of world politics as a type of politics in its own right. From the perspective of the theory of global society, the group aims to investigate the extent to which the emergence of world politics represents both a consequence and a precondition of the constitution of modern states. Researchers specialising in political science, sociology, history and law will collaborate to address this question. (Host university: University of Bielefeld, Spokesperson: Professor Dr. Mathias Albert) Perception, the authorship of action, emotions, and social and linguistic understanding are central cognitive phenomena. The Research Training Group "Situated Cognition - New Concepts in Investigating Core Mental Phenomena" will combine the philosophy of the mind and cognition with cognition sciences, which closely interact with cognitive neurosciences. The main aim of the group is to identify deficits in existing concepts of the human mind and further develop these concepts such as to give more attention to more recent developments in cognition sciences that are not yet adequately reflected in philosophical theory formation. (Host university: University of Bochum, Spokesperson: Professor Dr. Albert Newen; Additional applicant university: University of Osnabrück) Short-term dynamic loads such as impacts, detonations or earthquakes can cause structures to collapse. The aim of the Research Training Group "Mineral-Bonded Composites for Enhanced Structural Impact Safety" is to make existing buildings and structures more resilient through the addition of thin-layer reinforcements. With the help of new mineral-bonded materials known as composites, the researchers aim to improve the safety of people and the infrastructure essential to their lives. (Host university: Technical University of Dresden, Spokesperson: Professor Dr.-Ing. Viktor Mechtcherine) According to the World Health Organization, more than 422 million people worldwide suffer from diabetes, with approximately 3.7 million mortalities per year. In Germany, experts estimate the number of sufferers at 8 to 10 million. The German-British Research Training Group "Immunological and Cellular Strategies in Metabolic Disease (ICSMD)" aims to achieve a better understanding of the pathophysiology of type 1 and type 2 diabetes and develop strategies to halt the progress of the disease or even discover a cure. (Host university: Technical University of Dresden, Spokesperson: Professor Dr. Stefan R. Bornstein, Cooperation partner: King's College London, Great Britain) The German-Austrian Research Training Group "Resonant Self-World Relations in Ancient and Modern Socio-Religious Practices" will investigate ritual practices which generate, determine or express meaningful relations between people and the world - to other people, things, nature, self, heaven and God or the gods. The nature of these world relations, in turn, says much about a given culture and the social or gender positions which characterise it. The establishment of the group has been approved by the DFG's Grants Committee on Research Training Groups. The Austrian Science Fund (FWF) will reach a decision on co-funding at its next meeting. (Host university: University of Erfurt, Spokesperson: Professor Dr. Jörg Rüpke, Cooperation partner: University of Graz, Austria) The Research Training Group "Configurations of Cinema" understands film as a medium in constant transformation. In three working areas, 'formations', 'usages' and 'localisations', the group intends to analyse the genealogy and transformation of a wide variety of configurations of film, also in regard to the shift from cinemas to portable digital devices. The researchers will thus explore new modes of writing the history of a medium that is subject to constant change and examine film's defining features. (Host university: Goethe University of Frankfurt am Main, Spokesperson: Professor Dr. Vinzenz Hediger) How are authority and trust formed in US politics? How does this happen in American society, in religion and culture? The Research Training Group "Authority and Trust in American Culture, Society, History and Politics" intends to answer these questions. The chosen object of analysis is the USA because, due to its early democratization, egalitarian-libertarian political culture, ethnocultural heterogeneity and international hegemony, the country offers particularly fundamental insights into the problems of authority and trust in the modern age. (Host university: University of Heidelberg, Spokesperson: Professor Dr. Manfred Berg) The Research Training Group "Tip- and Laser-Based 3D-Nanofabrication in Extended Macroscopic Working Areas" will develop manufacturing methods for two-dimensional and three-dimensional structures on a nanometre scale using tip-based and laser-based techniques. The research work will primarily be based on nanopositioning and nanomeasuring machines, allowing structuring and measuring to take place on the same machine. With the aid of this equipment the researchers intend to give particular attention to larger and uneven surfaces, such as optical lenses. (Host university: Technical University of Ilmenau, Spokesperson: Professor Dr.-Ing. Eberhard Manske) Batteries are seen as key components of future technologies such as electric vehicles and energy supplies. The Research Training Group "SIMET - Simulation Mechano-Electro-Thermal Processes in Lithium-Ion Batteries" will work on numerical simulation methods for lithium-ion batteries. The researchers will address the problem in a multi-scale approach in several different orders of magnitude. As well as individual particles, they will simulate the electrode pair and the complete cell. (Host university: Karlsruhe Institute of Technology (KIT), Spokesperson: Professor Dr.-Ing. Thomas Wetzel) Patients with chronic diseases of the brain are normally treated with medication, but this is frequently associated with side effects. Neuroimplants, on the other hand, allow localised therapy, but must satisfy many requirements. The Research Training Group "Materials for Brain (M4B): Thin Film Functional Materials for Minimally Invasive Therapy of Brain Diseases" intends to study the use of nanoscale, therapeutically active coatings for implants of this type. Its aim is to achieve the controlled release of substances into the brain by means of the coating. (Host university: University of Kiel, Spokesperson: Professor Dr. Christine Selhuber-Unkel) We do not know enough about the reaction of lake ecosystems to environmental changes to be able to predict reliably whether they actually return to their original state following renaturation measures. Taking the example of Lake Constance, the Research Training Group "R3 - Responses to Biotic and Abiotic Changes, Resilience and Reversibility of Lake Ecosystems" aims to better understand the reactions of lake ecosystems to environmental changes, their resilience - the resistance of an ecosystem to disturbances - and their reversibility, in other words the ability to return to an original state following disturbance. (Host university: University of Constance, Spokesperson: Professor Dr. Frank Peeters) For many mathematical questions, approximation and dimension reduction are the most important tools for achieving simplified representation and therefore saving computing time. The Research Training Group "Mathematical Complexity Reduction (CoRe)" will approach complexity reduction in a more general sense and will also investigate when problems can be made easier to solve through embedding in higher dimensional spaces ('liftings'). The group also intends to systematically examine the influence of the costs of data collection. (Host university: University of Magdeburg, Spokesperson: Professor Dr. Sebastian Sager) One of the basic requirements for the economic success of a business is the efficient use of resources. In an increasingly networked world, several decision-makers are often involved in resource management and the amount of data available is growing. The Research Training Group "Advanced Optimization in a Networked Economy (AdONE)", based in the fields of operations research and management science, aims to develop models and processes and transfer these into software solutions designed to enable efficient use of resources through intelligent planning and control. (Host university: Technical University of Munich, Spokesperson: Professor Dr. Stefan Minner) Rapidly increasing antibiotic resistance and the growth of so-called lifestyle diseases confront humanity with enormous challenges. In the Research Training Group "Evolutionary Processes in Adaptation and Disease (RTG EvoPAD)", doctoral researchers in biology, medicine and the philosophy of science will therefore investigate adaptations and diseases by drawing on modern evolutionary research and approaches in the philosophy of science, in order to better understand them. (Host university: University of Münster, Spokesperson: Professor Dr. Joachim Kurtz) The development of metropolises prior to the age of industrialisation and globalisation has not, so far, been the subject of sufficient research. The "Pre-Modern Metropolitanism" Research Training Group intends to close this gap by investigating the establishment, impact and evolution of major urban centres from Ancient Greece and Rome to the dawn of the industrial age. (Host university: University of Regensburg, Spokesperson: Professor Dr. Jörg Oberste) Until now there have been few if any approaches to the improvement of robots that work with easily modifiable materials or handle soft tissue. In a German-New Zealand Research Training Group, doctoral researchers will investigate "Soft Tissue Robotics - Simulation-Driven Concepts and Design for Control and Automation for Robotic Devices Interacting with Soft Tissues". The aim is to further develop simulation techniques and sensors in order to enable new regulation and control technology for robots that interact with soft materials. (Host university: University of Stuttgart, Spokesperson: Professor Oliver Röhrle, Ph.D., Cooperation partner: University of Auckland, New Zealand) For many tumours there are no means of prevention, which is why they are usually diagnosed in advanced stages. It is also difficult to develop efficient therapies for tumours because there are genomic differences not only between different tumours (intertumoral) but also within a single tumour (intratumoral), which contributes to therapy resistance. The Research Training Group "Heterogeneity and Evolution in Solid Tumors (HEIST): Molecular Characterization and Therapeutic Consequences" aims to understand intra- and intertumoral heterogeneity, the evolutionary history of a tumour and the genes responsible for it in order to improve the treatment of tumours even in advanced stages. (Host university: University of Ulm, Spokesperson: Professor Dr. Thomas Seufferlein) Aberrations in what is known as the ubiquitin system in the body contribute to the development of a wide range of diseases such as cancer, neurodegenerative diseases and infectious diseases. The aim of the Research Training Group "Understanding Ubiquitylation: From Molecular Mechanisms To Disease" is therefore to understand the biochemical and pathogenic mechanisms which underlie diseases associated with the ubiquitin system. (Host university: University of Würzburg, Spokesperson: Professor Dr. Alexander Buchberger) Further information will also be provided by the spokespersons of the Research Training Groups. More details about the funding programme and the funded Research Training Groups is available at: http://www.


News Article | November 30, 2016
Site: www.nature.com

Ribosomes from E. coli MRE 600, initiation factors (IF1, IF2, IF3), and fMet-tRNAfMet were prepared as described47, 48, 49. E. coli SelA and SelD (gift from M. Wahl, Free University of Berlin) and SelB50 containing a hexahistidine tag (gift from A. Böck, LMU Munich) were expressed in BL21(DE3) cells and purified according to published protocols4, 51. Biochemical analysis showed that SelB carrying the His-tag is fully functional in the interactions with guanine nucleotides, SECIS elements, and Sec-tRNASec and in mediating UGA recoding in vivo4, 50. tRNASec was overexpressed in E. coli BL21 transformed with the plasmid pCB2013 (gift from A. Böck, LMU Munich)52 and purified and aminoacylated as described4, 53, 54. The mRNA UGA was a derivative of mLP75s54 (Extended Data Fig. 4d). The templates for mRNAs UUC and iSECIS (Extended Data Fig. 4e, f) were prepared by PCR mutagenesis. Transcription and refolding of the mRNAs were performed as described54, 55. 70S ribosomes (3 μM) were incubated with IF1, IF2, IF3 (4.5 μM), mRNA (15 μM), and f[3H]Met-tRNAfMet (7 μM) in buffer A (50 mM Tris-HCl (pH 7.5), 70 mM NH Cl, 30 mM KCl, 7 mM MgCl , 2 mM DTT) with 1 mM GTP for 30 min at 37 °C. Initiation efficiency was close to 100% as verified by nitrocellulose binding. Initiation complexes were purified by gel filtration on a Biosuite 450 HR 5 μm column (Waters). To prepare the ribosome–SelB complexes, ternary complexes SelB–GDPNP–Sec-tRNASec were prepared in buffer B (50 mM Hepes-KOH, pH 7.5, 70 mM NH Cl, 30 mM KCl, 7 mM MgCl , 2 mM DTT) by incubating SelB (1 μM) with GDPNP (2 mM) for 4 min at 37 °C, adding Sec-tRNASec (1 μM) and incubating for 2 min at 23 °C. Ternary complex (0.5 μM) was incubated with initiation complex (0.06 μM) at 0 °C in buffer B supplemented with 0.6 mM spermine and 0.4 mM spermidine before application onto EM grids. Initiation complexes were prepared as described42. Ternary complex SelB–[γ32P]GTP–Sec-tRNASec was prepared in buffer A, by incubating SelB (9 μM) with [γ32P]GTP (60 μM) for 20 min at room temperature (RT), followed by addition of Sec-tRNASec (9 μM) and incubation for 2 min at room temperature. Unbound [γ32P]GTP was removed by gel filtration56. The GTPase activity of SelB was determined at single round conditions, by mixing purified ternary complex (0.05 μM) with UGA, iSECIS and UUC mRNA-programmed initiation complexes at the indicated concentrations. Intrinsic GTP hydrolysis was measured in the absence of ribosomes. When necessary, quench-flow experiments were performed in a KinTek apparatus. Reactions were quenched with formic acid (25% v/v) and the extent of GTP cleavage was determined by thin layer chromatography and phosphor imaging57. The rate of GTP hydrolysis was determined by exponential fitting of the time courses using GraphPad Prism software (GraphPad Software, Inc.); time courses were normalized to the respective reaction end levels. Cryo-EM grids were prepared by applying 5 μl of initiation complex–SelB–GDPNP–Sec-tRNASec complexes onto EM grids (Quantifoil 3.5/1 μm, Jena) covered with pre-floated continuous carbon and subsequently vitrified using a Vitrobot Mark IV (FEI Company, Eindhoven) operated at 4 °C and 100% humidity. 4,000 × 4,000 images (12,681 in total) were acquired in the integration mode by spot-scanning (3 × 3 images per 3.5 μm hole in the Quantifoil carbon film) on a Falcon 2 direct detector (FEI Eindhoven) using a Titan Krios microscope (FEI Eindhoven), fitted with a XFEG electron source (FEI Eindhoven) and a spherical aberration (Cs)-corrector (CEOS Heidelberg). Acquisition was at 300 kV acceleration voltage, an electron dose of ~30 ± 5 electrons per Å2 (determination based on calibration with a Faraday cup), −0.7 to −2.6 μm defocus and a nominal magnification of 118,000× resulting in a final pixel size of ~1.16 Å (determined by optimizing correlation of the final 3D map with atomic coordinates from X-ray crystallography58). The Cs-corrector was tuned as described58 to reduce electron-optical aberrations, linear distortion (to <0.1%) and axial coma (usrimageshift tuning) resulting from the spot-scanning procedure. Ribosome particle images were selected and corrected locally for the contrast-transfer function as described58. Good quality particle images were selected according to power spectra quality (that is, showing Thon rings better than 3.5 Å), yielding a total of 969,526 ribosome particles. An initial 3D structure was computed from randomly selected 100,000 particles to judge the compositional and conformational homogeneity of the image dataset. Even at low-resolution (~10 Å) this average structure showed only very weak, scattered density in the factor-binding region, which disappeared completely upon further refinement to higher-resolution (~3.7 Å) (Extended Data Fig. 1c). This observation indicated that the occupancy of ribosome particles with SelB–Sec-tRNASec was low, in line with the low Sec incorporation efficiency in vivo and in vitro26. The dataset was sorted computationally in a hierarchical manner34 (Extended Data Fig. 1a, b). First, images were sorted according to global ribosome conformation, as described58 (step 1), which allowed us to discard low quality particles and 50S subunits. Subsequently (step 2), particles were sorted according to ligand occupancy using supervised classification by projection matching59 on the basis of a library of ribosome-ligand cryo-EM maps34, 60. Importantly, this library entailed a cryo-EM map of the canonical ribosome–EF-Tu complex60 as potential reference for the ribosome-SelB complex to avoid any reference bias for SelB-Sec-tRNASec, for which no structure was available. To further avoid any high-resolution reference bias, sorting in both steps was performed using low-pass filtered reference maps and particle images binned to about 6.9 Å per pixel. The resulting maps of ribosome-ligand complexes showed all specific features expected for the Sec system (that is, the SECIS in the mRNA, the extra-long variable arm of tRNASec, and domain 4 of SelB). In step 3, the resulting populations of ribosome-ligand particles were further rectified from low-quality particles by three-dimensional (3D) classification in Relion 1.2 and 1.3 (ref. 61). Focused 3D classification in Relion 1.3 without alignment was used to isolate three particle sub-populations that show distinct states of SelB–Sec-tRNASec on the ribosome (step 4); particle images were coarsened to 3.16 Å per pixel for this step to improve the speed and robustness of classification. Finally, to further enrich for ribosome particles of good quality containing SelB within these sub-populations, supervised classification was used in step 5 to assign particles either to the respective ribosome-SelB complex or ribosomes with only peptidyl-site tRNA, but not SelB–Sec-tRNASec bound; again a pixel sampling of 3.16 Å and low-pass filtered reference maps were used to avoid any high-resolution reference bias. In a similar manner, the particle populations of ribosomes carrying only the peptidyl-site tRNA or two tRNAs in the classical state were further computationally cleaned up by supervised classification. The six homogenous ribosome-ligand particle populations resulting from this sorting procedure were refined to high resolution according to the gold-standard procedure in Relion 1.3 and overall resolution of the final maps was determined using high-resolution noise substitution62 in Relion 1.4 (Extended Data Fig. 2a). The final cryo-EM maps were sharpened as described58; and for each reconstruction local, resolution maps were computed using Resmap63 (Extended Data Fig. 2f, g). If not denoted otherwise, densities in the figures are rendered at 2σ, except winged-helix motifs 3–4 and SECIS of the GTPase-activated state, which are rendered at 1.3–1.7σ. Figures were prepared using UCSF Chimera64. Pseudo-crystallographic refinement and model building. For initial model building and refinement, the cryo-EM density map of the GTPase-activated state was sharpened by applying a B factor of −120 Å2, filtered to the estimated highest resolution limit and masked using a pseudo bulk solvent envelope. The mask was obtained by merging the cryo-EM map filtered at different frequencies (9.0 Å, 6.0 Å and 4.0 Å) using the RAVE package65 and UCSF Chimera64. The masked cryo-EM density map was converted to reciprocal space structure factors using Crystallography and NMR System (CNS)66, 67 without employing phase significance blurring scale factors derived from FSC values. Initial rigid body fit of an atomic model of the kirromycin-stalled E. coli ribosome complex58 lacking EF-Tu and Phe-tRNAPhe was performed against the masked cryo-EM map of the GTPase-activated state using Chimera, followed by rigid body refinement of individual chains in PHENIX68 program. The atomic model of SelB with exception of tandem winged-helix motifs 3 and 4 was obtained by combining manual rebuilding and homology modelling with density-guided energy optimization, as implemented in the Rosetta package69, 70, employing a template derived from Methanococcus maripaludis SelB (PDB ID: 4AC9)9 and alignment provided by the HHPRED server71. SelB tandem winged-helix motifs (wh) 1 and 2 were modelled based on the crystal structure of the isolated domain 4 of SelB from Moorella thermoacetica (PDB ID: 1LVA)72; and wh3 and wh4 with mRNA SECIS were modelled on the basis of the crystal structure of E. coli SECIS RNA bound to the domain of elongation factor SelB (PDB ID: 2PJP)73 using Rosetta and Coot74. Sec-tRNASec was manually modelled on the basis of the crystal structure of tRNASec in complex with seryl-tRNA synthetase (PDB ID: 3W3S)6 with Coot and Rcrane75 and optimized by ERRASER76. The catalytic water molecule in the GTPase active centre of SelB was modelled on the basis of the superposition from PDB ID 4V5L35 into available density. Before global optimization of the atomic model of ribosome was performed, models of all individual protein chains were relaxed against the masked cryo-EM map filtered to 3.8 Å resolution (GTPase-activated state) using Rosetta. The assembled complete ribosome model was further minimized in both real and reciprocal space (ERRASER, phenix.real_space_refine77, phenix.refine) with alternating cycles of manual rebuilding in Coot and monitoring the local fit to the density with RESOLVE78. Refinement progress was additionally monitored by calculating the Pearson correlation coefficient (CC ; ref. 79), as well as the Fourier shell correlation between the cryo-EM reconstruction and a model map (FSC ). Both real and reciprocal space refinements in PHENIX employed automatically generated restraints and additional pseudo DEN (Deformable Elastic Network) restraints in order to maintain chemically important interactions. Group atomic displacement factors (ADP) were refined exclusively during reciprocal space refinement steps. During real space refinement steps in phenix.real_space_refine Ramachandran plot restraints were enabled. For parts of the model exhibiting larger conformational differences and/or lower local map resolution, additional cycles of real space refinement and manual fitting were performed against experimental map filtered to lower resolution, which was gradually increased between subsequent refinement steps until convergence. To maintain the intermolecular interactions of selected model fragments within local environment, all residues within at least 15 Å radius were included. For final refinement steps the cryo-EM map was sharpened58 and masked using a smoothed model-based envelope generated within 3.0 Å radius around atoms of the ribosome model of the GTPase-activated state before conversion to reciprocal space structure factors; for these steps and improved visualization the cryo-EM maps resolved at ≤3.6 Å resolution (initial complex, classical and GTPase-activated states) were resampled to a pixel size of 0.789 Å. The final model of the GTPase-activated state consisting of 154,136 individual atoms was refined to 24.90% and 0.936 for R and CC (definition is given below), respectively. The model of the GTPase-activated state exhibits a good stereochemistry with 90.87% of residues in the most favoured region and 0.88% residues in the disallowed region of the Ramachandran plot, protein side chain outliers of 2.83% and all atom clash score 15.09. The remaining states (initial complex, initial binding, codon reading, classical and hybrid states) were modelled based on the final model of GTPase-activated state in an analogous way. For cryo-EM reconstructions resolved at a resolution lower than 3.6 Å, a 3.8 Å radius for generating a smooth model-based envelope was chosen before generating reciprocal space structure factors used for the final refinement steps. FSC and CC , were calculated in a resolution-dependent manner using SFALL program (CCP4 suite80. Real space correlation coefficients (RSCC) were calculated using RESOLVE. All atomic models fit well the experimental cryo-EM map as judged based on the following criteria. (1) The Pearson correlation coefficient (CC ) calculated between model and map structure factors (F and F ) used for refinement is greater than 0.2 for the highest resolution shell and the overall correlation coefficient (CC ) is not lower than 0.9. (2) The calculated FSC value between model map coefficients (F , phase ) and structure factors derived from the cryo-EM map (F , phase ) used for refinement are not lower than 0.5 for the highest resolution shell and overall greater than 0.9. (3) The cumulative RSCC values are greater than 0.8, 0.6 and 0.4 for 53–75%, 88–94% and 95–97% of the residues, respectively. Detailed refinement statistics are presented in Extended Data Table 1, FSC and CC curves in Extended Data Fig. 2a–c. To build the initial recruitment complex, SelB domain 4 from the structure of the isolated SECIS-domain 4 complex (wh2 to wh4; PDB ID: 2PLY)73 was docked onto the initial complex by superimposing the SECIS. Then, wh2 was used to model our structure of SelB–GDPNP–Sec-tRNASec onto the initial complex-domain 4 complex. Refinements of final models against datasets obtained from two half maps were performed at 2.5 Å resolution in PHENIX using several cycles of real space refinement followed by reciprocal space refinement employing reference model restraints. To remove possible model bias a random shift of 0.3 Å was applied to all atomic positions before real space refinement. The FSC and CC were calculated between the models and the masked half-maps used for refinement, as well as between the model and the other half-map for cross-validation. The individual half-maps were masked using a smoothed mask derived from the respective refined model using a radius of 3.0 or 3.8 Å depending on the estimated highest resolution limit. Simulation setup. To obtain the energetics and dynamics of the free ternary complex, molecular dynamics simulations were started from the ribosome-bound conformations (initial binding, codon reading, and GTPase-activated states). Coordinates of Sec-tRNASec, SelB (amino acids 1–401), and GTP were extracted from the cryo-EM structures along with resolved water molecules and ions in the vicinity (<5 Å). The system was protonated, solvated, and ions were added as described earlier81. All simulations were carried out with Gromacs 5 (ref. 82) using the amberff12sb force field83, and the SPC/E water model84. Parameters for potassium and chloride ions were taken from ref. 85 and for modified nucleotides from Aduri et al.86. Atom types for selenocysteine were obtained with ANTECHAMBER87 and partial charges were determined using DFT-B3LYP with a 6–31/G* basis set. Bond and virtual-site constraints, temperature and pressure coupling were applied as described81. For each of the three starting structures, the system was pre-equilibrated as described81 with potential-energy minimization and 50-ns molecular dynamics simulations with position restraints followed by release of position restraints during 20 ns. Production runs started at 70 ns. At times 170, 270, and 370 ns, coordinates were extracted from the trajectory, new velocities were assigned and new simulations were started (12 simulations; total production run simulation time of 24 μs). To address the question of whether intrinsic conformational changes are rate-limiting for the transitions between the free ternary complex and the ribosome-bound states, we carried out a principal component analysis (PCA)88 on three subsets of atoms: ‘v-arm’ (P-atoms of variable arm), ‘no-v-arm’ (remaining peptidyl-atoms of tRNA), and ‘D1’ (Cα-atoms of SelB domain D1). The trajectories were rigid-body fitted using T-stem and acceptor-stem peptidyl-atoms for the ‘v-arm’ and ‘no-v-arm’ subsets and D2 Cα-atoms for the ‘D1’ subsets (Δt = 10 ps, discarding first 200 ns). The trajectories were concatenated and the atomic-displacement covariance-matrix was calculated. The first eigenvectors, sorted according to their eigenvalues, represent the most dominant conformational modes. For ‘no-v-arm’, the first two eigenvectors largely consist of a bending motion of the anticodon arm. To estimate the free-energy landscape of this motion, the projections of all frames onto these eigenvectors were binned. The relative free energy of each bin was calculated via ΔG  = −k T ln(c /c ), where k is the Boltzmann constant, T the temperature, c the number of frames in the bin and c is the maximum of all c (Fig. 4c, Extended Data Figs 6a, 7e). For ‘no-v-arm’ conformational modes 1 and 2, the bending angles (α and β) as a function of the projection onto the respective mode were calculated. The vector between the centres of mass of U34–A36 peptidyl-atoms and of T-stem peptidyl-atoms was calculated. For each projection, the angle between the vector and the vector corresponding to the bin with ΔG = 0 was calculated. To monitor the local geometry of the active site in the free ternary complex, the minimal distances between His61 imidazole atoms and GTP atoms (R ) as well as the van-der-Waals distance between Val9 and Met36 (R ) were calculated (Δt = 10 ps, discarding first 200 ns). The resulting free-energy landscape is shown in Extended Data Fig. 7f. To estimate the magnitudes of rates for transitions of tRNASec in the free ternary complex between the conformations corresponding to the ribosome-bound states, the projections onto the “no-v-arm” conformational modes 1 and 2 were calculated, thus obtaining 2-dimensional trajectories. For each simulation the number of transitions n between the region around the free-energy minimum (all bins with 0 ≤ ΔG ≤ 0.5 k T mol−1) and the ribosome-bound conformations was counted. For each ribosome-bound tRNA conformation a region was defined by an ensemble of 10,000 structures generated from the cryo-EM coordinates and b-factors. For each peptidyl-atom and ensemble structure, the coordinate obtained from cryo-EM was shifted in a random direction by distance d drawn from a normal distribution p(d). The normal distribution p(d) with μ = 0 and σ = rmsf (calculated from the b-factor) was set to zero for d < σ and d > σ. The resulting structures were projected onto the ‘no-v-arm’ conformational modes. The region was defined as all bins with entries from these structures. The transition rates were calculated for each simulation by dividing n by the simulation time t . The mean rates and standard deviations were obtained by weighting the individual transition rates by the corresponding t . To address a possible coupling of ‘v-arm’ and ‘no-v-arm’ conformational modes, we investigated whether the projections onto these modes are correlated as would be expected for coupled motions. For all four pairs of eigenvectors v and v , where v is either ‘no-v-arm’ mode 1 or 2 and v is either “v-arm” mode 1 or 2, the correlation coefficient of the projections was calculated. To estimate the statistical error, a bootstrapping method was applied. First, the autocorrelation time τ was defined by f (τ) = exp(−1), where f (Δt) is the autocorrelation function of the projection. For a given pair of eigenvectors v and v , the maximum of the two corresponding τ values (τ ) was used as an interval to resample the projections, resulting in sets of N = t /τ projections. This resampling was repeated 1,000 times and mean and standard deviations of the correlation coefficients were calculated for the simulations started from the individual ribosome-bound conformations and for all simulations combined (Extended Data Fig. 6b, red points). To check whether the resulting correlation coefficients are statistically significant, the standard deviations expected from uncorrelated projections were estimated by randomly drawing N projections (1,000 repetitions; Extended Data Fig. 6b, grey points). To address coupling between tRNA dynamics and motions of SelB domain 1 (D1), the same analysis was carried out for ‘no-v-arm’ and ‘D1’ conformational modes (Extended Data Fig. 6c). Cryo-EM maps/coordinates of the atomic models for each state have been deposited in the Electron Microscopy Data Bank/Protein Data Bank (http://www.emdatabank.org/) with the following accession codes: initial complex, EMD-4121/ 5ZLA; initial binding state, EMD-4122/ 5ZLB; codon reading state, EMD-4123/ 5ZLC; GTPase-activated state, EMD-4124/ 5ZLD; classical state, EMD-4125/ 5ZLE; hybrid state, EMD-4126/ 5ZLF. Cryo-EM micrographs and particle images have been deposited in the EMPIAR database (https://www.ebi.ac.uk/pdbe/emdb/empiar/) with accession code EMPIAR-10077.


Zeng N.,The Interdisciplinary Center | Zhao F.,The Interdisciplinary Center | Collatz G.J.,NASA | Kalnay E.,The Interdisciplinary Center | And 3 more authors.
Nature | Year: 2014

The atmospheric carbon dioxide (CO 2) record displays a prominent seasonal cycle that arises mainly from changes in vegetation growth and the corresponding CO 2 uptake during the boreal spring and summer growing seasons and CO 2 release during the autumn and winter seasons. The CO 2 seasonal amplitude has increased over the past five decades, suggesting an increase in Northern Hemisphere biospheric activity. It has been proposed that vegetation growth may have been stimulated by higher concentrations of CO 2 as well as by warming in recent decades, but such mechanisms have been unable to explain the full range and magnitude of the observed increase in CO 2 seasonal amplitude. Here we suggest that the intensification of agriculture (the Green Revolution, in which much greater crop yield per unit area was achieved by hybridization, irrigation and fertilization) during the past five decades is a driver of changes in the seasonal characteristics of the global carbon cycle. Our analysis of CO 2 data and atmospheric inversions shows a robust 15 per cent long-term increase in CO 2 seasonal amplitude from 1961 to 2010, punctuated by large decadal and interannual variations. Using a terrestrial carbon cycle model that takes into account high-yield cultivars, fertilizer use and irrigation, we find that the long-term increase in CO 2 seasonal amplitude arises from two major regions: the mid-latitude cropland between 25° N and 60° N and the high-latitude natural vegetation between 50° N and 70° N. The long-term trend of seasonal amplitude increase is 0.311 ± 0.027 per cent per year, of which sensitivity experiments attribute 45, 29 and 26 per cent to land-use change, climate variability and change, and increased productivity due to CO 2 fertilization, respectively. Vegetation growth was earlier by one to two weeks, as measured by the mid-point of vegetation carbon uptake, and took up 0.5 petagrams more carbon in July, the height of the growing season, during 2001-2010 than in 1961-1970, suggesting that human land use and management contribute to seasonal changes in the CO 2 exchange between the biosphere and the atmosphere.


Keller B.G.,Free University of Berlin | Kobitski A.,Fraunhofer Institute for Applied Solid State Physics | Jaschke A.,University of Heidelberg | Nienhaus G.U.,Fraunhofer Institute for Applied Solid State Physics | And 2 more authors.
Journal of the American Chemical Society | Year: 2014

We have developed a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes into account the trace-dependent background intensities. This analysis technique reveals an unprecedented amount of detail in the folding kinetics of the Diels-Alderase ribozyme. We find a multitude of extended (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified in two FRET constructs and at three Mg2+ concentrations. Structures generally tend to become more compact upon addition of Mg2+. Some compact structures are observed to significantly depend on Mg2+ concentration, suggesting a tertiary fold stabilized by Mg2+ ions. One compact structure was observed to be Mg2+-independent, consistent with stabilization by tertiary Watson-Crick base pairing found in the folded Diels-Alderase structure. A hierarchy of time scales was discovered, including dynamics of 10 ms or faster, likely due to tertiary structure fluctuations, and slow dynamics on the seconds time scale, presumably associated with significant changes in secondary structure. The folding pathways proceed through a series of intermediate secondary structures. There exist both compact pathways and more complex ones, which display tertiary unfolding, then secondary refolding, and, subsequently, again tertiary refolding. © 2014 American Chemical Society.


Hu J.,Free University of Berlin | Kehr B.,Free University of Berlin | Kehr B.,Max Planck Institute for Molecular Genetics | Reinert K.,Free University of Berlin
Bioinformatics | Year: 2014

Motivation: Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing.Results: We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments.Availability: The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.Contact: Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author.


Lustrino M.,University of Rome La Sapienza | Lustrino M.,CNR Institute of Environmental Geology and Geoengineering | Duggen S.,Leibniz Institute of Marine Science | Duggen S.,Minority | Rosenberg C.L.,Free University of Berlin
Earth-Science Reviews | Year: 2011

The central-western Mediterranean area is a key region for understanding the complex interaction between igneous activity and tectonics. In this review, the specific geochemical character of several 'subduction-related' Cenozoic igneous provinces are described with a view to identifying the processes responsible for the modifications of their sources. Different petrogenetic models are reviewed in the light of competing geological and geodynamic scenarios proposed in the literature.Plutonic rocks occur almost exclusively in the Eocene-Oligocene Periadriatic Province of the Alps while relatively minor plutonic bodies (mostly Miocene in age) crop out in N Morocco, S Spain and N Algeria. Igneous activity is otherwise confined to lava flows and dykes accompanied by relatively greater volumes of pyroclastic (often ignimbritic) products. Overall, the igneous activity spanned a wide temporal range, from middle Eocene (such as the Periadriatic Province) to the present (as in the Neapolitan of southern Italy). The magmatic products are mostly SiO2-oversaturated, showing calcalkaline to high-K calcalcaline affinity, except in some areas (as in peninsular Italy) where potassic to ultrapotassic compositions prevail. The ultrapotassic magmas (which include leucitites to leucite-phonolites) are dominantly SiO2-undersaturated, although rare, SiO2-saturated (i.e., leucite-free lamproites) appear over much of this region, examples being in the Betics (southeast Spain), the northwest Alps, northeast Corsica (France), Tuscany (northwest Italy), southeast Tyrrhenian Sea (Cornacya Seamount) and possibly in the Tell region (northeast Algeria).Excepted for the Alpine case, subduction-related igneous activity is strictly linked to the formation of the Mediterranean Sea. This Sea, at least in its central and western sectors, is made up of several young (<30Ma) V-shaped back-arc basins plus several dispersed continental fragments, originally in crustal continuity with the European plate (Sardinia, Corsica, Balearic Islands, Kabylies, Calabria, Peloritani Mountains). The bulk of igneous activity in the central-western Mediterranean is believed to have tapped mantle 'wedge' regions, metasomatized by pressure-related dehydration of the subducting slabs. The presence of subduction-related igneous rocks with a wide range of chemical composition has been related to the interplay of several factors among which the pre-metasomatic composition of the mantle wedges (i.e., fertile vs. refractory mineralogy), the composition of the subducting plate (i.e., the type and amount of sediment cover and the alteration state of the crust), the variable thermo-baric conditions of magma formation, coupled with variable molar concentrations of CO2 and H2O in the fluid phase released by the subducting plates are the most important.Compared to classic collisional settings (e.g., Himalayas), the central-western Mediterranean area shows a range of unusual geological and magmatological features. These include: a) the rapid formation of extensional basins in an overall compressional setting related to Africa-Europe convergence; b) centrifugal wave of both compressive and extensional tectonics starting from a 'pivotal' region around the Gulf of Lyon; c) the development of concomitant Cenozoic subduction zones with different subduction and tectonic transport directions; d) subduction 'inversion' events (e.g., currently along the Maghrebian coast and in northern Sicily, previously at the southern paleo-European margin); e) a repeated temporal pattern whereby subduction-related magmatic activity gives way to magmas of intraplate geochemical type; f) the late-stage appearance of magmas with collision-related 'exotic' (potassic to ultrapotassic) compositions, generally absent from simple subduction settings; g) the relative scarcity of typical calcalkaline magmas along the Italian peninsula; h) the absence of igneous activity where it might well be expected (e.g., above the hanging-wall of the Late Cretaceous-Eocene Adria-Europe subduction system in the Alps); i) voluminous production of subduction-related magmas coeval with extensional tectonic rìgimes (e.g., during Oligo-Miocene Sardinian Trough formation).To summarize, these salient central-western Mediterranean features, characterizing a late-stage of the classic 'Wilson Cycle' offer a 'template' for interpreting magmatic compositions in analogous settings elsewhere. © 2010 Elsevier B.V.


Muller A.C.,Free University of Berlin | Muller A.C.,Max Planck Institute for Molecular Genetics | Bockmayr A.,Free University of Berlin | Bockmayr A.,Research Center Matheon
Bioinformatics | Year: 2013

Motivation: Flux variability analysis (FVA) is an important tool to further analyse the results obtained by flux balance analysis (FBA) on genome-scale metabolic networks. For many constraint-based models, FVA identifies unboundedness of the optimal flux space. This reveals that optimal flux solutions with net flux through internal biochemical loops are feasible, which violates the second law of thermodynamics. Such unbounded fluxes may be eliminated by extending FVA with thermodynamic constraints.Results: We present a new algorithm for efficient flux variability (and flux balance) analysis with thermodynamic constraints, suitable for analysing genome-scale metabolic networks. We first show that FBA with thermodynamic constraints is NP-hard. Then we derive a theoretical tractability result, which can be applied to metabolic networks in practice. We use this result to develop a new constraint programming algorithm Fast-tFVA for fast FVA with thermodynamic constraints (tFVA). Computational comparisons with previous methods demonstrate the efficiency of the new method. For tFVA, a speed-up of factor 30-300 is achieved. In an analysis of genome-scale metabolic networks in the BioModels database, we found that in 485 of 716 networks, additional irreversible or fixed reactions could be detected. © 2013 The Author. Published by Oxford University Press. All rights reserved.


An overview of the established developmental models of antisocial behavior in children and adolescents is presented. Most of the established developmental models (e. g., by Patterson, Moffitt, or Loeber) consider - at least - an early-starter and a late-starter pathway. Additionally, several other pathways limited to childhood or adulthood have been suggested. Several recently conducted studies have revealed results which make a critical discussion and revision of the established developmental models necessary. The developmental models are summarized and results from recently conducted studies are discussed with regard to their implications for intervention and prevention strategies. © Hogrefe Verlag, Göttingen 2010.


Hsu C.-T.,Free University of Berlin | Jacobs A.M.,Free University of Berlin | Conrad M.,Free University of Berlin | Conrad M.,University of La Laguna
Cortex | Year: 2015

In this fMRI study we contrasted emotional responses to literary reading in late bilinguals' first or second language. German participants with adequate English proficiency in their second language (L2) English read short text passages from Harry Potter books characterized by a "negative" or "positive" versus "neutral" emotional valence manipulation. Previous studies have suggested that given sufficient L2 proficiency, neural substrates involved in L1 versus L2 do not differ (Fabbro, 2001). On the other hand, the question of attenuated emotionality of L2 language processing is still an open debate (see Conrad, Recio, & Jacobs, 2011). Our results revealed a set of neural structures involved in the processing of emotion-laden literature, including emotion-related amygdala and a set of lateral prefrontal, anterior temporal, and temporo-parietal regions associated with discourse comprehension, high-level semantic integration, and Theory-of-Mind processing. Yet, consistent with post-scan emotion ratings of text passages, factorial fMRI analyses revealed stronger hemodynamic responses to "happy" than to "neutral" in bilateral amygdala and the left precentral cortex that were restricted to L1 reading. Furthermore, multivariate pattern analyses (MVPA) demonstrated better classifiability of differential patterns of brain activity elicited by passages of different emotional content in L1 than in L2 for the whole brain level. Overall, our results suggest that reading emotion-laden texts in our native language provides a stronger and more differentiated emotional experience than reading in a second language. © 2014 Elsevier Ltd.


Robinson P.N.,Charité - Medical University of Berlin | Robinson P.N.,Max Planck Institute for Molecular Genetics | Robinson P.N.,Free University of Berlin | Webber C.,University of Oxford
PLoS Genetics | Year: 2014

The use of model organisms as tools for the investigation of human genetic variation has significantly and rapidly advanced our understanding of the aetiologies underlying hereditary traits. However, while equivalences in the DNA sequence of two species may be readily inferred through evolutionary models, the identification of equivalence in the phenotypic consequences resulting from comparable genetic variation is far from straightforward, limiting the value of the modelling paradigm. In this review, we provide an overview of the emerging statistical and computational approaches to objectively identify phenotypic equivalence between human and model organisms with examples from the vertebrate models, mouse and zebrafish. Firstly, we discuss enrichment approaches, which deem the most frequent phenotype among the orthologues of a set of genes associated with a common human phenotype as the orthologous phenotype, or phenolog, in the model species. Secondly, we introduce and discuss computational reasoning approaches to identify phenotypic equivalences made possible through the development of intra- and interspecies ontologies. Finally, we consider the particular challenges involved in modelling neuropsychiatric disorders, which illustrate many of the remaining difficulties in developing comprehensive and unequivocal interspecies phenotype mappings. © 2014 Robinson, Webber.


Georgieva Y.,Max Planck Institute for Molecular Genetics | Konthur Z.,Free University of Berlin
Molecules | Year: 2011

The last decade has seen a steady increase in screening of cDNA expression product libraries displayed on the surface of filamentous bacteriophage. At the same time, the range of applications extended from the identification of novel allergens over disease markers to protein-protein interaction studies. However, the generation and selection of cDNA phage display libraries is subjected to intrinsic biological limitations due to their complex nature and heterogeneity, as well as technical difficulties regarding protein presentation on the phage surface. Here, we review the latest developments in this field, discuss a number of strategies and improvements anticipated to overcome these challenges making cDNA and open reading frame (ORF) libraries more readily accessible for phage display. Furthermore, future trends combining phage display with next generation sequencing (NGS) will be presented. © 2011.


Benzmuller C.,Free University of Berlin | Pease A.,Articulate Software
Journal of Web Semantics | Year: 2012

This article addresses the automation of higher-order aspects in expressive ontologies such as the suggested upper merged ontology SUMO. Evidence is provided that modern higher-order automated theorem provers like LEO-II can be fruitfully employed for the task. A particular focus is on embedded formulas (formulas as terms), which are used in SUMO, for example, for modeling temporal, epistemic, or doxastic contexts. This modeling is partly in conflict with SUMO's assumption of a bivalent, classical semantics and it may hence lead to counterintuitive reasoning results with automated theorem provers in practice. A solution is proposed that maps SUMO to quantified multimodal logic which is in turn modeled as a fragment of classical higher-order logic. This way automated higher-order theorem provers can be safely applied for reasoning about modal contexts in SUMO. Our findings are of wider relevance as they analogously apply to other expressive ontologies and knowledge representation formalisms. © 2011 Elsevier B.V. All rights reserved.


Singh S.S.,University of Warwick | Typas A.,Free University of Berlin | Hengge R.,Free University of Berlin | Grainger D.C.,University of Warwick
Nucleic Acids Research | Year: 2011

In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ 70 factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generally considered unimportant. Here, we use a combination of bioinformatics, genetics and biochemistry to show that σ 70 can sense the sequence and conformation of the promoter spacer region. Our data illustrate how alterations in spacer region sequence can increase promoter activity. This stimulatory effect requires σ 70 side chain R451, which is located in close proximity to the non-template strand at promoter position-18. Conversely, R451 is not required to mediate transcriptional stimulation by improvement of the-10 element. Mutation of σ 70 residue R451, which is highly conserved, results in reduced growth rate, consistent with a central role in promoter recognition. © 2011 The Author(s).


Strozecka A.,Free University of Berlin | Eiguren A.,University of the Basque Country | Eiguren A.,Donostia International Physics Center | Pascual J.I.,Free University of Berlin
Physical Review Letters | Year: 2011

On surfaces with strong spin-orbit coupling, backscattering is forbidden since it requires flipping of the spin of the electron. It has been proposed that the forbidden scattering channels in such systems can be activated if time reversal symmetry is locally broken, for example, by a magnetic scattering center. Scanning tunneling spectroscopic maps of quasiparticle interference patterns around a single magnetic MnPc molecule on a Bi(110) surface reveal only spin-conserving scattering events. Simulations based on the Green's functions approach confirm that the charge-density interference patterns are unaffected by the magnetic state of the impurity. A fingerprint of backscattering processes appears, however, in the magnetization patterns, suggesting that only spin-polarized measurements can access this information. © 2011 American Physical Society.


Liu Z.,Beijing Computational Science Research Center | Liu Z.,CAS Institute of Physics | Bergholtz E.J.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

The possibility of realizing lattice analogs of fractional quantum Hall (FQH) states, so-called fractional Chern insulators (FCIs), in nearly flat topological (Chern) bands has attracted a lot of recent interest. Here, we make the connection between Abelian as well as non-Abelian FQH states and FCIs more precise. Using a gauge-fixed version of Qi's Wannier basis representation of a Chern band, we demonstrate that the interpolation between several FCI states, obtained by short-range lattice interactions in a spin-orbit-coupled kagome lattice model, and the corresponding continuum FQH states is smooth: the gap remains approximately constant and extrapolates to a finite value in the thermodynamic limit, while the low-lying part of the orbital entanglement spectrum remains qualitatively unaltered. The orbital entanglement spectra also provide a first glimpse of the edge physics of FCIs via the bulk-boundary correspondence. Corroborating these results, we find that the squared overlaps between the FCI and FQH ground states are as large as 98.7% for the 8-electron Laughlin state at ν=13 (consistent with an earlier study) and 97.8% for the 10-electron Moore-Read state at ν=12. For the bosonic analogs of these states, the adiabatic continuity is also shown to hold, albeit with somewhat smaller associated overlaps, etc. Although going between the Chern bands to the Landau-level problem is often smooth, we show that this is not always the case by considering fermions at filling fraction ν=45, where the interpolation between Hamiltonians describing the two systems results in a phase transition. © 2013 American Physical Society.


Serang O.,Free University of Berlin | Serang O.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Kall L.,KTH Royal Institute of Technology
Journal of Proteome Research | Year: 2015

In any high-throughput scientific study, it is often essential to estimate the percent of findings that are actually incorrect. This percentage is called the false discovery rate (abbreviated "FDR"), and it is an invariant (albeit, often unknown) quantity for any well-formed study. In proteomics, it has become common practice to incorrectly conflate the protein FDR (the percent of identified proteins that are actually absent) with protein-level target-decoy, a particular method for estimating the protein-level FDR. In this manner, the challenges of one approach have been used as the basis for an argument that the field should abstain from protein-level FDR analysis altogether or even the suggestion that the very notion of a protein FDR is flawed. As we demonstrate in simple but accurate simulations, not only is the protein-level FDR an invariant concept, when analyzing large data sets, the failure to properly acknowledge it or to correct for multiple testing can result in large, unrecognized errors, whereby thousands of absent proteins (and, potentially every protein in the FASTA database being considered) can be incorrectly identified. © 2015 American Chemical Society.


Keck C.M.,Free University of Berlin | Keck C.M.,Kaiserslautern University of Applied Sciences | Muller R.H.,Free University of Berlin
European Journal of Pharmaceutics and Biopharmaceutics | Year: 2013

There is an increasing discussion about potential toxicity of nanoparticles (nanotoxicity). A classification system is proposed classifying the nanoparticles in four classes (I to IV) from low/no risk to high risk. It is based on the nanoparticle size (>/<100 nm) and size-related differences in interaction with human cells, and on biodegradability/non-biodegradability in the body. This classification is superimposed by biocompatibility (B) and non-biocompatibility (NB) of the nanoparticle surface, resulting in a total of eight classes from I-B (best tolerated) to IV-NB (highest potential risk). The classification should help as a guideline in pharmaceutical formulation development, but also as a guide for risk assessment in other product areas and environmental exposure. © 2013 Elsevier B.V. All rights reserved.


Gielisch I.,Max Planck Institute for Molecular Genetics | Gielisch I.,Free University of Berlin | Meierhofer D.,Max Planck Institute for Molecular Genetics
Journal of Proteome Research | Year: 2015

Complex I (CI; NADH dehydrogenase) deficiency causes mitochondrial diseases, including Leigh syndrome. A variety of clinical symptoms of CI deficiency are known, including neurodegeneration. Here, we report an integrative study combining liquid chromatography-mass spectrometry (LC-MS)-based metabolome and proteome profiling in CI deficient HeLa cells. We report a rapid LC-MS-based method for the relative quantification of targeted metabolome profiling with an additional layer of confidence by applying multiple reaction monitoring (MRM) ion ratios for further identity confirmation and robustness. The proteome was analyzed by label-free quantification (LFQ). More than 6000 protein groups were identified. Pathway and network analyses revealed that the respiratory chain was highly deregulated, with metabolites such as FMN, FAD, NAD+, and ADP, direct players of the OXPHOS system, and metabolites of the TCA cycle decreased up to 100-fold. Synthesis of functional iron-sulfur clusters, which are of central importance for the electron transfer chain, and degradation products like bilirubin were also significantly reduced. Glutathione metabolism on the pathway level, as well as individual metabolite components such as NADPH, glutathione (GSH), and oxidized glutathione (GSSG), was downregulated. Overall, metabolome and proteome profiles in CI deficient cells correlated well, supporting our integrated approach. © 2014 American Chemical Society.


Ayarzaguena B.,Complutense University of Madrid | Langematz U.,Free University of Berlin | Serrano E.,Complutense University of Madrid
Journal of Geophysical Research: Atmospheres | Year: 2011

In January 2009 and 2010, two major stratospheric warmings (MSWs) took place in the boreal polar stratosphere. Both MSWs were preceded by nearly the strongest injection of tropospheric wave activity on record since 1958 and their central date was almost coincident. However, the typical external factors that influence the occurrence of MSWs (the Quasi-Biennial Oscillation, sunspot cycle, or El Nio) were dissimilar in the two midwinters: favorable in 2010 but unfavorable in 2009. In this study, the driving mechanisms of these two different MSWs were investigated focusing on the amplification of upward wave activity injection into the stratosphere before the MSW onset. By decomposing the total wave flux injection into contributions from the climatological planetary waves and from deviations from the latter we found clear differences in this amplification between both MSWs. The pre-MSW period in 2009 was characterized by a peak in the 100 hPa eddy heat flux with a predominance of wave number 2 activity. This was due to strong anomalies associated with Rossby wave packets originating from a deep ridge over the eastern Pacific. In contrast, the amplification of the upward wave propagation prior to the 2010 MSW was equally due to Rossby wave packets and to the interaction between the latter and the climatological waves. This amplification enhanced wave number 1 stationary waves in January 2010, which seemed at least partially due to the 2009/2010 El Nio event. Our results show the relevance of the internal tropospheric variability in generating MSWs, particularly when the external factors do not play any role. © 2011 by the American Geophysical Union.


Shebani Z.,Medical Research Council | Pulvermuller F.,Medical Research Council | Pulvermuller F.,Free University of Berlin
Cortex | Year: 2013

Language and action systems of the human brain are functionally interwoven. Speaking about actions and understanding action-related speech sparks the motor system of the human brain and, conversely, motor system activation has an influence on the comprehension of action words and sentences. Although previous research has shown that motor systems become active when we understand language, a major question still remains whether these motor system activations are necessary for processing action words. We here report that rhythmic movements of either the hands or the feet lead to a differential impairment of working memory for concordant arm- and leg-related action words, with hand/arm movements predominantly impairing working memory for words used to speak about arm actions and foot/leg movements primarily impairing leg-related word memory. The resulting cross-over double dissociation demonstrates that body part specific and meaning-related processing resources in specific cortical motor systems are shared between overt movements and working memory for action-related words, thus documenting a genuine motor locus of semantic meaning. © 2011.


Marsalek O.,Czech Institute of Organic Chemistry And Biochemistry | Uhlig F.,Wilhelm Ostwald Institute For Physikalische Und Theoretische Chemie | Frigato T.,Free University of Berlin | Schmidt B.,Free University of Berlin | Jungwirth P.,Czech Institute of Organic Chemistry And Biochemistry
Physical Review Letters | Year: 2010

The process of electron localization on a cluster of 32 water molecules at 20, 50, and 300 K is unraveled using ab initio molecular dynamics simulations. In warm, liquid clusters, the excess electron relaxes from an initial diffuse and weakly bound structure to an equilibrated, strongly bound species within 1.5 ps. In contrast, in cold, glassy clusters the relaxation processes is not completed and the electron becomes trapped in a metastable surface state with an intermediate binding energy. These results question the validity of extrapolations of the properties of solvated electrons from cold clusters of increasing size to the liquid bulk. © 2010 The American Physical Society.


Yang H.,University of Southern California | Robinson P.N.,Charité - Medical University of Berlin | Robinson P.N.,Max Planck Institute for Molecular Genetics | Robinson P.N.,Free University of Berlin | Wang K.,University of Southern California
Nature Methods | Year: 2015

Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text. © 2015 Nature America, Inc.


Siragusa E.,Free University of Berlin | Siragusa E.,Max Planck Institute for Molecular Genetics | Weese D.,Free University of Berlin | Reinert K.,Free University of Berlin
Nucleic Acids Research | Year: 2013

We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai. © 2013 The Author(s).


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2011.4.3-1 | Award Amount: 3.23M | Year: 2012

In an era of global flux, emerging powers and growing interconnectedness, transatlantic relations appear to have lost their bearings. As the international system fragments into different constellations of state and non-state powers across different policy domains, the US and the EU can no longer claim exclusive leadership in global governance. Not only the ability, but also the willingness of the US and the EU to exercise leadership together can no longer be taken for granted. Political, economic, and social elites on both shores of the Atlantic express different views on whether the US and the EU should be bound together, freelance, or seek alternative partnerships in a confusing multipolar world. Traditional paradigms to understand the transatlantic relationship are thus wanting. A new approach is needed to pinpoint the direction transatlantic relations are taking. TRANSWORLD provides such an approach. By combining an inter-disciplinary analysis of transatlantic relations, including desk research, in-depth interviews, an elite survey and a sophisticated Delphi exercise to elaborate solid policy proposals, TRANSWORLD would: a) ascertain, differentiating among four policy domains (economic, security, environment, and human rights/democracy), whether transatlantic relations are drifting apart, adapting along an ad hoc cooperation-based pattern, or evolving into a different but resilient special partnership; b) assess the role of a re-defined transatlantic relationship in the global governance architecture; c) provide tested policy recommendations on how the US and the EU could best cooperate to enhance the viability, effectiveness, and accountability of governance structures. In so doing, TRANSWORLD, which features a thirteen-partner transatlantic consortium of attested academic, policy, dissemination and management excellence, would contribute to an inter-disciplinary transatlantic research area, with in-built connections to policy-making.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2010-ITN | Award Amount: 3.58M | Year: 2010

GeoWeb 2.0 is the geographic embodiment of the Web 2.0 moniker for the next generation Web, i.e., the next generation of geographic information publishing, discovery and use. With the proliferation of the Internet as the primary medium for data publishing and information exchange, we have seen an explosion in the amount of online content available on the Web. In addition to professionally-produced material being offered free on the Internet, the public has also been encouraged to make its content available online to everyone as User-Generated Content (UGC). The goal of the GEOCROWD project is to establish a fertile research environment by means of a training network that will promote the GeoWeb 2.0 vision and advance the state of the art in collecting, storing, analyzing, processing, reconciling, and making large amounts of semantically rich user-generated geospatial information available on the Web. Specifically, activities will be centered on (i) exploiting user-contributed geospatial data, (ii) Web-geodata management and (iii) efficient means for data collection and dissemination, e.g., mobile computing. Our goal is to tame this data explosion, which applied to the geospatial domain translates to massively collecting and sharing knowledge to ultimately digitize the world.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.30M | Year: 2014

Organofluorine chemistry has played a significant role in the majority of the spectacular scientific and technological developments of the past century although this is not widely recognised even by the scientific community. Fluoroorganic molecules are key components in an ever increasing number of high-value commercially important products particularly in the life science industries. The use of fluorinated systems in drug discovery programmes has continued to grow and, at present, approximately 30% of new pharmaceutical and agrochemical systems that enter the market bear fluorine atoms or fluorinated substituents, contributing enormously to the economic wellbeing of the EU as a whole and the health of its citizens. All useful fluoroorganic systems are man-made and the key step in developing new products and applications involving fluorinated derivatives is the synthesis of carbon-fluorine bonds. We will develop new selective fluorination processes by using both innovative chemoselective methodology and the emerging field of synthetic biology to provide new technology platforms beyond the current state-of-the-art. The desire to introduce a fluorine atom into an organic system is often driven by the fact that the C-F bond imparts unique and highly tuneable control of both geometric and stereoelectronic phenomena within a molecular structure. The Networks expertise in handling and analysing fluorinated molecules will allow us to engineer the properties of organic and biological molecules through the strategic introduction of C-F bonds by molecular editing. A large number of world-leading research scientists in academia in the various fields of organofluorine chemistry have retired in the recent past and, consequently, if training of ESRs and support of youthful research groups is not continued, the EU will lose very competitive, highly valuable, high technology, research expertise that contributes significantly to all chemical, life science and materials sectors.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: NMP-2010-1.3-1 | Award Amount: 12.48M | Year: 2011

While there are standard procedures for product life cycle analysis, exposure, hazard, and risk assessment for traditional chemicals, is not yet clear how these procedures need to be modified to address all the novel properties of nanomaterials. There is a need to develop specific reference methods for all the main steps in managing the potential risk of ENM. The aim of MARINA is to develop such methods. MARINA will address the four central themes in the risk management paradigm for ENM: Materials, Exposure, Hazard and Risk. The methods developed by MARINA will be (i) based on beyond-state-of-the-art understanding of the properties, interaction and fate of ENM in relation to human health and the quality of the environment and will either (ii) be newly developed or adapted from existing ones but ultimately, they will be compared/validated and harmonised/standardised as reference methods for managing the risk of ENM. MARINA will develop a strategy for Risk Management including monitoring systems and measures for minimising massive exposure via explosion or environmental spillage.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.71M | Year: 2012

The overall objective of this project is the creation of an ITN network for the structured interdisciplinary training of researchers in advanced thin film photovoltaic (PV) technologies. The project proposes the development of new technologies compatible with the cost, efficiency, sustainability and mass production requirements that are needed to become a reliable and future alternative to conventional non renewable energy sources. With this objective in mind, the project will focus on the development of kesterite based solar cells. Kesterites are quaternary compounds with a crystalline structure very similar to that of chalcopyrites (CIGS: Cu(In,Ga)(S,Se)2). They have a strong potential for thin film low cost PV technologies, related to their direct bandgap and high optical absorption. In contrast with CIGS -where the potential for high mass production is compromised by the scarcity of In- they are constituted by abundant elements. For this, a consortium formed by research institutes, universities and companies with strongly complementary expertises has been formed. This includes groups that are leaders on the development of kesterite cells (Univ. Northumbria, HZB, Univ. Luxembourg) with groups with strong expertise on CIGS technologies (that are the parent technologies for kesterite solar cells) (EMPA, UU-ASC, NEXCIS, IREC, Free Univ. Berlin, Univ. dAix-Marseille, Autonomous Univ. Madrid). Free Univ. Berlin has also significant experience in the crystalline analysis of kesterites. Involvement of private companies (NEXCIS, Abengoa) devoted to the production and exploitation of PV technologies provides with complementary training aspects related to transferability of processes to industrial production and exploitation issues. All these aspects are relevant for the definition of a structured interdisciplinary training programme for the formation of high level researchers that will be required in Europe for the development of competitive PV technologies.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2012-1.1.16. | Award Amount: 10.15M | Year: 2013

SYNTHESYS3 will create an accessible, integrated European resource for researchers in the natural sciences in Europe and globally. Building on the success of the previous SYNTHESYS IA, the NA will focus on improving collections management of new physical and virtual collections. By focusing the JRA on extracting and enhancing data from digitised collections, SYNTHESYS3 will increase the accessibility of these 390 million strong collections. A wide range of services and access both physical and digital will be provided to a broad range of scientific Users (from biological and geological related disciplines) in a consistent and accessible way. The natural history collections, held within the museums and herbaria, of Europe are World-class in terms of their magnitude and taxonomic coverage. They represent a resource unique in Europe as a model of the diversity of life on earth and are a physical dataset enabling Users to research how the human activity (including climate change) is having an increasingly negative impact on the diversity and distribution of biodiversity, which is threatening the continued provision of ecosystem services essential to human well-being.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ENV.2012.6.2-2 | Award Amount: 11.59M | Year: 2012

Sustainable governance of our biological resources requires reliable scientific knowledge that meets the needs of society. Current biodiversity observation systems and environmental datasets are unbalanced in coverage and not integrated, limiting integrative analyses and implementation of environmental policies. EU BON presents an innovative approach towards integration of biodiversity information systems from on-ground to remote sensing data, for addressing policy and information needs in a timely and customized manner. EU BON will provide integration between social networks of science and policy and technological networks of interoperating IT infrastructures, resulting in a new open-access platform for sharing biodiversity data and tools, and greatly advance biodiversity knowledge in Europe. EU BONs 30 partners from 18 countries are members of networks of biodiversity data-holders, monitoring organisations, and leading scientific institutions. EU BON will build on existing components, in particular GBIF, LifeWatch infrastructures, and national biodiversity data centres. EU BON will 1) enable greater interoperability of data layers and systems through adoption of new standards; 2) advance data integration by new (modelling) technologies; 3) increase data mobilisation via scientific communities, citizen scientists, and potential data users; 4) develop strategies for future harmonizing and mainstreaming of biodiversity recording and monitoring; 5) improve analytical tools and services interpreting biodiversity data; 6) support the science-policy interface by timely information and scenario development; 7) link integrated, customized information to relevant stakeholders, and 8) strengthen overall European capacities and infrastructures for environmental information management. EU BONs deliverables include a comprehensive European Biodiversity Portal for all stakeholder communities, and strategies for a global implementation of GEO BON and supporting IPBES.


Grant
Agency: Cordis | Branch: FP7 | Program: | Phase: | Award Amount: 4.37M | Year: 2008

The European Theoretical Spectroscopy Facility addresses an important need of European science and technology by providing experimental, industrial and other researchers with access to state-of-the-art computer simulation tools for electronic excited states in matter, together with high-quality support from ETSF personnel, mirroring the massive progress in the power and resolution of new European experimental facilities. All domains that need knowledge about electronic excitations, transport and spectroscopy will benefit from the ETSF, such as condensed matter physics and chemistry, biology, materials science and nanoscience, atmospheric science, and astrophysics. The ETSF provides users with computer codes, background knowledge, customised support and development, training, and collaborators to enhance their studies of the electronic and transport properties of complex or nanoscale materials. Its focus is on the rapid transfer of ground-breaking fundamental knowledge of matter, at the quantum-mechanical level, to detailed understanding and future-oriented design of prototypical or technologically relevant systems. The ETSF has been successfully designed and recently brought into operation by the Nanoquanta Network of Excellence with the support of national and local institutions. In the present ETSF-I3 project, the ETSF is partnered by the Barcelona Supercomputing Centre to create a framework for deploying the ETSF infrastructure to a much wider range of users, through user training and projects supported by ETSF scientists. The ETSF-I3 project will monitor the scientific and technological needs of users, and will boost the user-oriented development of ETSF software, algorithms and libraries made available on the most advanced computational platforms. ETSF-I3 will be crucial to keep the ETSF at the forefront of knowledge and establish it as the world-wide reference centre for modelling of electronic excited states.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2011.1.6 | Award Amount: 6.24M | Year: 2011

Community networks are an emerging and successful model for the Future Internet across Europe and far beyond. The CONFINE project complements existing FIRE infrastructure by establishing a new facility built on the federation of existing community IP networks constituted by more than 20,000 nodes and 20,000 Km of links. These community networks incorporate a large and wide variety of commodity wireless and optical links, heterogeneous nodes, different routing protocols, applications and a large number of end-users, following an innovative model of self-provisioning using unlicensed and public spectrum. The project develops a unified access to an open testbed with tools that allow researchers to deploy, run, monitor and experiment with services, protocols and applications on real-world community IP networks. This integrated platform will provide user-friendly access to these emerging networks supporting any stakeholder interested in developing and testing experimental technologies for open and interoperable network infrastructures, strengthening open community networks. The project will take a multi-disciplinary and integrated view to this emerging network model as part of the Future Internet across Europe and beyond. The project includes as partners well established community networks with large end-user bases and diverse application providers (e.g. content distribution, voice, data and multimedia communication), research institutions with experience in key related areas, non-profit organizations and SMEs.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: ICT-35-2016 | Award Amount: 499.98K | Year: 2017

One of the major terminological forces driving ICT development today is that of big data. While the phrase may sound inclusive and integrative, in fact, big data approaches are highly selective, excluding any input that cannot be effectively structured, represented, or, indeed, digitised. Data of this messy, dirty sort is precisely the kind that humanities and cultural researchers deal with best. It will therefore be the contribution of the K-PLEX project to investigate these elements of humanities and cultural data, and the strategies researchers have developed to deal with them. In doing so it will remain at the margins of ICT so as to better shed light on the gap between analogue or augmented digital practices and fully computational ones. As such, it will expand our awareness of the risks inherent in big data and to suggest ways in which phenomena that resist datafication can still be represented (if only by their absence) in knowledge creation approaches reliant upon the interrogation of large data corpora. K-PLEX approaches this challenge in a comparative, multidisciplinary and multisectoral fashion, focusing on 3 key challenges to the knowledge creation capacity of big data approaches: the manner in which data that are not digitised or shared become hidden from aggregation systems; the fact that data is human created, and lacks the objectivity often ascribed to the term; the subtle ways in which data that are complex almost always become simplified before they can be aggregated. It will approach these questions via a humanities research perspective, but using social science research tools to look at both the humanistic and computer science approaches to the term data and its many possible meanings and implications. As such, K-PLEX project defines and describes key aspects of data that are at risk of being left out of our knowledge creation processes in a system where large scale data aggregation is becoming ever more the gold standard.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: INT-08-2015 | Award Amount: 2.67M | Year: 2016

Ten years after its inception, the European Neighbourhood Policy (ENP) has fallen short of accomplishing its mission. The war in Ukraine and the rising tensions with Russia have made a re-assessment of the ENP both more urgent and more challenging. EU-STRAT will address two questions: First, why has the EU fallen short of creating peace, prosperity and stability in its Eastern neighbourhood? Second, what can be done to strengthen the EUs transformative power in supporting political and economic change in the six Eastern Partnership (EaP) countries? Adopting an inside-out perspective on the challenges of transformation the EaP countries and the EU face, EU-STRAT will develop a conceptual framework for the varieties of social orders in EaP countries to explain the propensity of domestic actors to engage in change; investigate how bilateral, regional and global interdependencies shape the scope of action and the preferences of domestic actors in the EaP countries; de-centre the EU by studying the role of selected member states and other external actors active in the region; evaluate the effectiveness of the Association Agreements and alternative EU instruments, including scientific cooperation, in supporting change in the EaP countries; analyse normative discourses used by the EU and Russia to enhance their influence over the shared neighbourhood. formulate policy recommendations to strengthen the EUs capacity to support change in the EaP countries by advancing different scenarios for developmental pathways. EU-STRAT features an eleven-partner consortium including six universities, three think-tanks, one civil society organization and one consultancy. This consortium will achieve the research and policy relevant objectives of the project by bringing together various disciplinary perspectives and methodologies and strengthening links with academics and policy makers across six EU member states, Switzerland and three of the EaP countries.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 2.70M | Year: 2009

The large scale production of commodity polymers is increasingly shifting overseas. Europe still plays a major role in polymer processing and product development, but the competition with the US and Asia requires distinctive efforts to sustain this leadership. Thus, it is decisive for European researchers and companies to design innovative, specialised commodities and optimise current production strategies. NANOPOLYs main scientific objective is to further create, exchange and spread-out such know-how systematically within a European network in order to make this progress available and exploitable for European industries and coming generations of researchers. NANOPOLY will be unique in combining the strengths of applied mathematics/software engineering on the one hand and macro-molecular chemistry/reaction engineering on the other hand. These two sets of competences are currently rather unrelated but represent an important source of innovation for creating new models and associated software tools that permit new rational designs of polymer materials. NANOPOLYs main training objective is the education of a new generation of researchers who are able to bridge the still significant gap between the two mentioned sets of competences. The job market urgently calls for researchers with suchlike sophisticated knowledge and interdisciplinary training. These prospects will make participation in the network a rewarding career option. Through superior training, intense cooperation, and outreach the network will build-up an exeptional multi-disciplinary, European-based community that is able to achieve the crucial transfer of knowledge between the associated fields and thus permit major innovation in improving technological processes that allow tailoring nano-architectures of polymers to specific requirements.


Grant
Agency: Cordis | Branch: FP7 | Program: CPCSA | Phase: INFRA-2010-1.2.3 | Award Amount: 3.09M | Year: 2010

Partners to this proposal include the six major global programmes exploring the full extent of species diversity, a core dimension in human knowledge of global biodiversity.\nThey are: GBIF and distribution modelling, the EBI/INDSC, and Barcode of Life initiatives and molecular diversity, IUCN Red Lists and the species conservation movement, and the Species 2000 Catalogue of Life taxonomic framework. These will work closely with ELIXIR and LifeWatch, the ESFRI Infrastructures covering biodiversity, and build on the 4D4Life Project that develops the internal e-infrastructure of the Catalogue of Life.\nThe i4Life project is to establish a Virtual Research Community that will enable each of these global projects to engage in a common programme enumerating the extent of life on earth. It builds on the common need of each organisation to specify the entire set of organisms, their growing use of the Catalogue of Life as a common taxonomic resource alongside their own catalogues, and the different expertise that each programme brings to the task.\nThese key players present particular hurdles to Catalogue integration because they a) have established their own architectures, standards and protocols, b) have special requirements, and c) have their own partial catalogues that need to be integrated with the Catalogue of Life in a two way flow.\nIn each case i4Life will design, implement and test the necessary special pipelines, as well as contributing significantly to enhancement of the Catalogue of Life for all to use through the inflows from the partners. By providing access to a common species catalogue within each of the organisations, we expect to contribute a much needed level of knowledge integrity across the various scientific and community studies of the global biota. To make sense of global biodiversity it is vital that these organisations can communicate through a unified view of the extent of life.


Grant
Agency: Cordis | Branch: FP7 | Program: NoE | Phase: ENV.2009.4.2.1.1 | Award Amount: 8.35M | Year: 2009

Existing research points out that the full potential of Impact Assessment (IA) for delivering sustainable development is not being realised. Many tools to support IA are not yet being fully employed by policy makers. This is symptomatic of a large and deep gap between the two broad communities of IA researchers and IA practitioners. Practitioners tend to look for tools that are simple and transparent while the researchers are more interested in the sophistication and innovative aspects of assessment tools. The main purpose of LIAISE is to identify and exploit opportunities to bridge between these two communities in a way that leads to an enhanced use of IA tools in policy making. Its centrepiece will be a shared toolbox simultaneously accessible and useful for policy makers as well as for the research community. The LIAISE consortium will: Unite the multi-disciplinary competences of a core of large European institutes, that in turn consolidate the expertise from large FP6 projects. Combine researchers that analyse current policy needs and link them in innovative ways to those who maintain and develop IA tools; Develop a roadmap towards a virtual centre of excellence on IA, that can operate as the durable hub of existing academic and practitioner networks relevant to the themes of the NoE; Maintain the flexibility to support real life IA processes, informed by a structured dialogue with the IA user community; Develop a business plan to ensure durable operation, scientific credibility and efficient usability of the shared toolbox, also in the post-project period. Resulting in: A shared toolbox: a durable and flexible infrastructure to support IA with improved tools; A continuously updated shared research agenda; Capacity building and training components to spread the results of research activities to target groups in communities of IA users and IA researchers; A virtual centre of excellence on IA


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH-2007-2.1-02 | Award Amount: 1.98M | Year: 2008

CONSENSUS aims to improve our understanding of trade-offs and synergies between economic, environmental and social aspects of sustainable development. In so doing, the project applies a selective focus in order to shed light on several issues that are of particular relevance in this respect both in practical and analytical terms. First, the project places particular emphasis on a systematic analysis of the interlinkage between different levels of economic pressure and social and environmental policy. Second, in line with the political emphasis on better regulation and deregulation, the project applies a highly innovative perspective on policy change and sustainable development. Third, this interlinkage between economic pressure on the one side, and environmental and social sustainability on the other, is analyzed on the basis of a systematic comparison across 25 OECD countries over a period of thirty years (1975-2005) Fourth, this focus offers the opportunity for a comparison of regulatory adjustments across different policy areas. The focus on two crucial policy fields social and environmental policy allows us to study whether regulatory responses to economic pressures differ between these areas. Fifth, with regard to environmental and social policy, we focus on those subfields that have been identified as priority areas of sustainable development The projects proceeds in the following steps. In the first step, the theoretical framework will be further elaborated. In the second step, a quantitative analysis of the major driving forces of policy dismantling will be acrried out. For this purpose, cross-national data on social and environmental policy dismantling for the period from 1975 to 2005 will be collected. In the third part of the study, theoretiaccly interesting cases will be selected and subject to an in-depth qualitative analysis. The final part refers to the publication of the research reprot and the dissemination of the results.


Biodiversity core data and information constitutes an important source of knowledge for many disciplines. In order to facilitate access to this knowledge, technical and semantic interoperability barriers need to be addressed.\n\nThe objectives of Pro-iBiosphere are, to: a) Coordinate towards and prepare the foundations for a long-term viable, evolving knowledge management, aggregation and integration platform needed to replace and improve the present system of taxonomic literature, especially as presented in Floras and Faunas; b) Provide new methods to synthesize distributed knowledge and a strategy to adapt methods of acquisition, curation, and dissemination of biodiversity data to the digital era; c) Help to align ongoing and forthcoming semantic mark up of taxonomic literature, and to link elements of biodiversity literature (ie. taxonomic treatments) to the original data, such as the individual observation record (being the essential foundation of any biodiversity information); d) Promote and monitor the development and adoption of common mark up standards and specifications for making biodiversity knowledge more accessible and re-usable; e) Provide the community with technical solutions for the enhancement and use of these data; f) Analyze and evaluate business models for supporting Open Science and provide recommendations to achieve sustainable delivery of biodiversity information to target audiences; g) Develop and agree on a shared data and IPR policy; h) Promote and increase cooperation between the major biodiversity projects, initiatives and platforms at EU and global levels.\n\nThese activities will prepare the ground for an integrative system for intelligent management of biodiversity knowledge. A system that facilitates open access to taxonomic data is essential because it will allow a sustainable provision of high quality data to partners and users, including e-science infrastructure projects as well as global initiatives on biodiversity informatics.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2008-1.1.1 | Award Amount: 9.66M | Year: 2008

EUFAR is the Integrating Activity for airborne research in Geo-science. It will integrate the airborne community, to ensure that researchers may have access to the most suited infrastructure they need, irrespective of the location of the infrastructure. The EUFAR consortium comprises 32 legal entities. 14 operators of airborne facilities, and 18 experts in airborne research. They contribute to 9 Networking Activities, Trans-national Access to 26 installations, and 3 Joint Research Activities. A Scientific Advisory Committee, constituted of eminent scientists, contributes to a better integration of the users with the operators to tackle new user driven developments. Transnational Access coordination aims at providing a wider and more efficient access to the infrastructures. The working group for the Future of the Fleet fosters the joint development of airborne infrastructures in terms of capacity and performance. The Expert Working Groups facilitate a wider sharing of knowledge and technologies across fields. The activity for Education and Training provides training courses to new users. The working group on Standards and Protocols contributes to better structure the way research infrastructures operate. The development of a distributed data base for airborne activities improves the access to the data collected by the aircraft. All these activities rely on an unique web portal to airborne research in Europe. The working group on the Sustainable Structure aims at promoting solutions for the long term sustainability of EUFAR. Among the JRA, one will develop and characterize airborne hygrometers, the second one will develop and implement quality layers in the processing chains of hyperspectral imagery, and the third one will develop an airborne drop spectrometer based on a new principle.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH-2007-2.1-01 | Award Amount: 1.57M | Year: 2009

The aim of the project is to analyse, within a comparative institutionalist analytical framework, the trajectories of socio-economic development models. Comparative analyses of forms of capitalism have underlined the diversity in institutional configurations. Within the EU, it is assumed that four types of socio-economic models exist: market-oriented, continental, Nordic, and Southern, with the position of transitional CEEC under discussion. The project will reconstitute the historical trajectories of these socio-economic models, in order to understand how their institutional configuration mediates the synergies and trade-offs between the economic, social and environmental dimensions of development. By focusing on complementarities and conflicts as well as changes in socio-political compromises, by contesting the hypothesis of convergence towards a specific European model and by analysing the impacts of globalisation and structural reforms, the possible future for these models will be discussed. The project will combine three approaches Firstly, a quantitative analysis of the trajectories of socio-economic models. Using long-term data bases for industrialized countries, statistical and econometrical analyses will allow for a quantitative historical analysis of trajectories for the period 1975-2005. The analysis will be completed with analysis of CEEC and emerging countries for the period 1990-2010. Secondly, a comparative analysis of socio-political dynamics and institutional changes. Twelve European and four non-European countries will be examined in order to identify, from an historical perspective, the evolution of socio-political compromises and their influence on the dynamics of institutional changes. Thirdly, sectoral analyses of institutional configurations and industrial dynamics, which will combine statistical and socio-political approaches in order to analyse the long term dynamics of four industries within different socio-economic models.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2008-1.1.1 | Award Amount: 9.65M | Year: 2009

SYNTHESYS IA will aid in the evolution of a European resource through the creation an accessible, integrated infrastructure for researchers in the natural sciences in Europe and globally. By focusing the JRA on DNA extraction, SYNTHESYS IA will increase the opportunities for Users to exploit a largely untapped facet of the 337 million strong collections. Users will be able to play an active role in generating new knowledge based on molecular and morphological studies. A range of new services and improved access both physical and digital will be provided to a broad range of scientific Users (from biological and geological related disciplines) in a consistent and more easily accessible way. The new tools to be developed and disseminated will give Users the chance to pursue new avenues for independent studies at the leading edge of biodiversity and environmental research.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.3.4-1 | Award Amount: 3.82M | Year: 2013

Background Ixodes ricinus transmits bacterial, protozoal and viral pathogens that cause Lyme borreliosis, babesiosis and tick-borne encephalitis respectively and exceedingly affect Central and Eastern Europe (CEE). During feeding, ticks introduce salivary proteins in the skin that interfere with host defense mechanisms. However, in animals repeated tick infestations as well as vaccination against selected tick proteins can lead to decreased pathogen transmission by inhibiting tick feeding - known as tick immunity - or by neutralizing tick proteins that facilitate the transmission of tick-borne pathogens (TBPs). Also humans with hypersensitivity to tick-bites have a lower risk of contracting tick-borne diseases (TBDs). Therefore, anti-tick vaccines encompass an innovative strategy to prevent TBDs in humans, or animals and wildlife to indirectly reduce the risk of contracting TBDs for humans. Overall Objective To identify and characterize tick proteins involved in tick immunity and TBP transmission and to use this knowledge to develop anti-tick vaccines to prevent multiple human TBDs. Methods Using state of the art proteomic and transcriptomic approaches we will identify and characterize novel tick salivary gland proteins, which will be subsequently assessed as anti-tick vaccines to protect against LB, babesiosis and TBE in animal models. In addition, through an integrated and multidisciplinary approach involving CEE public health institutes, health organizations and industrial companies we will examine how to develop anti-tick vaccines and implement these in public health systems. Impact ANTIDotE will deliver 1) essential knowledge on the biological mechanisms involved in the pathogenesis of TBDs, 2) proof of concept of an anti-tick vaccine protecting against multiple human TBPs and 3) plans for exploitation and implementation of anti-tick vaccines, significantly contributing to downscaling the severe medical and economic burden that TBDs have on societies.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2011-1.1.3. | Award Amount: 8.84M | Year: 2012

The Collaborative EuropeaN Digital Archive Infrastructure (CENDARI) will provide and facilitate access to existing archives and resources in Europe for the study of medieval and modern European history through the development of an enquiry environment. This environment will increase access to records of historic importance across the European Research Area, creating a powerful new platform for accessing and investigating historical data in a transnational fashion overcoming the national and institutional data silos that now exist. It will leverage the power of the European infrastructure for Digital Humanities (DARIAH) bringing these technical experts together with leading historians and existing research infrastructures (archives, libraries and individual digital projects) within a programme of technical research informed by cutting edge reflection on the impact of the digital age on scholarly practice. The enquiry environment that is at the heart of this proposal will create new ways to discover meaning, a methodology not just of scale but of kind. It will create tools and workspaces that allow researchers to engage with large data sets via federated multilingual searches across heterogeneous resources while defining workflows enabling the creation of personalized research environments, shared research and teaching spaces, and annotation trails, amongst other features. This will be facilitated by multilingual authority lists of named entities (people, places, events) that will harness user involvement to add intelligence to the system. Moreover, it will develop new visual paradigms for the exploration of patterns generated by the system, from knowledge transfer and dissemination, to language usage and shifts, to the advancement and diffusion of ideas.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.1.6 | Award Amount: 3.63M | Year: 2008

The aim of this project is to provide a multi-level infrastracture of interconnected testbeds of large-scale wireless sensor networks for research purposes, pursuing an interdisciplinary approach that integrates the aspects of hardware, software, algorithms, and data. This will demonstrate how heterogeneous small-scale devices and testbeds can be brought together to form well-organized, large-scale structures, rather than just some large network; it will allow research not only at a much larger scale, but also in different quality, due to heterogeneous structure and the ability to deal with dynamic scenarios, both in membership and location. For the interdisciplinary area of wireless sensor networks, establishing the foundations of distributed, interconnected testbeds for an integrated approach to hardware, software, algorithms, and data will allow a new quality of practical and theoretical collaboration, possibly marking a turning point from individual, hand-tailored solutions to large-scale, integrated ones. For this end, we will engage in implementing recent theoretical results on algorithms, mechanisms and protocols and transform them into software. We will apply the resulting code to the scrutiny of large-scale simulations and experiments, from which we expect to obtain valuable feedback and derive further requirements, orientations and inputs for the long-term research. We intend to make these distributed laboratories available to the European scientific community, so that other research groups will take advantage of the federated infrastructure. Overall, this means pushing the new paradigm of distributed, self-organizing structures to a different level.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2007-2.2-01 | Award Amount: 6.37M | Year: 2008

The Life Watch e-Science and Technology Infrastructure for biodiversity data and observatories will be a large-scale European research infrastructure bringing together: -a system of marine, terrestrial and freshwater observatories; -common access to a huge amount of interlinked, distributed data from databases and monitoring sites; -computational facilities in virtual laboratories with analytical and modelling tools; -targeted user and training support and a programme for public services. The biodiversity research infrastructure will open up new and exciting research opportunities, and will help to enhance the understanding and sustainable management of our natural environment. This preparatory project brings together the interested EU Member and Associated States with the objective to prepare a cooperation agreement on the construction and maintenance of the Life Watch research infrastructure. In addition, the leading networks in biodiversity science and stakeholder institutes are preparing the organisation and logistics for the following construction phase. The current project delivers the technical, legal and financial preparations required for entering and managing the Construction Phase. A range of policy issues are resolved with respect the organisation of the distributed infrastructure, its legal implications, construction logistics, user service, cost analysis and planning. In addition the project makes the necessary preparations in the domain of risk management and quality control. The project is planned to take three years. A Policy and Science Board, populated by the representatives of fourteen potentially interested partner countries and eight cooperating scientific networks, oversees the progress of the preparations. The individual members of the Board act as the liaison with their political domains and the research communities, respectively.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2010-IRSES | Award Amount: 180.50K | Year: 2011

The key objective of this multidisciplinary project is to intensify and consolidate cooperation between research groups from member states and Third countries on topics of synergy in research, innovation, sharing common expertise and technology transfer in the area of photovoltaic, more specifically in Kesterite materials. This project will provide the possibility to the involved research organizations, to reinforce their research cooperation on the long term. They will establish through this joint program, new opportunities for a further exploration of solar cell materials science, which plays nowadays a critical role in the implementation of technologies into area of photovoltaic devices. In this sense, the project aims to investigate absorber materials for thin film solar cells that only contain abundant and non-toxic elements as a contribution to a sustainable energy economy. Currently, earth-abundant copper-zinc-tin-chalcogenide kesterites Cu2ZnSn(Se,S)4, are potential alternatives for the two leading technologies Cu(In,Ga)(S,Se) (CIGS) and CdTe, reaching promising efficiencies over 9.6% . The obtained knowledge of these materials will help to understand their physics and give routes to engineer technologies of growing of structural perfect crystals, films and devices on their base. There is still a large need for an ample scientific study in order to support a future implementation of kesterites in the European industry. This multidisciplinary project comprises research activities in materials science and physics and includes the structural, optical and transport characterization of kesterite films and crystals. Throughout the exchange program the individual expertise available at the partners will be combined to study kesterites that are especially appropriate for use as materials for high-efficient, ecologically lovely and low-cost photovoltaic devices. Finally all ideas/developments will be turned into one device that will find applications in photovoltaics


Grant
Agency: Cordis | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2015-ETN | Award Amount: 3.90M | Year: 2016

We propose a Multi-Partner ITN-ETN network on Transport of Soft Matter at the Nanoscale. The scientific topic, which is the focus of the proposal, is an emerging field of science and technology. Challenges such as design of environmentally friendly engineering materials or understanding the principles of biological organization crucially depend on fundamental understanding of transport of fluids and colloids at the nanoscale. Topics we will study within NANOTRANS are at the core of modern technology (i.e. active design of smart nanomaterials, nanofluidic and lab on a chip devices, sustainable nanocompounds, energy storage, contaminants dissemination in environment, oil recovery, drug delivery and disease treatment). The main objective of the ITN network is to train students. We will offer a balanced and timely supradisciplinary research training program providing a range of skills in various scientific and technological disciplines and fostering creativity and entrepreneurial mindset. Both, private and academic sectors are strongly represented in the network and will substantially contribute to the NANOTRANS training program, which will offer the participating fellows unparalleled education unavailable in standard academic programs at Universities, as well as excellent career opportunities both in academia and industry. NANOTRANS research will result in improved fundamental understanding of soft matter systems out of equilibrium, novel experimental and theoretical methods for nanoscale exploration, as well as in designing advanced aterials, products and applications. In turn, it will contribute to issues connected to energy production and storage, sustainable development, and novel disease treatment strategies. The NANOTRANS research, training and outreach activities will have a substantial and lasting impact on the society, environment, international scientific community, industry and on the European Union.


Dommert F.,University of Stuttgart | Wendler K.,Max Planck Institute for Polymer Research | Berger R.,TU Darmstadt | Delle Site L.,Free University of Berlin | Holm C.,University of Stuttgart
ChemPhysChem | Year: 2012

Classical molecular dynamics simulations are a valuable tool to study the mechanisms that dominate the properties of ionic liquids (ILs) on the atomistic and molecular level. However, the basis for any molecular dynamics simulation is an accurate force field describing the effective interactions between all atoms in the IL. Normally this is done by empirical potentials which can be partially derived from quantum mechanical calculations on simple subunits or have been fitted to experimental data. Unfortunately, the number of accurate classical non-polarizable models for ILs that allow a reasonable description of both dynamical and statical properties is still low. However, the strongly increasing computational power allows one to apply computationally more expensive methods, and even polarizable-force-field-based models on time and length scales long enough to ensure a proper sampling of the phase space. This review attempts to summarize recent achievements and methods in the development of classical force fields for ionic liquids. As this class of salts covers a large number of compounds, we focus our review on imidazolium-based ionic liquids, but show that the main conclusions are valid for non-imidazolium salts, too. Insight obtained from recent electronic density functional results into the parametrization of partial charges and on the influence of polarization effects in bulk ILs is highlighted. An overview is given of different available force fields, ranging from the atomistic to the coarse-grained level, covering implicit as well as explicit modeling of polarization. We show that the recently popular usage of the ion charge as fit parameter can looked upon as treating polarization effects in a mean-field matter. © 2012 Wiley-VCH Verlag GmbH& Co. KGaA, Weinheim.


Cubitt T.S.,Complutense University of Madrid | Eisert J.,Free University of Berlin | Wolf M.M.,TU Munich
Physical Review Letters | Year: 2012

The behavior of any physical system is governed by its underlying dynamical equations. Much of physics is concerned with discovering these dynamical equations and understanding their consequences. In this Letter, we show that, remarkably, identifying the underlying dynamical equation from any amount of experimental data, however precise, is a provably computationally hard problem (it is NP hard), both for classical and quantum mechanical systems. As a by-product of this work, we give complexity-theoretic answers to both the quantum and classical embedding problems, two long-standing open problems in mathematics (the classical problem, in particular, dating back over 70 years). © 2012 American Physical Society.


Stroecka A.,Free University of Berlin | Soriano M.,Autonomous University of Madrid | Soriano M.,University of Alicante | Pascual J.I.,Free University of Berlin | Palacios J.J.,Autonomous University of Madrid
Physical Review Letters | Year: 2012

We show that the magnetic state of individual manganese phthalocyanine (MnPc) molecules on a Bi(110) surface is modified when the Mn2+ center coordinates to CO molecules adsorbed on top. Using scanning tunneling spectroscopy we identified this change in magnetic properties from the broadening of a Kondo-related zero-bias anomaly when the CO-MnPc complex is formed. The original magnetic state can be recovered by selective desorption of individual CO molecules. First principles calculations show that the CO molecule reduces the spin of the adsorbed MnPc from S=1 to S=1/2 and strongly modifies the respective screening channels, driving a transition from an underscreened Kondo state to a state of mixed valence. © 2012 American Physical Society.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2012.5.2-1 | Award Amount: 2.99M | Year: 2013

The big bang enlargement of the European Union (EU) has nurtured vivid debates among both academics and practitioners about the consequences of an ever larger Union for the EUs integration capacity. The research project MAXCAP will start with a critical analysis of the effects of the 2004- 2007 enlargement on stability, democracy and prosperity of candidate countries, on the one hand, and the EUs institutions, on the other. We will then investigate how the EU can maximize its integration capacity for current and future enlargements. Adopting an inter-disciplinary and mixed methods approach that combines desk research, in-depth interviews and Q-methodology, MAXCAP will a) explain the effects of the EUs integration modes and strategies on democracy and socio-economic development in the new members, candidates and neighbourhood countries; b) inquire into the relationship between the widening and deepening of the EU by establishing conditions for effective decision-making and implementation in an enlarged EU; c) identify the social limits to the EUs integration capacity related to citizens perceptions of the last and future enlargements; d) study the EUs current and past negotiation strategies in the context of enlargement and investigate to what extent they need to be adjusted to changing conditions in the EU and the candidate countries; e) examine how the EU employs different modes of integrating countries with highly diverse economic powers, democratic qualities of governance, and institutional capacities and f) assess whether alternative models, such as the European Neighbourhood Policy, can be successful in bringing countries closer to the EU. MAXCAP which features a nine-partner consortium of academic, policy, dissemination and management excellence will create new and strengthen existing links within and between the academic and the policy world on matters relating to the current and future enlargement of the EU.


News Article | November 29, 2016
Site: www.eurekalert.org

Research networks to investigate topics such as practices of comparison, neutrinos, dark matter, and the robustness of vision; around €120 million in funding for an initial 4-year period The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) will establish 14 new Collaborative Research Centres (CRCs). This was decided by the responsible Grants Committee during its autumn session in Bonn. The new CRCs will receive a total of 117.4 million euros in funding. There will also be a 22 percent programme allowance for indirect project costs. Seven of the 14 networks set up are CRC/Transregios, which will be spread across multiple research sites. All of the new CRCs will be funded for an initial four-year period starting on 1 January 2017. In addition to the 14 new Collaborative Research Centres, the Grants Committee also approved the extension of 15 existing CRCs for an additional funding period. As a result, the DFG will be funding a total of 268 Collaborative Research Centres from January 2017. The new Collaborative Research Centres in detail (in alphabetical order by their host universities, including the name of the applicant universities): Little is currently known about the history, social and cultural causes, functions and impacts of comparison - despite frequent speculation about the increase in comparisons in certain epochs and in modern societies. In the Collaborative Research Centre "Practices of Comparisons: Ordering and Changing the World", researchers from the fields of history, literature studies, philosophy, history of art, political science and law will investigate how the historically variable practices of comparison link to routines, rules, institutions and discourses - and can thus create structures but also trigger medium-range dynamics or overarching change. (Host university: Bielefeld University, Spokesperson: Professor Dr. Angelika Epple) Industrial forming processes for metals cause damage within the material. It is not known how the damage caused by forming processes such as rolling or deep-drawing is influenced, how it changes throughout the process chain or what impact it has on subsequent component behaviour. The CRC/Transregio "Damage Controlled Forming Processes" therefore aims to develop new methods and technologies to control and predict damage as well as component characteristics. (Host university: Technical University of Dortmund, Spokesperson: Professor Dr.-Ing. A. Erman Tekkaya; additional applicant university: RWTH Aachen University) The aim of the CRC/Transregio "Mobile Material Characterisation and Localisation by Electromagnetic Sensing" is to trial new approaches to mobile material detectors. This would enable the material properties of any object to be determined, even if it were concealed behind a wall, making it possible to locate unconscious persons in a building filled with smoke or contaminated with poisonous gases, or to detect burning cables inside walls, for example. To achieve this it is necessary to develop mobile detectors that record data in a frequency range from several gigahertz to terahertz, which can be used to precisely localise and characterise a complex environment. (Host university: University of Duisburg-Essen, Spokesperson: Professor Dr.-Ing. Thomas Kaiser; additional applicant university: University of Bochum) Myeloid cells - the immune cells of the brain - play an important role in the function of the central nervous system. They are the focus of the work of the CRC/Transregio "Development, Function and Potential of Myeloid Cells in the Central Nervous System (NeuroMac)". Using some of the latest methods in molecular immunology and neuroscience, such as in-vivo microscopy and genome editing, the researchers will investigate the role of myeloid cells in diseases such as stroke, multiple sclerosis, Alzheimer's and Huntington's disease. (Host university: University of Freiburg, Spokesperson: Professor Dr. Marco Prinz; additional applicant universities: Free University of Berlin and Humboldt University of Berlin) The Collaborative Research Centre "N-Heteropolycycles as Functional Materials" is concerned with the field of organic electronics and will investigate new, entirely organic semiconductors. As the fundamental building blocks for semiconductors, the research network will use what are known as N-heteropolycycles and study their characteristics. The researchers intend to address the complete spectrum of chemical synthesis, method development and the physical and theoretical characterisation of organic semiconductors, including the question of the effects of the material properties of N-heteropolycycles in optoelectronic components, such as solar cells. (Host university: University of Heidelberg, Spokesperson: Professor Dr. Lutz H. Gade) In algebra, where exact calculations are essential, modern high-performance computers with mathematical software have enormous computing potential which so far has not been fully exploited. The researchers in the CRC/Transregio "Symbolic Tools in Mathematics and their Application" plan to further develop existing computer algebra systems which they have largely developed themselves and in doing so, answer fundamental questions in mathematics. They also plan to make the software available as an open-source system. (Host university: Technical University of Kaiserslautern, Spokesperson: Professor Dr. Gunter Malle; additional applicant universities: RWTH Aachen University; Saarland University) Symplectic geometry has its roots in classical mechanics, where it enables a coordinate-free formulation of the basic equations of motion and therefore a deeper understanding of the underlying dynamics. The CRC/Transregio "Symplectic Structures in Geometry, Algebra and Dynamics" will investigate symplectic structures and the application of symplectic techniques to topics in geometry, algebra, dynamic systems, topology, combinatorics and optimisation. The network will forge links with disciplines in which the potential of a symplectic approach has been little or not fully realised or which themselves can contribute new methodologies to the study of symplectic questions, for example computer science. (Host university: University of Cologne, Spokesperson: Professor Dr. Hansjörg Geiges; additional applicant university: University of Bochum) How is information organised and structured in language? The factor of 'prominence' plays a central role in the formation of language structures. Through its formulated question, the Collaborative Research Centre "Prominence in Language" will bring together many areas of linguistics, such as phonetics/phonology, morphology, syntax, semantics, pragmatics and discourse. It will also investigate the relationships between linguistic prominence and general cognitive mechanisms such as the accentuation of attention, thus forging links with psychology and clinical linguistics. (Host university: University of Cologne, Spokesperson: Professor Dr. Klaus von Heusinger) Contrary to a long-held view, bacteria are highly organised units whose function is guaranteed by the precise positioning of biomolecules inside them. The CRC/Transregio "Spatiotemporal Dynamics of Bacterial Cells" will consider many different aspects of cellular organisation, such as the spatiotemporal regulation of cell division, growth and morphogenesis, the organisation and segregation of chromosomal DNA and the dynamics of the formation of (membrane) protein complexes. In this way, the CRC/Transregio aims to identify the molecular systems responsible for controlling these cellular processes and better understand the spatiotemporal dynamics of bacterial cells. (Host university: University of Marburg, Spokesperson: Professor Dr. Martin Rudolf Thanbichler; additional applicant university: LMU Munich) The CRC/Transregio "Rationality and Competition: The Economic Performance of Individuals and Firms" brings together representatives of behavioural economics and neoclassical economics. They aim to explain how distortions and anomalies in the behaviour of individuals and companies are connected and what economic policy measures can effectively protect consumers and employees against poor decisions and exploitation. (Host university: LMU Munich, Spokesperson: Professor Dr. Klaus Schmidt; additional applicant university: Humboldt University of Berlin) A Munich-based Collaborative Research Centre will investigate "Neutrinos and Dark Matter in Astro- and Particle Physics (NDM)". The researchers are primarily interested in neutrinos, the most common particles of matter in the universe, and dark matter, which is responsible for cosmic dynamics on galactic and even larger scales. Among the topics they will address is the still unanswered question of whether neutrinos are their own antiparticles and whether they have sterile partners. The answer to this question could explain why our world consists of more matter than antimatter. (Host university: Technical University of Munich, Spokesperson: Professor Dr. Elisa Resconi) The high resource demands of construction, a fast-growing world population, especially in urban areas, and the changing needs of inhabitants create a need for fundamentally new architectural concepts. The aim of the Collaborative Research Centre "Adaptive Envelopes and Structures for the Future Built Environment" is therefore to develop concepts for adaptive buildings. The network will investigate the potential of adaptive elements for load-bearing structures, envelope systems and interior fittings, with a view to designing buildings which can actively react to external influences. (Host university: University of Stuttgart, Spokesperson: Professor Dr.-Ing. Werner Sobek) Our sense of sight enables us to identify objects reliably even under very different conditions; we therefore have robust visual inference. This ability demands complex calculations, which are performed by the nerve cells in the visual system. The aim of the Collaborative Research Centre "Robust Vision - Inference Principles and Neural Mechanisms" is to uncover the principles and algorithms that make robust vision possible. The researchers will also use technical algorithms of human learning and computer vision research to draw conclusions about biological vision. (Host university: University of Tübingen, Spokesperson: Professor Dr. Matthias Bethge) Predicting the extent to which pollutants will remain in and alter our landscapes in the long term is a major challenge in geosciences and environmental research, all the more so as the extremely complex processes are very difficult to measure with laboratory experiments. The Collaborative Research Centre "Catchments as Reactors: Metabolism of Pollutants on the Landscape Scale (CAMPOS)" will therefore investigate the transport and conversion of pollutants in the large-scale and long-term process chains found in nature. The researchers will utilise innovative observation systems and numerical landscape models with a view to laying the foundations for more reliable predictions about future soil and water quality in the face of climate and land use change. (Host university: University of Tübingen, Spokesperson: Professor Dr. Peter Grathwohl) Further information will be provided by the spokespersons of the Collaborative Research Centres. Contact at the DFG Head Office: Dr. Klaus Wehrberger, Head of the Research Centres Division, Tel. +49 228 885-2355, Klaus.Wehrberger@dfg.de More details about the funding programme and the funded Collaborative Research Centres are available at: http://www.


HONG KONG, CHINA--(Marketwired - Dec 16, 2016) - The Yidan Prize Foundation has visited Europe to encourage nominations for the Yidan Prize and engage in discussions on the future of education with a cross-section of stakeholders in the region. This high-level engagement brings together for the first time the world's largest international award in education and the European education community. In early December, Charles Chen Yidan, founder of the Yidan Prize and a core founder of Chinese internet company Tencent visited the UK and Germany to introduce the Yidan Prize to leading members of the academic and education community. In addition to visiting the Universities of Oxford and Cambridge and University College London, he also had meetings with the Sutton Trust, the Bertelsmann Stiftung, Humboldt University of Berlin, Free University of Berlin, the Robert Bosch Stiftung, the German Academic Exchange Service (DAAD) and other universities, foundations and research institutes. During his stay in the UK, Mr. Chen spoke at the Milken Institute London Summit 2016, which was attended by almost a thousand business leaders, investors, philanthropists and decision-makers. Speaking about his visit to Europe, Mr. Chen said: "I founded the Yidan Prize to support ideas that can change the lives of people around the world by encouraging innovation and forward thinking in education, so Europe, with its long tradition of giving birth to ideas and educational initiatives that have found global audiences and applications, is an obvious and essential place to promote the prize. During my visit to Europe, I had some fruitful meetings and I was impressed by how Europe emphasizes humanities and constant innovation in education system." "From my own experience with Tencent and since then as a philanthropist supporting educational initiatives in China, I understand the potential of technology to transform global education, and with 47 percent of people globally now using the internet this potential is growing by the day. Such tremendous advances in connectivity now mean that we can bring learning opportunities to communities that previously did not have them, and leverage technology and innovation to raise standards and levels of education worldwide." Established in 2016, the Yidan Prize recognizes individuals whose work transforms education in innovative ways that can be repeated around the world to provide access and improve the quality of education for all. Nominations for the Prize are currently open, and will be accepted until March next year. Founded in 2016 by Charles Chen Yidan, the Yidan Prize reaches out to the world to give recognition to individuals whose work makes profound contributions to education research and development, with the ultimate aim of creating a better world through education. The Yidan Prize consists of two awards: the Yidan Prize for Education Research, which recognizes outstanding research that amounts to significant contributions to education; and the Yidan Prize for Education Development, which recognizes innovative ideas that tackle pressing challenges in the field of education. Nominees can be either individuals or teams of up to three representatives, who can be teachers, researchers, academics, policymakers and advocates among others. Yidan Prize Laureates each receive a gold medal and a total sum of HK$30 million (about $3.8 million) including a cash prize and a project fund of HK$15 million (about $1.9 million). To ensure transparency and sustainability, the prize is managed by the Yidan Prize Foundation and governed by an independent trust with an endowment of HK$2.5 billion (about $320 million). Through a series of initiatives, the prize serves to establish a platform that allows the global community to engage in conversation around education and to play a role in education philanthropy. As a part of the project, the Yidan Prize Foundation commissioned the Economist Intelligence Unit (EIU) to conduct a study on future trends in education across 25 economies. The results can be viewed here: https://www.eiuperspectives.economist.com/talent-education/education-2030 For more information on the Yidan Prize: www.yidanprize.org/en/


News Article | December 14, 2016
Site: www.eurekalert.org

The latest recipients of Germany's most prestigious research funding prize have been announced. In Bonn today, the Joint Committee of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) chose ten researchers, three women and seven men, to receive the 2017 Leibniz Prize. The recipients of the prize were selected by the Nominations Committee from 134 nominees. Of the ten new prizewinners, three are from the natural sciences, three from the humanities and social sciences, two from the life sciences and two from the engineering sciences. Each of the ten winners will receive €2.5 million in prize money. They can use these funds for their research work in any way they wish, without bureaucratic obstacles, for up to seven years. The awards ceremony for the 2017 Leibniz Prizes will be held on 15 March in Berlin. The following researchers will receive the 2017 "Funding Prize in the Gottfried Wilhelm Leibniz Programme" awarded by the DFG: The Gottfried Wilhelm Leibniz Prize has been awarded by the DFG annually since 1986. Each year a maximum of ten prizes can be awarded, each with prize money of €2.5 million. With the ten prizes for 2017, a total of 348 Leibniz Prizes have been awarded to date. Of these, 115 were bestowed on researchers in the natural sciences, 101 in the life sciences, 79 in the humanities and social sciences, and 53 in the engineering sciences. The number of award recipients is higher than the number of awarded prizes because, in exceptional cases, the prizes and money can be shared. Accordingly, a total of 374 nominees have received the prize, including 326 men and 48 women. The Leibniz Prize is the most significant research prize in Germany. Seven past prizewinners have subsequently received the Nobel Prize: 1988 Professor Dr. Hartmut Michel (Chemistry), 1991 Professor Dr. Erwin Neher and Professor Dr. Bert Sakmann (Medicine), 1995 Professor Dr. Christiane Nüsslein-Volhard (Medicine), 2005 Professor Dr. Theodor W. Hänsch (Physics), 2007 Professor Dr. Gerhard Ertl (Chemistry) and most recently in 2014 Professor Dr. Stefan W. Hell (Chemistry). Professor Dr. Lutz Ackermann (43), Organic Molecular Chemistry, Institute of Organic and Biomolecular Chemistry, University of Göttingen Lutz Ackermann has been selected for the 2017 Leibniz Prize for his outstanding work in the field of organic chemistry. His international reputation is based especially on his research into the catalytic activation of carbon-hydrogen bonds. These bonds, which occur in all organic substances, are usually extremely inert and permit only very poor and frequently non-selective transformation. The methods developed by Ackermann and his colleagues have paved the way for fundamentally new and low-impact manufacturing methods for important chemical products including active substances, agrochemicals and fine chemicals. Through his other work, Ackermann has also created new concepts for environmentally friendly chemical synthesis. Lutz Ackermann studied chemistry in Kiel, and, after further studies in Rennes and Mülheim an der Ruhr, he obtained his doctorate from the University of Dortmund. He did postdoctoral research at Berkeley before going to Munich in 2003 to work as the leader of a DFG-funded Emmy Noether independent junior research group. Ackermann has held his current chair in Göttingen since 2007 and has headed the Institute of Organic and Biomolecular Chemistry there since 2015. He is one of the most frequently cited researchers in his field in the world. Professor Dr. Beatrice Gründler (52), Arabic Studies, Seminar for Semitic and Arabic Studies, Free University of Berlin Beatrice Gründler will receive the Leibniz Prize for her studies on the diversity of voices in Arabic poetry and culture. She has been interested in the medium of script and its fundamental importance to Arabic traditions since an early stage in her career, as evidenced for example by her book "The Development of the Arabic Script" (1993). Through her research she has developed a complex media history of the Arab world, from the introduction of paper to book printing and beyond - indeed, she refers to an 'Arabic book revolution'. In a pilot project for a critical, annotated digital edition of the "Kalila wa-Dimna", begun in 2015, Gründler has unravelled the history of the text, development and impact of this collection of fables, considered one of the earliest Arabic prose works and a central text of Arabic wisdom literature. Gründler's own approach puts into practice in an exemplary way the encounters between Arabic and European knowledge traditions that she investigates in her work - another reason for the importance of her research. Beatrice Gründler studied at Strasbourg, Tübingen and Harvard, where she received her doctorate in 1995. After a period at Dartmouth College, she began teaching at Yale University in 1996, first as an assistant professor and from 2002 as Professor of Arabic Literature. In 2014 she returned to Germany, and has since been undertaking research at the Free University of Berlin. Ralph Hertwig will be recognised with the 2017 Leibniz Prize for his pioneering work in the psychology of human judgement and decision-making. His research has expanded our understanding of the possibilities and limitations of human rationality. Hertwig investigates the strategies which humans use, faced with limited knowledge, limited cognitive resources and often limited time, to nonetheless make good decisions and organise their actions. Central to his work is the question why a limitation also constitutes a strength, in other words how adaptive heuristics, as simple rules of thumb for problem-solving, can be as effective as complex optimisation models. Another of Hertwig's important contributions to decision research is the distinction between experience-based and description-based assessment of risk. This explains why the dramatic consequences of climate change, for example, are systematically underestimated by society, because although there is plenty of information available to describe the problem, there is little everyday experience - the main thing that people base their decisions on. Ralph Hertwig has been the director of the Max Planck Institute for Human Development since 2012 and heads the Center for Adaptive Rationality. Hertwig began his scientific career in 1995 at the Max Planck Institute for Psychological Research in Munich. In 1997 he moved to the Max Planck Institute in Berlin. Between 2000 and 2002 he was a Research Fellow at Columbia University. In 2003 he obtained his habilitation from the Free University of Berlin. In 2005 he was appointed Professor of Cognitive Science and Decision Psychology at the University of Basel, and moved from there to his current position. Karl-Peter Hopfner will receive the Leibniz Prize for his outstanding work in structural molecular biology and genome biology, with which he has made pioneering contributions to the field of DNA repair and the cellular detection of foreign nucleic acids. Hopfner's research focused on the molecular mechanisms of multiprotein complexes, which play an important role in the detection of damaged or viral nucleic acids. These detection processes are crucial to the protection of the genome; errors in detection and repair are among the main reasons for the development of cancer. Building on that work, Hopfner has carried out essential work on DNA double-strand break repair and in recent years has decoded the mechanism of the central MRN complex Mre11-Rad50-Nbs1, a DNA damage sensor. He also contributed substantially to answering the question of how cellular sensors of the innate immune system recognise viral or bacterial nucleic acids in the case of infection. Here, the sensors must distinguish between the body's own RNA and foreign RNA. Karl-Peter Hopfner studied biology in Regensburg and in St. Louis, USA. He completed his doctorate at the Max Planck Institute for Biochemistry in Martinsried as part of the Division led by Nobel Prize winner Robert Huber. Between 1999 and 2001 he carried out postdoctoral research at the Scripps Research Institute in La Jolla, before accepting a tenure track professorship at the Gene Center at LMU Munich. He has been a full professor at LMU since 2007. Professor Dr. Frank Jülicher (51), Theory of Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden The award of the Leibniz Prize to Frank Jülicher recognises a world-leading researcher in biophysics with the ability to identify universal physical principles in the complex world of living matter. He had already attracted attention with his early work on the physics of hearing and cell mechanics. Through his investigation of active matter - the components of which exhibit autonomous activity, such as molecular motors, which play a key role in cell movement and division - Jülicher has established a new field of research. This raises many fundamental questions in non-equilibrium physics and has also inspired numerous new applications as well as biomimetic design. In collaboration with French researchers, the biophysicist laid the foundations for the dynamics of active matter by formulating a general hydrodynamic theory of active matter. Most recently, Jülicher has turned his attention to the control and organisation of cells in tissue. His seminal work is contributing to our understanding of cell self-organisation in tissue. This phenomenon, as yet poorly understood, is of enormous importance to developmental biology and medical applications. Frank Jülicher studied physics in Stuttgart and Aachen, received his doctorate in Cologne in 1994 and then spent two years researching in the USA and Canada. He subsequently worked with leading researchers in Paris in the field of soft matter and biophysics, before obtaining his habilitation in 2000 at Paris Diderot University (Paris 7). Since 2002, Jülicher has been the director of the Max Planck Institute for the Physics of Complex Systems in Dresden and Professor of Biophysics at the Technical University of Dresden. Professor Dr. Lutz Mädler (45), Mechanical Process Engineering, Stiftung Institut für Werkstofftechnik (IWT) and Department of Production Engineering, University of Bremen Lutz Mädler will receive the Leibniz Prize in recognition of his pioneering work in the targeted reactive formation of nanoparticles in the gas phase and their effect on living matter. He has developed an improved variant of flame spray pyrolysis for the cost-effective synthesis of nanoparticles, involving the thermochemical splitting of organic compounds. His work has made flame spray pyrolysis available for industrial applications. Mädler subsequently refined this pyrolysis technique when he discovered the droplet explosion phenomenon in flame sprays and its effects on material synthesis. However, as well as looking at the tailored synthesis of nanoparticles, Mädler has also investigated how toxic these particles are to the human body. This is important because many applications, for example paints, textiles and dental fillings, have direct impacts on humans. Mädler was able to demonstrate that interactions between synthetic nanoparticles and biological tissue produce reactive oxygen species which can trigger undesirable reactions. Lutz Mädler studied physics at the Technical University of Zwickau and then process engineering at Technische Universität Bergakademie Freiberg, where he obtained his doctorate in 1999. He completed his habilitation at ETH Zurich and then, with the support of a DFG fellowship, became a Senior Researcher at the University of California, Los Angeles. In 2008 he was appointed professor at the University of Bremen. Britta Nestler has been selected to receive the 2017 Leibniz Prize for her significant, internationally recognised research in computer-assisted materials research and the development of new material models with multiscale and multiphysical approaches. Nestler has developed extremely flexible and high-performing simulation environments to simulate the microstructure of materials for use on supercomputers. These are based on her own quantitative models for the description of multicomponent systems. She has thus achieved a new quality of microstructure representation in the thermomechanical simulation of materials and the simulation of solidification processes and thus depicted these processes through realistic 3D simulation for the first time. Through her creative application and further development of the phase field method, Nestler has achieved outstanding fundamental insights which are also of enormous practical relevance. For example, her simulation calculations are used to predict the spread of cracks in design materials such as brake discs and therefore help to extend their lifetime. Britta Nestler studied physics and mathematics in Aachen, where she also received her doctorate. Research visits took her to Southampton, UK and Paris. In 2001 Nestler accepted a professorship in the Faculty of Computer Science at Karlsruhe University of Applied Sciences and in 2009 her current chair at KIT. Professor Dr. Joachim P. Spatz (47), Biophysics, Max Planck Institute for Intelligent Systems, Stuttgart, and Institute of Physical Chemistry, University of Heidelberg Joachim Spatz will be recognised with the Leibniz Prize for his outstanding research at the boundaries of materials sciences and cell biophysics. His research is concerned with cell adhesion, that is, the adhesion and bonding of cells to one another and to surfaces. His exemplary experimental approach has garnered precise insights into the control of cell adhesion and indeed physiological processes. To achieve this, Spatz used artificial, molecularly structured boundary surfaces to reduce possible interactions to a minimum of molecular components. Joachim Spatz' scientific achievement lies in the fact that he can study the communication mechanisms between cells in a new way with the help of concepts from materials science and physics. Using these resources, he was able to explain how the molecular mechanism of collective cell migration works in wound healing. Joachim Spatz studied physics in Ulm and at Colorado State University. He obtained his doctorate in macromolecular chemistry in Ulm, and it was also there that he completed his habilitation with a topic on cell mechanics. Since 2000 he has been a professor of biophysical chemistry in Heidelberg. In 2004 he was appointed director of the Max Planck Institute for Metals Research, now the Max Planck Institute for Intelligent Systems, in Stuttgart. Since 2008 he has also held a visiting professorship in molecular cell biology at the Weizmann Institute in Rehovot, Israel. Professor Dr. Anne Storch (48), African Studies, Institute for African Studies and Egyptology, University of Cologne In awarding the 2017 Leibniz Prize to Anne Storch, the DFG is honouring an extremely innovative and world-renowned researcher in African Studies who has contributed to a far-reaching reorientation of her field through her pioneering work. Drawing on questions and methods from cultural anthropology and the social sciences, Storch has introduced new thematic and methodological dimensions, both theoretical and practical, to African Studies. Her exemplary studies have also shown how linguistically based analyses can be used in an interdisciplinary approach to develop a cultural-anthropological understanding of contemporary Africa. Of particular significance was her study of taboos and secret languages in central Africa, published in 2011, which describes linguistic observations in such a way that they lead to complex sociological descriptions of power practices and political mechanisms of effect. Storch's case studies, rooted in, yet transcending, linguistic speech description, have become internationally significant model studies for a modern, self-critical approach to African Studies. Anne Storch has been Professor of African Studies in Cologne since 2004. She trained in anthropology, African Studies, Oriental Studies and archaeology in Frankfurt am Main and Mainz. Between 2006 and 2009 she served as president of the Fachverband Afrikanistik, the specialist society for Africa-related scholarship in Germany. Since 2014 she has been the president of the International Association for Colonial and Postcolonial Linguistics. Awarding the Leibniz Prize to Jörg Vogel recognises one of the world's leading researchers in the field of ribonucleic acid biology. He was selected for his pioneering contributions to our understanding of regulatory RNA molecules in infection biology. Vogel recognised the importance of RNA biochemistry in prokaryotes very early on and has done pioneering work in the application and development of high-throughput sequencing for RNA analysis. Using this method, he has studied the influence of pathogens on the host cell. Vogel has also discovered how small regulatory RNA molecules control protein synthesis and the breakdown of RNA. This in turn has contributed to the development of new methods which can be used in gene therapy. Together with Emmanuelle Charpentier, who won the Leibniz Prize in 2016, Vogel was able to understand tracrRNA (trans-activating RNA) and its function, which made the application of the CRISPR/Cas9 system possible. Vogel thus uncovered general biological principles which play a major role in our understanding of pathogenic microorganisms and are resulting in new treatment approaches. Jörg Vogel studied biochemistry at the Humboldt University of Berlin, where he also obtained his doctorate on RNA splicing in plants. After doing postdoctoral research in Uppsala and Jerusalem, in 2004 he was appointed Head of Division at the Max Planck Institute for Infection Biology in Berlin. Since 2009 he has been a professor at the University of Würzburg, where he heads the Institute for Molecular Infection Biology. The Leibniz Prizes will be awarded on 15 March 2017 at 3.00 pm at the Berlin-Brandenburg Academy of Sciences and Humanities in Berlin. A separate invitation will be sent to members of the media. Additional information about the 2017 prizewinners can be requested at the start of the new year by contacting the DFG Press and Public Relations Office or at http://www. . Detailed information about the Gottfried Wilhelm Leibniz Programme is available at: http://www.


News Article | November 23, 2015
Site: cen.acs.org

Last July, Carmen Bachmann had an idea. The University of Leipzig professor wanted to help the growing influx of refugees arriving in Germany from conflict-ridden Syria, as well as from Afghanistan, Iraq, and elsewhere. With the help of an undergraduate student, Bachmann built an online platform called “Chance for Science” designed to connect refugee scientists with local academics. Bachmann’s organization is one of several efforts reaching out to scientists and engineers thought to be among the hundreds of thousands of refugees, asylum seekers, and others in Europe looking for temporary safety from conflict in the Middle East. Many European countries are tightening their borders to refugees after this month’s deadly terrorist attacks in Paris. But given how many people have already arrived, nonprofits and government agencies reckon there must be some highly qualified scientists among them. Finding those trained in the sciences will be difficult. And figuring out how to help them might be even harder, given that the migrants’ challenges include finding housing, language barriers, and asylum applications. The United Nations High Commissioner for Refugees estimates that well over 800,000 refugees and asylum seekers arrived in Europe by sea alone so far this year, more than half of whom came from Syria, and nearly one-fifth of whom came from Afghanistan. Those numbers dwarf efforts in the U.S., which accepted just 132 in 2014, according to the U.S. Department of Health & Human Services. Earlier this year, President Barack Obama promised to accept 10,000 refugees from Syria in the next year. However, there has been a backlash against that plan in the U.S. after the Paris attacks. Refugees who want to stay in Europe—many hope to make it to Germany or Sweden—must obtain visas that allow either temporary asylum or permission to immigrate. Only then can they think about procuring permission to work—and searching for jobs in what are already tight academic and industry markets. This is just the most recent of Europe’s waves of immigrants. Before the current flood of Syrians, for example, Iraqis arrived in droves in the 1990s and again in the 2000s. Statistics from the European Union show that since 2009, non-EU citizens’ rates of employment have dropped relative to that of EU citizens. These numbers suggest it will be harder for current refugees to find jobs if and when they receive permission to work. Last month, the European Commission’s research and innovation directorate announced its Science4Refugees initiative. The agency hopes its online platform—tied to its existing jobs portal, Euraxess—will act as a kind of matchmaker for refugees seeking science jobs and raise the profile of immigration issues among scientists. But it offers no financial support. Those working on the program say that it’s too soon to evaluate success; meanwhile, the initiative’s staff is working to boost awareness of the program among refugees. They acknowledge that finding their target audience will be difficult and take some time; they hope to find other networks and websites in different countries working on the same goals. As of mid-November, universities have already flagged some 150 jobs on Euraxess with the Science4Refugees label, highlighting their willingness to consider assisting applicants with visas and other red tape. But only around 20 CVs were posted by people with refugee status. That could be because many refugees are still getting settled. First-time asylum seekers have registered in Germany, Hungary, Austria, France, Italy, and Sweden in the greatest numbers. Germany is the number one destination of choice for current refugees: 343,000 applied for asylum between January and October. But getting a work visa could take several months to a year, even after getting asylum papers. The situation is easier in Sweden, which welcomed more than 112,000 refugees from January to October. Although it can take months to grant an individual asylum seeker status, individuals have permission to work in the country the day after receiving their papers. Earlier waves of migration to Sweden have led to assistance programs that eventually could be useful to recent arrivals. For example, the Swedish government offers to pay salaries for researchers in six-month internships with universities and companies; that offer is open to educated immigrants with the right to work as well as Swedes who have been unemployed for six months or more. But in Sweden, as in other EU countries, language could prove to be a stumbling block for even educated asylum seekers: State-sponsored intensive language courses for engineers, medical personnel, and others take one-and-a-half years to complete to teach proficiency in workaday Swedish. Still, the language of science is English, and that may be the case in Lebanon or Syria just as much as it is in Sweden or Germany. Back at the University of Leipzig, refugees who may have had their studies disrupted can audit courses taught in German or English if they are proficient in these languages. (The university has no numbers yet on how many students are taking advantage of these resources.) The Free University of Berlin is also opening courses to refugees even though they are not officially enrolled as students. The university sees this as preparation for enrollment at a later stage, once they have received visas or other kinds of permission to attend classes. In the meantime, already-enrolled students can volunteer to assist refugees in getting familiar with the university, work that counts for credit in job-qualification courses. Meanwhile, Bachmann’s “Chance for Science” now has 200 people registered on the online platform. Only 20 are refugees and might have asylum status. Bachmann is not sure that her efforts will make a difference, but she hopes she can help keep knowledgeable people in their fields.


Klippel S.,Leibniz Institute for Molecular Pharmacology | Klippel S.,Free University of Berlin | Freund C.,Free University of Berlin | Schroder L.,Leibniz Institute for Molecular Pharmacology
Nano Letters | Year: 2014

We demonstrate a concept for multichannel MRI cell-labeling using encapsulated laser-polarized xenon. Conceptually different Xe trapping properties of two nanocarriers, namely macrocyclic cages as individual hosts or compartmentalization into nanodroplets, ensure a large chemical shift separation for Xe bound in either of the carriers even after cellular internalization. Two differently labeled mammalian cell populations were imaged by frequency selective saturation transfer resulting in a switchable "two-color" xenon-MRI contrast at micro- to nanomolar Xe carrier concentrations. © 2014 American Chemical Society.


Rao Y.,Free University of Berlin | Rao Y.,Max Planck Institute of Biochemistry | Haucke V.,Free University of Berlin | Haucke V.,Charité - Medical University of Berlin | Haucke V.,Leibniz Institute for Molecular Pharmacology
Cellular and Molecular Life Sciences | Year: 2011

BAR domain superfamily proteins have emerged as central regulators of dynamic membrane remodeling, thereby playing important roles in a wide variety of cellular processes, such as organelle biogenesis, cell division, cell migration, secretion, and endocytosis. Here, we review the mechanistic and structural basis for the membrane curvature-sensing and deforming properties of BAR domain superfamily proteins. Moreover, we summarize the present state of knowledge with respect to their regulation by autoinhibitory mechanisms or posttranslational modifications, and their interactions with other proteins, in particular with GTPases, and with membrane lipids. We postulate that BAR superfamily proteins act as membrane-deforming scaffolds that spatiotemporally orchestrate membrane remodeling. © Springer Basel AG 2011.


von Kleist L.,Free University of Berlin | Haucke V.,Free University of Berlin | Haucke V.,Charité - Medical University of Berlin | Haucke V.,Leibniz Institute for Molecular Pharmacology
Traffic | Year: 2012

Intracellular membrane traffic regulates cell physiology at multiple levels ranging from cell growth and development to the function of the nervous and immune systems. Multiple endocytic routes are used by distinct cargoes including ligands bound to their receptors but also viruses and pathogens to gain access to the cell interior. Within the endosomal system, proteins and lipids are sorted for degradation or recycling allowing cells to dynamically respond to environmental signals and to regulate cell shape and morphology. Some receptors or toxins are sorted along the retrograde pathway from endosomes to the Golgi complex, where they intersect with secretory cargo destined for exocytosis. Genetic manipulations of these pathways frequently cause problems with regard to data interpretation as the resulting phenotypes may be indirect consequences resulting from perturbation of multiple steps or trafficking routes. Hence, novel approaches are needed to acutely and reversibly perturb intracellular membrane traffic, e.g. by small molecule inhibitors. Such drugs may also be pharmacologically important as they offer new avenues to fight human diseases. Here, we provide an overview of the small molecules available to interfere with intracellular membrane traffic and outline strategies for future research. © 2011 John Wiley & Sons A/S.


Wloka C.,University of Pennsylvania | Wloka C.,Free University of Berlin | Bi E.,University of Pennsylvania
Cytoskeleton | Year: 2012

Cytokinesis is essential for cell proliferation in all domains of life. Because the core components and mechanisms of cytokinesis are conserved from fungi to humans, the budding yeast Saccharomyces cerevisiae has served as an attractive model for studying this fundamental process. Cytokinesis in budding yeast is driven by two interdependent cellular events: actomyosin ring (AMR) constriction and the formation of a chitinous cell wall structure called the primary septum (PS), the functional equivalent of extracellular matrix remodeling during animal cytokinesis. AMR constriction is thought to drive efficient plasma membrane ingression as well as to guide PS formation, whereas PS formation is thought to stabilize the AMR during its constriction. Following the completion of the PS formation, two secondary septa (SS), consisting of glucans and mannoproteins, are synthesized at both sides of the PS. Degradation of the PS and a part of the SS by a chitinase and glucanases then enables cell separation. In this review, we discuss the mechanics of cytokinesis in budding yeast, highlighting its common and unique features as well as the emerging questions. © 2012 Wiley Periodicals, Inc.


Koeppe B.,Free University of Berlin | Tolstoy P.M.,Free University of Berlin | Tolstoy P.M.,Saint Petersburg State University | Limbach H.-H.,Free University of Berlin
Journal of the American Chemical Society | Year: 2011

Combined low-temperature NMR/UV-vis spectroscopy (UVNMR), where optical and NMR spectra are measured in the NMR spectrometer under the same conditions, has been set up and applied to the study of H-bonded anions A· middot;H middot; middot;X- (AH = 1-13C-2-chloro-4-nitrophenol, X- = 15 carboxylic acid anions, 5 phenolates, Cl-, Br -, I-, and BF4 -). In this series, H is shifted from A to X, modeling the proton-transfer pathway. The 1H and 13C chemical shifts and the H/D isotope effects on the latter provide information about averaged H-bond geometries. At the same time, red shifts of the π-π* UV-vis absorption bands are observed which correlate with the averaged H-bond geometries. However, on the UV-vis time scale, different tautomeric states and solvent configurations are in slow exchange. The combined data sets indicate that the proton transfer starts with a H-bond compression and a displacement of the proton toward the H-bond center, involving single-well configurations A-H⋯X-. In the strong H-bond regime, coexisting tautomers A · ·H⋯X- and A-⋯H ··X are observed by UV. Their geometries and statistical weights change continuously when the basicity of X- is increased. Finally, again a series of single-well structures of the type A-⋯H-X is observed. Interestingly, the UV-vis absorption bands are broadened inhomogeneously because of a distribution of H-bond geometries arising from different solvent configurations. © 2011 American Chemical Society.


Sinnhuber B.-M.,Karlsruhe Institute of Technology | Meul S.,Free University of Berlin
Geophysical Research Letters | Year: 2015

Bromine from very short lived substances (VSLS), primarily from natural oceanic sources, contributes substantially to the stratospheric bromine loading. This source of stratospheric bromine has so far been ignored in most chemistry climate model calculations of stratospheric ozone trends. Here we present a transient simulation with the chemistry climate model EMAC for the period 1960-2005 including emissions of the five brominated VSLS CHBr3, CH2Br2, CH2BrCl, CHBrCl2, and CHBr2Cl. The emissions lead to a realistic stratospheric bromine loading of about 20 pptv for present-day conditions. Comparison with a standard model simulation without VSLS shows large differences in modeled ozone in the extratropical lowermost stratosphere and in the troposphere. Differences in ozone maximize in the Antarctic Ozone Hole, resulting in more than 20% less ozone when VSLS are included. Even though the emissions of VSLS are assumed to be constant in time, the model simulation with VSLS included shows a much larger ozone decrease in the lowermost stratosphere during the 1979-1995 period and a faster ozone increase during 1996-2005, in better agreement with observed ozone trends than the standard simulation without VSLS emissions. ©2015. American Geophysical Union. All Rights Reserved.


Ahsanullah,Free University of Berlin | Rademann J.,University of Leipzig | Rademann J.,Leibniz Institute for Molecular Pharmacology
Angewandte Chemie - International Edition | Year: 2010

Support and guidance: Azidopeptidyl phosphoranes on a solid support react very efficiently through cyclative cleavage to yield cyclopeptides with an incorporated triazole ring. The solid support is advantageous as cyclization is favored strongly over oligomerization reactions and thus only cyclized products are released. "Chemical equation presented". © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.


Vent-Schmidt T.,Albert Ludwigs University of Freiburg | Riedel S.,Free University of Berlin
Inorganic Chemistry | Year: 2015

The chemistry of the lanthanides is mostly dominated by compounds in the oxidation state +III. Only few compounds of Ce, Pr, and Tb are known with the metal in the +IV oxidation state. Removal of the last f-electron on praseodymium +IV would lead to a closed-shell system with formal oxidation state V. In this work we investigated the stability of the PrF5 molecule by theory and matrix-isolation techniques through the reaction of laser-ablated praseodymium atoms with fluorine in excess of neon, argon, krypton, or neat fluorine. Besides the known PrF3 molecule, unreported IR bands for PrF4 could be observed, and there is evidence for the formation of PrF and PrF2 but not for the formation of PrF5. © 2015 American Chemical Society.


Lemos J.P.S.,University of Lisbon | Lemos J.P.S.,Free University of Berlin | Zaslavskii O.B.,University of Kharkiv
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

The entropy of extremal black holes (BHs) is obtained using a continuity argument from extremal quasiblack holes (QBHs). It is shown that there exists a smooth limiting transition in which (i) the system boundary approaches the extremal Reissner-Nordström (RN) horizon, (ii) the temperature at infinity tends to zero and quantum backreaction remains bounded on the horizon, and (iii) the first law of thermodynamics is satisfied. The conclusion is that the entropy S of extremal QBHs and of extremal BHs can take any non-negative value, only in particular cases it coincides with S=A/4. The choice S=0 with non-zero temperature at infinity is rejected as physically unsatisfactory. © 2010 Elsevier B.V.


Jaeger P.A.,Free University of Berlin | Jaeger P.A.,Stanford University | Wyss-Coray T.,Stanford University | Wyss-Coray T.,Geriatric Research Education and Clinical Center
Archives of Neurology | Year: 2010

Beclin 1 is a protein involved in the regulation of autophagy and has been shown to be reduced in patients with Alzheimer disease. This review summarizes the current research data that link disturbances in autophagy, a cellular degradation and maintenance pathway, to the development of Alzheimer disease and related neurodegenerative diseases. It also provides a brief overview of the existing pharmacological interventions available to modulate autophagy activity in mammalian cells. ©2010 American Medical Association. All rights reserved.


Lanzer P.,Hospitals and Clinics Bitterfeld Wolfen | Prechelt L.,Free University of Berlin
Catheterization and Cardiovascular Interventions | Year: 2011

Objectives: Accelerate and improve the training and learning process of operators performing percutaneous coronary interventions (PCI). Background: Operator cognitive, in particular decision-making skills and technical skills are a major factor for the success of coronary interventions. Currently, cognitive skills are commonly developed by three methods: (1) Cognitive learning of rules for which statistical evidence is available. This is very incomprehensive and isolates cognitive learning from skill acquisition. (2) Informal tutoring received from experienced operators, and (3) personal experience by trial-and-error are both very slow. Methods: We propose in this concept article a conceptual framework to elicit, capture, and transfer expert PCI skills to complement the current approach. This includes the development of an in-depth understanding of the nature of PCI skills, terminology, and nomenclature needed to streamline communication, propensity of reproducible performance assessment, and in particular an explication of intervention planning and intra-intervention decision-making. We illustrate the impact of improved decision-making by simulation results based on a stochastic model of intervention risk. Results: We identify several key concepts that form the basis of this conceptual framework, in particular different risk types and the notions of strategy, interventional module, and tactic. Conclusions: The increasing complexity of cases have brought PCI to the point where the decision-making skills of master operators need to be made explicit to make them systematically learnable such that the skills of beginner and intermediate operators can be improved much faster than is currently possible. © 2010 Wiley-Liss, Inc.


Inhofer A.,Albert Ludwigs University of Freiburg | Bercioux D.,Albert Ludwigs University of Freiburg | Bercioux D.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

We propose a device that allows for the emission of pairs of spin-polarized electrons into the edge states of a two-dimensional topological insulator. Charge and spin emission is achieved using a periodically driven quantum dot weakly coupled to the edge states of the host topological insulator. We present calculations of the emitted time-dependent charge and spin currents of such a dynamical scatterer using the Floquet scattering matrix approach. Experimental signatures of spin-polarized two-particle emission can be found in noise measurements. Here a new form of noise suppression, named Z2 antibunching, is introduced. Additionally, we propose a setup in which entanglement of the emitted electrons is generated. This entanglement is based on a postselection procedure and becomes manifest in a violation of a Clauser-Horne-Shimony-Holt inequality. © 2013 American Physical Society.


Raz R.,Leibniz Institute for Molecular Pharmacology | Raz R.,Free University of Berlin | Rademann J.,University of Leipzig | Rademann J.,Leibniz Institute for Molecular Pharmacology
Organic Letters | Year: 2011

tert-Butyl thioesters display an astonishing stability toward secondary amines in basic milieu, in contrast to other alkyl and aryl thioesters. Exploiting this enhanced stability, peptide thioesters were synthesized in a direct manner, applying a tert-butyl thiol linker for Fmoc-based solid-phase peptide synthesis. © 2011 American Chemical Society.


Talotta C.,University of Salerno | Gaeta C.,University of Salerno | Qi Z.,Free University of Berlin | Schalley C.A.,Free University of Berlin | Neri P.,University of Salerno
Angewandte Chemie - International Edition | Year: 2013

Partner preferences in pseudorotaxane formation were exploited to establish an integrative self-sorting system able to discriminate simultaneously at the sequence and stereochemical level (see picture). It was found that calix[6]arenes were threaded selectively with a preferred orientation onto bisammonium axles, even when the structural differences between the possible building blocks were small and located remote from the binding sites. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Daumke O.,Max Delbruck Centrum fur Molekulare Medizin | Daumke O.,Free University of Berlin | Roux A.,University of Geneva | Haucke V.,Leibniz Institute for Molecular Pharmacology | Haucke V.,Charité - Medical University of Berlin
Cell | Year: 2014

Biological membranes undergo constant remodeling by membrane fission and fusion to change their shape and to exchange material between subcellular compartments. During clathrin-mediated endocytosis, the dynamic assembly and disassembly of protein scaffolds comprising members of the bin-amphiphysin-rvs (BAR) domain protein superfamily constrain the membrane into distinct shapes as the pathway progresses toward fission by the GTPase dynamin. In this Review, we discuss how BAR domain protein assembly and disassembly are controlled in space and time and which structural and biochemical features allow the tight regulation of their shape and function to enable dynamin-mediated membrane fission. © 2014 Elsevier Inc.


Dias G.A.S.,University of Porto | Lemos J.P.S.,University of Lisbon | Lemos J.P.S.,Free University of Berlin
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

We construct thin-shell electrically charged wormholes in d-dimensional general relativity with a cosmological constant. The wormholes constructed can have different throat geometries, namely, spherical, planar, and hyperbolic. Unlike the spherical geometry, the planar and hyperbolic geometries allow for different topologies and in addition can be interpreted as higher-dimensional domain walls or branes connecting two universes. In the construction we use the cut-and-paste procedure by joining together two identical vacuum spacetime solutions. Properties such as the null energy condition and geodesics are studied. A linear stability analysis around the static solutions is carried out. A general result for stability is obtained from which previous results are recovered. © 2010 The American Physical Society.


Lemos J.P.S.,University of Lisbon | Lemos J.P.S.,Free University of Berlin | Zanchin V.T.,Federal University of ABC
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

In general relativity coupled to Maxwell's electromagnetism and charged matter, when the gravitational potential W2 and the electric potential field φ obey a relation of the form W2=a(-εφ+b)2+c, where a, b, and c are arbitrary constants, and ε=±1 (the speed of light c and Newton's constant G are put to one), a class of very interesting electrically charged systems with pressure arises. We call the relation above between W and φ, the Weyl-Guilfoyle relation, and it generalizes the usual Weyl relation, for which a=1. For both, Weyl and Weyl-Guilfoyle relations, the electrically charged fluid, if present, may have nonzero pressure. Fluids obeying the Weyl-Guilfoyle relation are called Weyl-Guilfoyle fluids. These fluids, under the assumption of spherical symmetry, exhibit solutions which can be matched to the electrovacuum Reissner-Nordström spacetime to yield global asymptotically flat cold charged stars. We show that a particular spherically symmetric class of stars found by Guilfoyle has a well-behaved limit which corresponds to an extremal Reissner-Nordström quasiblack hole with pressure, i.e., in which the fluid inside the quasihorizon has electric charge and pressure, and the geometry outside the quasihorizon is given by the extremal Reissner- Nordström metric. The main physical properties of such charged stars and quasiblack holes with pressure are analyzed. An important development provided by these stars and quasiblack holes is that without pressure the solutions, Majumdar-Papapetrou solutions, are unstable to kinetic perturbations. Solutions with pressure may avoid this instability. If stable, these cold quasiblack holes with pressure, i.e., these compact relativistic charged spheres, are really frozen stars. © 2010 The American Physical Society.


Flammia S.T.,University of Washington | Gross D.,Albert Ludwigs University of Freiburg | Liu Y.-K.,U.S. National Institute of Standards and Technology | Eisert J.,Free University of Berlin
New Journal of Physics | Year: 2012

Intuitively, if a density operator has small rank, then it should be easier to estimate from experimental data, since in this case only a few eigenvectors need to be learned. We prove two complementary results that confirm this intuition. Firstly, we show that a low-rank density matrix can be estimated using fewer copies of the state, i.e. the sample complexity of tomography decreases with the rank. Secondly, we show that unknown low-rank states can be reconstructed from an incomplete set of measurements, using techniques from compressed sensing and matrix completion. These techniques use simple Pauli measurements, and their output can be certified without making any assumptions about the unknown state. In this paper, we present a new theoretical analysis of compressed tomography, based on the restricted isometry property for low-rank matrices. Using these tools, we obtain near-optimal error bounds for the realistic situation where the data contain noise due to finite statistics, and the density matrix is full-rank with decaying eigenvalues. We also obtain upper bounds on the sample complexity of compressed tomography, and almost-matching lower bounds on the sample complexity of any procedure using adaptive sequences of Pauli measurements. Using numerical simulations, we compare the performance of two compressed sensing estimators-the matrix Dantzig selector and the matrix Lasso-with standard maximum-likelihood estimation (MLE). We find that, given comparable experimental resources, the compressed sensing estimators consistently produce higher fidelity state reconstructions than MLE. In addition, the use of an incomplete set of measurements leads to faster classical processing with no loss of accuracy. Finally, we show how to certify the accuracy of a low-rank estimate using direct fidelity estimation, and describe a method for compressed quantum process tomography that works for processes with small Kraus rank and requires only Pauli eigenstate preparations and Pauli measurements. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.


Kliesch M.,Free University of Berlin | Gross D.,Albert Ludwigs University of Freiburg | Eisert J.,Free University of Berlin
Physical Review Letters | Year: 2014

Tensor network states constitute an important variational set of quantum states for numerical studies of strongly correlated systems in condensed-matter physics, as well as in mathematical physics. This is specifically true for finitely correlated states or matrix-product operators, designed to capture mixed states of one-dimensional quantum systems. It is a well-known open problem to find an efficient algorithm that decides whether a given matrix-product operator actually represents a physical state that in particular has no negative eigenvalues. We address and answer this question by showing that the problem is provably undecidable in the thermodynamic limit and that the bounded version of the problem is NP-hard (nondeterministic-polynomial-time hard) in the system size. Furthermore, we discuss numerous connections between tensor network methods and (seemingly) different concepts treated before in the literature, such as hidden Markov models and tensor trains. © 2014 American Physical Society.


Alexiev U.,Free University of Berlin | Farrens D.L.,Oregon Health And Science University
Biochimica et Biophysica Acta - Bioenergetics | Year: 2014

Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks. © 2013 The Authors.


Bergholtz E.J.,Free University of Berlin | Liu Z.,Beijing Computational Science Research Center
International Journal of Modern Physics B | Year: 2013

Topological insulators and their intriguing edge states can be understood in a single-particle picture and can as such be exhaustively classified. Interactions significantly complicate this picture and can lead to entirely new insulating phases, with an altogether much richer and less explored phenomenology. Most saliently, lattice generalizations of fractional quantum Hall states, dubbed fractional Chern insulators, have recently been predicted to be stabilized by interactions within nearly dispersionless bands with nonzero Chern number, C. Contrary to their continuum analogues, these states do not require an external magnetic field and may potentially persist even at room temperature, which make these systems very attractive for possible applications such as topological quantum computation. This review recapitulates the basics of tight-binding models hosting nearly flat bands with nontrivial topology, C≠0, and summarizes the present understanding of interactions and strongly correlated phases within these bands. Emphasis is made on microscopic models, highlighting the analogy with continuum Landau level physics, as well as qualitatively new, lattice specific, aspects including Berry curvature fluctuations, competing instabilities as well as novel collective states of matter emerging in bands with |C|>1. Possible experimental realizations, including oxide interfaces and cold atom implementations as well as generalizations to flat bands characterized by other topological invariants are also discussed. © World Scientific Publishing Company.


Michalak J.,Witten/Herdecke University | Schultze M.,Free University of Berlin | Heidenreich T.,Esslingen University of Applied Sciences | Schramm E.,Albert Ludwigs University of Freiburg
Journal of Consulting and Clinical Psychology | Year: 2015

Objective: Mindfulness-based cognitive therapy (MBCT) has recently been proposed as a treatment option for chronic depression. The cognitive behavioral analysis system of psychotherapy (CBASP) is the only approach specifically developed to date for the treatment of chronically depressed patients. The efficacy of MBCT plus treatment-as-usual (TAU), and CBASP (group version) plus TAU, was compared to TAU alone in a prospective, bicenter, randomized controlled trial. Method: One hundred and six patients with a current DSM-IV defined major depressive episode and persistent depressive symptoms for more than 2 years were randomized to TAU only (N = 35), or to TAU with additional 8-week group therapy of either 8 sessions of MBCT (n = 36) or CBASP (n = 35). The primary outcome measure was the Hamilton Depression Rating Scale (24-item HAM-D, Hamilton, 1967) at the end of treatment. Secondary outcome measures were the Beck Depression Inventory (BDI; Beck, Steer, & Brown, 1996) and measures of social functioning and quality of life. Results: In the overall sample as well as at 1 treatment site, MBCT was no more effective than TAU in reducing depressive symptoms, although it was significantly superior to TAU at the other treatment site. CBASP was significantly more effective than TAU in reducing depressive symptoms in the overall sample and at both treatment sites. Both treatments had only small to medium effects on social functioning and quality of life. Conclusions: Further studies should inquire whether the superiority of CBASP in this trial might be explained by the more active, problem-solving, and interpersonal focus of CBASP. © 2015 American Psychological Association.


Hapke M.,Leibniz Institute for Catalysis at the University of Rostock | Tzschucke C.C.,Free University of Berlin
Angewandte Chemie - International Edition | Year: 2013

Chiral possibilities (Cp): In two approaches for introducing chirality into reactions of half-sandwich Rh complexes, dihydroisoquinolones have been synthesized from benzamides and olefins. In one approach C2-symmetric Cp ligands were utilized, while in the other an artificial metalloenzyme was employed as the chiral catalyst, leading to high levels of enantioselectivity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Zilberberg O.,Weizmann Institute of Science | Romito A.,Karlsruhe Institute of Technology | Romito A.,Free University of Berlin | Gefen Y.,Weizmann Institute of Science
Physical Review Letters | Year: 2011

A protocol employing weak values (WVs) to obtain ultrasensitive amplification of weak signals in the context of a solid-state setup is proposed. We consider an Aharonov-Bohm interferometer where both the orbital and the spin degrees of freedom are weakly affected by the presence of an external charge to be detected. The interplay between the spin and the orbital WVs leads to a significant amplification even in the presence of finite temperature, voltage, and external noise. © 2011 American Physical Society.


Steinigeweg R.,TU Braunschweig | Khodja A.,University of Osnabrück | Niemeyer H.,University of Osnabrück | Gogolin C.,Free University of Berlin | Gemmer J.,University of Osnabrück
Physical Review Letters | Year: 2014

In the ongoing discussion on thermalization in closed quantum many-body systems, the eigenstate thermalization hypothesis has recently been proposed as a universal concept and has attracted considerable attention. So far this concept is, as the name states, hypothetical. The majority of attempts to overcome this hypothetical character are based on exact diagonalization, which implies for, e.g., spin systems a limitation of roughly 15 spins. In this Letter we present an approach that pushes this limit up to system sizes of roughly 35 spins, thereby going significantly beyond what is possible with exact diagonalization. A concrete application to a Heisenberg spin ladder which yields conclusive results is demonstrated. © 2014 American Physical Society.


Markov A.G.,Saint Petersburg State University | Aschenbach J.R.,Free University of Berlin | Amasheh S.,Free University of Berlin
IUBMB Life | Year: 2015

Claudins are tetraspan tight junction proteins which have been attributed to primarily determine epithelial barrier function in a wide variety of different organs and tissues. Among this protein family with currently 27 members, single claudins contribute in an organ- and tissue-specific manner to defined properties such as cation-, anion- or water-selective pore functions, sealing functions or ambiguous functions. As the size of tight junction strand particles visualized by freeze-fracture electron microscopy have a diameter of approximately 10 nm, multimeric assembly of tight junction proteins appears to be a basic principle for barrier formation. Moreover, expression patterns of different tissues showed that single claudins appear to specifically co-localize with other claudins, which indicates a cluster formation within tight junction strand particles with a fixed stoichiometry. This review provides a critical view on the current understanding of tight junction protein co-localization within strands. We analyze how tissue specific differences of claudin functions could be dependent on their specific partners for barrier formation. Furthermore, a model of claudin clusters as structural and functional units within tight junction strands is provided. © 2015 IUBMB Life, 67(1):29-35, 2015 © 2015 International Union of Biochemistry and Molecular Biology.


Alho A.,University of Lisbon | Hell J.,Free University of Berlin | Uggla C.,Karlstad University
Classical and Quantum Gravity | Year: 2015

We consider a minimally coupled scalar field with a monomial potential and a perfect fluid in flat Friedmann-Lemaître-Robertson-Walker cosmology. We apply local and global dynamical systems techniques to a new three-dimensional dynamical systems reformulation of the field equations on a compact state space. This leads to a visual global description of the solution space and asymptotic behavior. At late times we employ averaging techniques to prove statements about how the relationship between the equation of state of the fluid and the monomial exponent of the scalar field affects asymptotic source dominance and asymptotic manifest self-similarity breaking. We also situate the 'attractor' solution in the three-dimensional state space and show that it corresponds to the one-dimensional unstable center manifold of a de Sitter fixed point, located on an unphysical boundary associated with the dynamics at early times. By deriving a center manifold expansion we obtain approximate expressions for the attractor solution. We subsequently improve the accuracy and range of the approximation by means of Padé approximants and compare with the slow-roll approximation. © 2015 IOP Publishing Ltd.


Baccarelli I.,Supercomputing Consortium for University and Research | Baccarelli I.,University of Rome La Sapienza | Bald I.,Free University of Berlin | Bald I.,University of Aarhus | And 3 more authors.
Physics Reports | Year: 2011

It is now over ten years since the seminal experiments of Leon Sanche's group in Sherbrooke have compellingly shown that subexcitation electrons interacting with DNA could cause the occurrence of specific resonant processes which in turn would eventually lead to either single or double strand breaks in DNA materials, to the damaging of its molecular components and possibly to biological apoptosis. Since then a great deal of activity has been spurred by that initial work, with experiments and computations being carried out in several laboratories around the world. Hence, several components of the DNA molecular structure and make-up, i.e. from the purinic and pyrimidinic bases to the sugar and phosphate fragments, have been analysed in detail in the gas phase, on thin-film deposits on noble metals, and in some form of condensed phase, in interaction with low energy electrons. Likewise, several theoretical and computational approaches have been directed at the study of the molecular processes deemed to be crucially involved in the various steps of the energy deposition by the impinging electron onto the molecular networks. The aim of the present review is therefore to put together, after these ten years of intense activity, the major findings which have been consolidated from the broad variety of existing experiments and, at the same time, the main computational approaches which describe the extent of molecular damage following the initial electron attachment process. The present field, in fact, is becoming mature enough to profitably stand an overall evaluation of its experimental and theoretical/computational results and to further construct, from such a review, a starting point for the assessment of its future directions. After a detailed analysis of the experimental data, in the gas phase and in other phases, we shall therefore report the main computational tools and theoretical concepts employed today for the interpretation of the measurements at the molecular level. An overall analysis of the subject will be attempted in the last Section of this review. © 2011 Elsevier B.V.


Wagner D.O.,Free University of Berlin | Aspenberg P.,Linköping University
Acta Orthopaedica | Year: 2011

Bone is specific to vertebrates, and originated as mineralization around the basal membrane of the throat or skin, giving rise to tooth-like structures and protective shields in animals with a soft cartilage-like endoskeleton. A combination of fossil anatomy and genetic information from modern species has improved our understanding of the evolution of bone. Thus, even in man, there are still similarities in the molecular regulation of skin appendages and bone. This article gives a brief overview of the major milestones in skeletal evolution. Some molecular machineries involving members of core genetic networks and their interactions are described in the context of both old theories and modern genetic approaches. © 2011 Nordic Orthopaedic Federation.


Pechstein A.,Free University of Berlin | Shupliakov O.,Karolinska Institutet | Haucke V.,Leibniz Institute for Molecular Pharmacology
Biochemical Society Transactions | Year: 2010

During neurotransmitter release, SVs (synaptic vesicles) fuse at the active zone and are recovered predominantly via clathrin-mediated endocytosis at the presynaptic compartment surrounding the site of release, referred to as the periactive zone. Exo- and endo-cytosis in synapses are tightly temporarily and spatially coupled to sustain synaptic transmission. The molecular mechanisms linking these two cellular events, which take place in separate compartments of the nerve terminal, remain largely enigmatic. Several lines of evidence indicate that multiple factors may be involved in exocytic-endocytic coupling including SV integral membrane proteins, SV membrane lipids and the membrane-associated actin cytoskeleton. A number of recent studies also indicate that multimodular adaptor proteins shuttling between the active and periactive zones aid the dynamic assembly of macromolecular protein complexes that execute the exo- and endo-cytic limbs of the SV cycle. Here, we discuss recent evidence implicating the multidomain scaffolding and adaptor protein ITSN1 (intersectin 1) as a central regulator of SV cycling. © The Authors Journal compilation.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2009.8.2 | Award Amount: 6.51M | Year: 2010

Quantum entanglement has the capacity to enable disruptive technologies that solve outstanding issues in: - Trust, privacy protection, and security in two- and multi-party transactions; - Novel or enhanced modes of operation of ICT devices; - Reference standards, sensing, and metrology. The development of entanglement-based strategies addresses these challenges and provides the foundations for quantum technologies of the 21st century. The practical exploitation of entanglement requires groundbreaking levels of robustness and flexibility for deployment in real-world environments. This ambitious goal can be reached only through radically new designs of protocols, architectures, interfaces, and components. Q-ESSENCE will achieve this by a concerted application-driven effort covering relevant experimental, phenomenological, and fundamental aspects. Our consortium will target three main outcomes: 1) Development of entanglement-enabled and entanglement-enhanced ICT devices: atomic clocks, quantum sensors, and quantum random-number generators; 2) Novel physical-layer architectures for long-distance quantum communication that surpass current distance limitations through the deployment of next-generation components; 3) Distributed quantum information protocols that provide disruptive solutions to multiuser trust, privacy-protection, and security scenarios based on multipartite entanglement. These outcomes will be reached through the underpinning science and enabling technologies of: light-matter interfaces providing faithful interconversion between different physical realizations of qubits; entanglement engineering at new scales and distances; robust architectures protecting quantum information from decoherence; quantum information concepts that solve problems of limited trust and privacy intrusion. The project builds on the outstanding expertise of the consortium demonstrated by pioneering works over the past decades, enhanced by a strong industrial perspective.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP-SICA | Phase: ENV.2011.3.1.1-2 | Award Amount: 4.78M | Year: 2011

Saph Pani addresses the improvement of natural water treatment systems such as river bank filtration (RBF), managed aquifer recharge (MAR) and wetlands in India building on a combination of local and international expertise. The project aims at enhancing water resources and water supply particularly in water stressed urban and peri-urban areas in different parts of the sub-continent. The objective is to strengthen the scientific understanding of the performance-determining processes occurring in the root, soil and aquifer zones of the relevant processes considering the removal and fate of important water quality parameters such as pathogenic microorganisms and respective indicators, organic substances and metals. Moreover the hydrologic characteristics (infiltration and storage capacity) and the eco-system function will be investigated along with the integral importance in the local or regional water resources management concept (e.g. by providing underground buffering of seasonal variations in supply and demand). The socio-economic value of the enhanced utilisation of the attenuation and storage capacity will be evaluated taking into account long-term sustainability issues and a comprehensive risk management. The project focuses on a set of case study areas in India covering various regional, climatic, and hydrogeological conditions as well as different treatment technologies. The site investigations will include hydrological and geochemical characterisation and, depending on the degree of site development, water quality monitoring or pre-feasibility studies for new treatment schemes. Besides the actual natural treatment component the investigation may encompass also appropriate pre- and post treatment steps to potabilise the water or avoid clogging of the sub-surface structures. The experimental and conceptual studies will be complemented by modelling activities which help to support the transferability of results.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SPA.2013.2.1-01 | Award Amount: 2.55M | Year: 2013

The iMars project will focus on developing tools and value-added datasets to massively increase the exploitation of space-based data from NASA and ESA mission imaging and 3D data beyond the PI teams. iMars proposes to add value by creating more complete and fused 3D models of the surface from combined stereo and laser altimetry and use these 3D models to create a set of co-registered imaging data through time, permitting a much more comprehensive interpretation of the Martian surface to be made. Emphasis will be placed on co-registration of multiple datasets from different space agencies and orbiting platforms around Mars and their synergistic use to discover what surface changes have occurred since NASAs Viking Orbiter spacecraft in the mid-1970s. iMars brings together the best expertise in Europe for the processing of Martian orbital data within a single environment for handling, visualising and interpreting these data. The ESA Mars Express High Resolution Camera (HRSC) will provide the base data, where possible. The iMars base data can then be used by the ESA ExoMars Trace Gas Orbiter 2016 and subsequent ESA missions to provide the necessary inputs for selection of a future landing site for the ESA ExoMars 2018 rover and for any Mars Sample Return missions in the 2020s. It will greatly extend the use of archived data by providing mapped and co-registered images. The resultant time-stamped imagery will be interfaced to automated data mining analysis software based on techniques developed for Earth surveillance. We will also build on the huge momentum, developed in the Zoouniverse system by building a MarsZoo project for mass public participation in the feature mapping of Mars. Co-operation with US colleagues will be through the Technical Advisory board at annual project meetings and with European scientists through the workshops as well as the exploitation of the 3D datasets in visualisation engines such as Google Mars. The iMars datasets and tools will allow the creation of new communities of geoscientists. iMars will also allow much greater public participation in data analysis so stimulating a much greater interest in space-based data.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2008.4.2.3.1. | Award Amount: 1.52M | Year: 2009

The objective of the project is to provide the EU with conceptual tools and applicable ideas to make sustainable development an operational paradigm framing EU policy making in the globalization process. Broadening the utilitarian, state-centred, and market failure approach often mobilised in globalisation analysis, we develop a reflexive framework within which time and irreversibility, institutional path-dependency and multiple actors, with heterogeneous knowledge, beliefs, preferences, technology and power, interfere in the process of policy making. In this procedural approach, the policy making process itself will be scrutinised and integrated as a key determinant of the policy outcome itself. Within this renewed framework, globalization core challenges will be intersected with sustainable development conceptual challenges, which will be tackled specifically before nurturing back EU policy-making in the globalization process. The ultimate test case for collective action according to recent statement by Nick Stern - namely the governance of climate change and the bottom billion interlinked issue - will be used as an application case study throughout the project. The projects main outputs are threefold: firstly, identify methodological tools to fulfil the empirical deficit in the measure of world citizens heterogeneous preferences across a range of sustainable development issues; second, develop conceptual tools to better understand sustainable development implications on EU social contracts and policy making processes; third, propose building blocks for a renewed dialogue on global governance within the EU and outside as if sustainable development really mattered to paraphrase Dani Rodrick.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: ICT-03-2016 | Award Amount: 3.10M | Year: 2017

The main objective of the project is to design and implement a parameterized, knowledge-based, multi-target food sensitive mini-portable system, with heterogeneous micro-scale photonics for on-the-spot food quality sensing and shelf-life prediction. In particular, the miniaturized smart integrated system will be able to detect food hazards, spoilage (incl. early sign of spoilage) and food fraud through the combined bio-chemical data analysis and additionally will be able to perform food components/additives analysis, food identification and prediction of food shelf-life. The following use case will be addressed during the project: Use case 1: Detection of mycotoxins in various grains and nuts. Aflatoxins detection. A simple, convenient ultraviolet test makes it possible to detect the possible presence of aflatoxin. Use case 2: Detection of early sign of spoilage and spoilage in fruits, vegetables, meat, fish: combined with estimation on product expiration date. Use case 3: Detection of food fraud: Adulteration of alcoholic beverages, oil, milk and meat. 3 sensor devices will be integrated in the miniaturised smart sensor node: i) a MEMS-based near IR spectrometer (950-1900 nm), ii) a UV-VIS spectrometer (450-900 nm) and iii) a micro-camera. Moreover 3 light sources will also be integrated to support the sensing functionality: i) UV-LED, ii) white LED and iii) a miniaturised IR emitter. Smart signal processing of the spectrum images will be performed by an advanced microcontroller, integrated in the sensing device. The data will be communicated to a smartphone device, where the spectroscopy analysis will take place with the help of a cloud-base application connected to a reference database. Advanced detection algorithms will be deployed both in the level of cloud and the smartphone application. PhasmaFOOD system will enable common consumers for on the spot food quality sensing and shelf-life prediction.


Rieder M.-T.,Free University of Berlin | Brouwer P.W.,Free University of Berlin | Adagideli I.,Sabanci University
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

In a one-dimensional spinless p-wave superconductor with coherence length ξ, disorder induces a phase transition between a topologically nontrivial phase and a trivial insulating phase at the critical mean-free path l=ξ/2. Here, we show that a multichannel spinless p-wave superconductor goes through an alternation of topologically trivial and nontrivial phases upon increasing the disorder strength, the number of phase transitions being equal to the channel number N. The last phase transition, from a nontrivial phase into the trivial phase, takes place at a mean-free path l=ξ/(N+1), parametrically smaller than the critical mean-free path in one dimension. Our result is valid in the limit that the wire width W is much smaller than the superconducting coherence length ξ. © 2013 American Physical Society.


Eckmann A.,University of Manchester | Felten A.,Free University of Berlin | Felten A.,Karlsruhe Institute of Technology | Mishchenko A.,University of Manchester | And 5 more authors.
Nano Letters | Year: 2012

Raman spectroscopy is able to probe disorder in graphene through defect-activated peaks. It is of great interest to link these features to the nature of disorder. Here we present a detailed analysis of the Raman spectra of graphene containing different type of defects. We found that the intensity ratio of the D and D′ peak is maximum (∼13) for sp 3-defects, it decreases for vacancy-like defects (∼7), and it reaches a minimum for boundaries in graphite (∼3.5). This makes Raman Spectroscopy a powerful tool to fully characterize graphene. © 2012 American Chemical Society.


Von Blanckenburg F.,Helmholtz Center Potsdam | Von Blanckenburg F.,Free University of Berlin | Willenbring J.K.,University of Pennsylvania
Elements | Year: 2014

Cosmogenic nuclides are very rare isotopes that are produced when particles generated in supernovas in our galaxy hit the atmosphere and then the Earth's surface. When the rocks and soils in this thin, ever-changing surface layer are bombarded by such cosmic radiation, the nuclide clock begins to tick, thus providing dates and rates of Earth-surface processes. The measurement of cosmogenic nuclides tells us when earthquakes created topography at faults, when changing climate led to the growth of glaciers, how fast rivers grind mountains down, and how fast rocks weather to soil and withdraw atmospheric CO2. The use of cosmogenic nuclides is currently revolutionizing our understanding of Earth-surface processes and has signifi cant implications for many Earth science disciplines.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2012-1.1.13. | Award Amount: 7.04M | Year: 2014

EUFAR aims at providing researchers with Open Access to the airborne facilities the most suited to their needs. EUFAR thus allocates Transnational Access to 21 installations, develops a culture of co-operation between scientists and operators, and organizes training courses to attract young scientists to airborne research. To improve the quality of the service, EUFAR supports the experts on airborne measurements, constitutes a central data base and develops standards and protocols for this data base to be fully interoperable with Earth observation data bases. EUFAR supports two Joint Research Activities dedicated to (i) the development of methodologies and tools for the integrated use of airborne hyperspectral imaging data and airborne laser scanning data and (ii) the development of robust calibration systems for the core gas-phase chemical measurements currently made on-board research aircraft. To optimise the use and development of airborne research infrastructure, the EUFAR Strategy and European Integration will (i) constitute a Strategic Advisory Committee in which representatives of research institutions will define scientific priorities, jointly support Open Access with in kind contributions to the operation and the harmonized development of the European fleet and (ii) constitute the EUFAR sustainable legal structure. Following the Innovation Union objectives, EUFAR will invite representatives of end user industries to participate in the SAC and constitute a Technology Transfer Office to support both market pull and technology push driven innovation. Workshops will be organized like Innovation Conventions where EUFAR experts and SMEs will closely interact and develop partnerships to transfer airborne research instruments, methodologies and software into new products.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2013.3.2-2 | Award Amount: 3.29M | Year: 2014

In line with the EU strategies for 2020 and the need for a systemic and integrated approach to Early Childhood education and Care (ECEC), the project identifies eight key issues and questions for which effective policy measures and instruments should be developed. They concern assessing the impact of ECEC, optimizing quality and curricula for ECEC to increase effectiveness, raising the professional competencies of staff, monitoring and assuring quality of ECEC, increasing the inclusiveness of ECEC, in particular for socioeconomically disadvantaged children, funding of ECEC, and the need for innovative European indicators of childrens wellbeing. The project will address these issues in an integrative way by combining state-of-the-art knowledge of factors determining personal, social and economic benefits of ECEC with knowledge of the mechanisms determining access to and use of ECEC. In developing a European knowledge base for ECEC, we will add to the existing knowledge in two ways. First, we will include recent and ongoing ECEC research from several European countries. Second, we will include the perspectives of important stakeholders and integrate cultural beliefs and values. The central aim is to develop an evidence-based and culture-sensitive framework of (a) Developmental goals, quality assessment, curriculum approaches and policy measures for improving the quality and effectiveness of ECEC; and (b) Effective strategies of organizing, funding and governing ECEC that increase the impact of ECEC. Our interdisciplinary research team will construct this framework, based on the competencies and skills that young children need to develop in current societies, identify the conditions that have to be fulfilled to promote child development and wellbeing, and identify strategies and policy measures that support access to high quality provisions, and likely to receive broad support of stakeholders, thereby enhancing the impact of ECEC.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-1.3-1 | Award Amount: 16.43M | Year: 2008

The overall aim of Predict-IV is to develop strategies to improve the assessment of drug safety in the early stage of development and late discovery phase, by an intelligent combination of non animal-based test systems, cell biology, mechanistic toxicology and in-silico modelling, in a rapid and cost effective manner. A better prediction of the safety of an investigational compound in early development will be delivered. Margins-of-safety will be deduced and the data generated by the proposed approach may also identify early biomarkers of human toxicity for pharmaceuticals. The results obtained in Predict-IV will enable pharmaceutical companies to create a tailored testing strategy for early drug safety. The project will integrate new developments to improve and optimize cell culture models for toxicity testing and to characterize the dynamics and kinetics of cellular responses to toxic effects in vitro. The target organs most frequently affected by drug toxicity will be taken into account, namely liver and kidney. Moreover, predictive models for neurotoxicty are scarce and will be developed. For each target organ the most appropriate cell model will be used. The approach will be evaluated using a panel of drugs with well described toxicities and kinetics in animals and partly also in humans. This approach will be highly advantageous as it will allow a direct comparison between the in vivo to the in vitro data. A parallel analysis of several dynamic and kinetic models with a broad spectrum of endpoints should allow for the identification of several relevant biomarkers of toxicity. Inter-individual susceptibilities will be taken into account by integrating the polymorphisms of the major drug metabolizing enzymes and correlating the observed effects in the human cell models with their genotype. Environmental influences on cellular toxicity to these compounds will also be evaluated using hypoxic stress as a relevant test model.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SEC-2013.2.1-2 | Award Amount: 4.77M | Year: 2014

The RAIN vision is to provide an operational analysis framework that identifies critical infrastructure components impacted by extreme weather events and minimise the impact of these events on the EU infrastructure network. The project has a core focus on land based infrastructure with a much wider consideration of the ancillary infrastructure network in order to identify cascading and inter-related infrastructure issues. A core component of the research will consider the implications of climate change and the subsequent impacts that this may have on an already ageing and vulnerable infrastructure system. The impact of these disruptions on both the key components and the wider pan-European network will be assessed using economic and social markers that will identify and rank a series of worst case scenarios. Technical and Logistic solutions will be developed to minimise the impact of these extreme events, which will include novel early warning systems, decision support tools and engineering solutions to ensure rapid reinstatement of the network. These tools will be implemented within a fresh Europe-wide operational and response strategy that will build on previous European infrastructure models. The robustness of the existing transport and energy networks to deal with changing weather conditions will be analysed in detail. The ability of this response plan to transcend borders will be guaranteed by the multi-disciplinary consortium. The project grouping will have expertise in climatology, operational analysis, transportation economics, risk analysis and mitigation, emergency planning, transportation engineering as well as engineering design and assessment. The outputs from the project will result in enhanced safety and reliability of critical infrastructure networks in the case of major weather induced disruptions and will address European policy in the areas of safety and security, inter-modality and emergency response planning.


News Article | December 23, 2015
Site: www.sciencenews.org

For Earth’s early inhabitants, living in a bubble was a good thing. Pockets of gas trapped along ancient shorelines gave microbes a cozy place to call home about 3.2 billion years ago, scientists suggest December 4 in Geology. Such a snug hideout could have shielded microbes from ultraviolet radiation not only on Earth, but perhaps on Mars as well. The new work is “exciting and very plausible,” says geologist Frances Westall of the French National Center for Scientific Research in Orléans. “It expands the known habitats for early life.” Earth was a tough place to live a few billion years ago. No oxygen in the atmosphere meant no ozone, and therefore no protection from the sun’s ultraviolet rays, says study coauthor Alessandro Airo, a geobiologist at the Free University of Berlin in Germany. Still, microbes found a way to survive. In many places around the world, these organisms glued sand and cells together, forming slimy carpetlike biofilms, or mats, underwater. Iron dissolved in the water could have screened out radiation, Airo says. During low tide, “surface microbes might get zapped by UV and die,” he says, but communities of microbes living below them may have thrived. Such communities could have colonized trapped bubbles of gas — perhaps a by-product of microbial metabolism. Inside the sheltered bubble chambers, ancient bacteria might have weathered the harsh conditions of early Earth, says study coauthor Martin Homann, also of the Free University of Berlin. Until now, the oldest evidence of bubble-dwelling microbes came from 2.75-billion-year-old rocks from Western Australia. Homann and colleagues examined even older rocks, from the oldest records of tidal environments on Earth: 3.22-billion-year-old sandstone from South Africa. From 2011 to 2013, Homann collected 350 kilograms of this sandstone and then cut and polished slices to look for signs of life. The gas pockets, or cavities, that once formed within the mats have long since filled with fine-grained crystals of quartz. But in the quartz, the researchers saw several clues. What appeared to be ancient biofilms hung down from the tops of shallow cavities, like tiny stalactites dripping from cave ceilings. And the biofilms exhibited a chemical hallmark of life: a ratio of heavy to light forms of carbon that’s typically found only in living organisms. The quartz also contained microfossil imprints of cells. High-powered microscopes revealed ghostly impressions of these cells linked together in chains, just like those formed by bacteria today. Taken together, the clues are “hard evidence for the presence of microbes,” Airo says. Geomicrobiologist Mark Van Zuilen of the Institute of Earth Physics of Paris agrees. The work is a “sound, basic observation that there were traces of life in these rocks,” he says. If microbes once survived in these pockets on early Earth, they could potentially have done so on other planets too, Airo says. On Mars, in particular, he says, “little cavities below the surface are a wonderful niche for rovers and future missions to hunt for life.”


Kolisek M.,Free University of Berlin | Nestler A.,Free University of Berlin | Vormann J.,Institute for Prevention and Nutrition | Schweigel-Rontgen M.,Leibniz Institute for Farm Animal Biology
American Journal of Physiology - Cell Physiology | Year: 2012

Magnesium (Mg 2+), the second most abundant divalent intracellular cation, is involved in the vast majority of intracellular processes, including the synthesis of nucleic acids, proteins, and energy metabolism. The concentration of intracellular free Mg 2+ ([Mg 2+]i) in mammalian cells is therefore tightly regulated to its optimum, mainly by an exchange of intracellular Mg 2+ for extracellular Na +. Despite the importance of this process for cellular Mg 2+ homeostasis, the gene(s) encoding for the functional Na +/ Mg 2+ exchanger is (are) still unknown. Here, using the fluorescent probe mag-fura 2 to measure [Mg 2+]i changes, we examine Mg 2+ extrusion from hSLC41A1-overexpressing human embryonic kidney (HEK)-293 cells. A three- to fourfold elevation of [Mg 2+]i was accompanied by a five- to ninefold increase of Mg 2+ efflux. The latter was strictly dependent on extracellular Na + and reduced by 91% after complete replacement of Na + with N-methyl- D-glucamine. Imipramine and quinidine, known unspecific Na +/ Mg 2+ exchanger inhibitors, led to a strong 88% to 100% inhibition of hSLC41A1-related Mg 2+ extrusion. In addition, our data show regulation of the transport activity via phosphorylation by cAMP-dependent protein kinase A. As these are the typical characteristics of a Na +/ Mg 2+ exchanger, we conclude that the human SLC41A1 gene encodes for the Na +/ Mg 2+ exchanger, the predominant Mg 2+ efflux system. Based on this finding, the analysis of Na +/ Mg 2+ exchanger regulation and its involvement in the pathogenesis of diseases such as Parkinson's disease and hypertension at the molecular level should now be possible. © 2012 the American Physiological Society.


Kirmaci M.,Adnan Menderes University | Kurschner H.,Free University of Berlin
Nova Hedwigia | Year: 2013

Four species, S. contortum, S. fallax, S. magellanicum and S. rubellum are recorded for the first time from Southwest Asia respectively Turkey, increasing the total known number of species to 22 (resp. 21 from Turkey). Five species (S. capillifolium, S. girgensohnii, S. inundatum, S. teres, S. warnstorfii) are re-collected after more than 100 resp. 40 years. In addition, first hints to the occurence of Oxycocco-Sphagnetea communities (e.g., Sphagnetalia magellanici) in Turkey are given. © 2013 J. Cramer in Gebr. Borntraeger Verlagsbuchhandlung, Stuttgart, Germany.


Veresoglou S.D.,Free University of Berlin | Menexes G.,Aristotle University of Thessaloniki | Rillig M.C.,Free University of Berlin
Mycorrhiza | Year: 2012

Arbuscular mycorrhizas (AM) are ubiquitous root symbioses with often pervasive effects on the plant host, one of which may be above- and belowground biomass allocation. A meta-analysis was conducted on 516 trials that were described in 90 available articles to examine whether AM colonization could result in a modification of partitioning of plant biomass in shoots and roots. It was hypothesized that alleviating plant nutrient limitations could result in a decrease of root to shoot (R/S) ratio in AM plants or, alternatively, the direction of shifts in the R/S ratio would be determined by the changes in total dry biomass. In our analysis, we considered four types of stresses: drought stress, single heavy metal stress, multiple heavy metal stress, and other potential abiotic plant stress factors. When disregarding any factors that could regulate effects, including stress status and mode of propagation, the overall AM effect was a significant modification of biomass towards shoot growth. However, the responses of stressed and clonally propagated plants differed from those of seed-grown unstressed plants. Our meta-analysis detected a considerable decline in the R/S ratio when plants were grown from seeds in the absence of abiotic stresses. Moreover, we demonstrate that additional regulators of the AM-mediated impact on R/S ratio were presence of competition from other plants, plant growth outcome of the symbiosis, growth substrate volume, experimental duration, and the identities of both plant and AM fungus. Our results indicate that a prediction of AM effects on R/S allocation becomes more accurate when considering regulators, most notably propagation mode and stress. We discuss possible mechanisms through which stress and other regulators may operate. © 2011 Springer-Verlag.


Gogolin C.,Free University of Berlin | Gogolin C.,ICFO - Institute of Photonic Sciences | Gogolin C.,Max Planck Institute of Quantum Optics | Eisert J.,Free University of Berlin
Reports on Progress in Physics | Year: 2016

We review selected advances in the theoretical understanding of complex quantum many-body systems with regard to emergent notions of quantum statistical mechanics. We cover topics such as equilibration and thermalisation in pure state statistical mechanics, the eigenstate thermalisation hypothesis, the equivalence of ensembles, non-equilibration dynamics following global and local quenches as well as ramps. We also address initial state independence, absence of thermalisation, and many-body localisation. We elucidate the role played by key concepts for these phenomena, such as Lieb-Robinson bounds, entanglement growth, typicality arguments, quantum maximum entropy principles and the generalised Gibbs ensembles, and quantum (non-)integrability. We put emphasis on rigorous approaches and present the most important results in a unified language. © 2016 IOP Publishing Ltd.


Noe F.,Free University of Berlin | Clementi C.,Rice University
Journal of Chemical Theory and Computation | Year: 2015

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets. © 2015 American Chemical Society.


Gallego R.,Free University of Berlin | Riera A.,Free University of Berlin | Riera A.,ICFO - Institute of Photonic Sciences | Eisert J.,Free University of Berlin
New Journal of Physics | Year: 2014

How much work can be extracted from a heat bath using a thermal machine? The study of this question has a very long history in statistical physics in the weak-coupling limit, when applied to macroscopic systems. However, the assumption that thermal heat baths remain uncorrelated with associated physical systems is less reasonable on the nano-scale and in the quantum setting. In this work, we establish a framework of work extraction in the presence of quantum correlations. We show in a mathematically rigorous and quantitative fashion that quantum correlations and entanglement emerge as limitations to work extraction compared to what would be allowed by the second law of thermodynamics. At the heart of the approach are operations that capture the naturally non-equilibrium dynamics encountered when putting physical systems into contact with each other. We discuss various limits that relate to known results and put our work into the context of approaches to finite-time quantum thermodynamics. © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.


Soleyman R.,Research Institute of Petroleum Industry RIPI | Adeli M.,Lorestan University | Adeli M.,Free University of Berlin
Polymer Chemistry | Year: 2015

For many years scientists have employed dendritic polymers (dendrimers and hyperbranched polymers) in association with other nanomaterials (such as graphene, carbon nanotubes, proteins and peptides, as well as metallic nanoparticles) to synthesize hybrid nanomaterials with improved biocompatibility, biodegradability, functionality, physicochemical properties and the capability of carrying other molecules. However, more recent studies demonstrate that one of the less noticed effects and newly observed facets of dendritic polymers is their role in changing the structure (shape, size and sheet multiplicity) of the obtained hybrid nanomaterials, upon covalent and noncovalent interactions. In this review, we intend to have a more specialized look at these reports and discuss the 'whys' and 'hows' of this phenomenon. © 2015 The Royal Society of Chemistry.


Correia C.A.,Max Planck Institute of Colloids and Interfaces | Gilmore K.,Max Planck Institute of Colloids and Interfaces | McQuade D.T.,Florida State University | Seeberger P.H.,Max Planck Institute of Colloids and Interfaces | Seeberger P.H.,Free University of Berlin
Angewandte Chemie - International Edition | Year: 2015

Efavirenz is an essential medicine for the treatment of HIV, which is still inaccessible to millions of people worldwide. A novel, semi-continuous process provides rac-Efavirenz with an overall yield of 45 %. This streamlined proof-of-principle synthesis relies on the efficient copper-catalyzed formation of an aryl isocyanate and a subsequent intramolecular cyclization to install the carbamate core of Efavirenz in one step. The three-step method represents the shortest synthesis of this life-saving drug to date. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Krumnow C.,Free University of Berlin | Pelster A.,Bielefeld University | Pelster A.,University of Duisburg - Essen
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

A homogeneous polarized dipolar Bose-Einstein condensate is considered in the presence of weak quenched disorder within mean-field theory at zero temperature. By first solving perturbatively the underlying Gross-Pitaevskii equation and then performing disorder ensemble averages for physical observables, it is shown that the anisotropy of the two-particle interaction is passed on to both the superfluid density and the sound velocity. © 2011 American Physical Society.


Ataka K.,Free University of Berlin | Kottke T.,Free University of Berlin | Heberle J.,Bielefeld University
Angewandte Chemie - International Edition | Year: 2010

New techniques in vibrational spectroscopy are promising for the study of biological samples as they provide exquisite spatial and/or temporal resolution with the benefit of minimal perturbation of the system during observation. In this Minireview we showcase the power of modern infrared techniques when applied to biological and biomimetic systems. Examples will be presented on how conformational changes in peptides can be traced with femtosecond resolution and nanometer sensitivity by 2D IR spectroscopy, and how surfaceenhanced infrared difference absorption spectroscopy can be used to monitor the effect of the membrane potential on a single protontransfer step in an integral membrane protein. Vibrational spectra of monolayers of molecules at basically any interface can be recorded with sum-frequency generation, which is strictly surface-sensitive. Chemical images are recorded by applying scanning near-field infrared microscopy at lateral resolutions better than 50 nm. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Aguilar-Trigueros C.A.,Free University of Berlin | Aguilar-Trigueros C.A.,Berlin Brandenburg Institute of Advanced Biodiversity Research | Powell J.R.,University of Western Sydney | Anderson I.C.,University of Western Sydney | And 3 more authors.
Trends in Plant Science | Year: 2014

Classification schemes have been popular to tame the diversity of root-infecting fungi. However, the usefulness of these schemes is limited to descriptive purposes. We propose that a shift to a multidimensional trait-based approach to disentangle the saprotrophic-symbiotic continuum will provide a better framework to understand fungal evolutionary ecology. Trait information reflecting the separation of root-infecting fungi from free-living soil relatives will help to understand the evolutionary process of symbiosis, the role that species interactions play in maintaining their large diversity in soil and in planta, and their contributions at the ecosystem level. Methodological advances in several areas such as microscopy, plant immunology, and metatranscriptomics represent emerging opportunities to populate trait databases. © 2014 Elsevier Ltd.


Ushakov D.B.,Max Planck Institute of Colloids and Interfaces | Gilmore K.,Max Planck Institute of Colloids and Interfaces | Kopetzki D.,Max Planck Institute of Colloids and Interfaces | McQuade D.T.,Florida State University | And 2 more authors.
Angewandte Chemie - International Edition | Year: 2014

Primary and secondary amines can be rapidly and quantitatively oxidized to the corresponding imines by singlet oxygen. This reactive form of oxygen was produced using a variable-temperature continuous-flow LED-photoreactor with a catalytic amount of tetraphenylporphyrin as the sensitizer. α- Aminonitriles were obtained in good to excellent yields when trimethylsilyl cyanide served as an insitu imine trap. At 25°C, primary amines were found to undergo oxidative coupling prior to cyanide addition and yielded secondary α-aminonitriles. Primary α-aminonitriles were synthesized from the corresponding primary amines for the first time, by an oxidative Strecker reaction at -50 °C. This atom-economic and protecting-group-free pathway provides a route to racemic amino acids, which was exemplified by the synthesis of tert-leucine hydrochloride from neopentylamine. The mild synthesis of imines paves the way to aminonitriles and amino acids. Aerobic oxidation of primary and secondary amines in a continuous photoreactor with singlet oxygen generated insitu led to the rapid formation of imines, which were quantitatively trapped as α-aminonitriles (see scheme; TMS=trimethylsilyl). Benzylic and primary α-aminonitriles, precursors for amino acids, could be efficiently produced in three minutes. © 2014 WILEY-VCH Verlag GmbH.


Rohrmeier M.,Free University of Berlin | Fu Q.,CAS Institute of Psychology | Dienes Z.,University of Sussex
PLoS ONE | Year: 2012

Context-free grammars are fundamental for the description of linguistic syntax. However, most artificial grammar learning experiments have explored learning of simpler finite-state grammars, while studies exploring context-free grammars have not assessed awareness and implicitness. This paper explores the implicit learning of context-free grammars employing features of hierarchical organization, recursive embedding and long-distance dependencies. The grammars also featured the distinction between left- and right-branching structures, as well as between centre- and tail-embedding, both distinctions found in natural languages. People acquired unconscious knowledge of relations between grammatical classes even for dependencies over long distances, in ways that went beyond learning simpler relations (e.g. n-grams) between individual words. The structural distinctions drawn from linguistics also proved important as performance was greater for tail-embedding than centre-embedding structures. The results suggest the plausibility of implicit learning of complex context-free structures, which model some features of natural languages. They support the relevance of artificial grammar learning for probing mechanisms of language learning and challenge existing theories and computational models of implicit learning. © 2012 Rohrmeier et al.


Kupferschmidt J.N.,Cornell University | Kupferschmidt J.N.,Free University of Berlin | Brouwer P.W.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

Andreev reflection at the interface between a half-metallic ferromagnet and a spin-singlet superconductor is possible only if it is accompanied by a spin flip. Here we calculate the Andreev reflection amplitudes for the case where the spin flip originates from a spatially nonuniform magnetization direction in the half-metal. We calculate both the microscopic Andreev reflection amplitude for a single reflection event and an effective Andreev reflection amplitude describing the effect of multiple Andreev reflections in a ballistic thin film geometry. It is shown that the angle and energy dependence of the Andreev reflection amplitude strongly depends on the orientation of the gradient of the magnetization with respect to the interface. We calculate the resulting effects on the subgap conductance as well as Josephson current for a few exemplary cases. Establishing a connection between the scattering approach employed here and earlier work that employs the quasiclassical formalism, we connect the symmetry properties of the Andreev reflection amplitudes to the symmetry properties of the anomalous Green function in the half-metal. © 2011 American Physical Society.


Eisert J.,Free University of Berlin | Friesdorf M.,Free University of Berlin | Gogolin C.,Free University of Berlin | Gogolin C.,ICFO - Institute of Photonic Sciences | Gogolin C.,Max Planck Institute of Quantum Optics
Nature Physics | Year: 2015

How do closed quantum many-body systems driven out of equilibrium eventually achieve equilibration? And how do these systems thermalize, given that they comprise so many degrees of freedom? Progress in answering these - and related - questions has accelerated in recent years - a trend that can be partially attributed to success with experiments performing quantum simulations using ultracold atoms and trapped ions. Here we provide an overview of this progress, specifically in studies probing dynamical equilibration and thermalization of systems driven out of equilibrium by quenches, ramps and periodic driving. In doing so, we also address topics such as the eigenstate thermalization hypothesis, typicality, transport, many-body localization and universality near phase transitions, as well as future prospects for quantum simulation. © 2015 Macmillan Publishers Limited.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 4.11M | Year: 2009

The Initial Training Network - Language, Cognition, and Gender (ITN LCG) investigates European languages from an interdisciplinary perspective to expand current knowledge of how language influences and forms the cognitive representations of women and men. The diversity of Europe offers a unique opportunity to investigate the impact of language and culture in establishing and maintaining gender inequality. This issue has not yet been systematically addressed on a large scale, although the reduction of gender inequality is generally considered an important issue within Europe. Therefore, ITN LCG will provide a structured interdisciplinary research training programme for young researchers in the emerging supra-disciplinary field of language, cognition, and gender to enhance the scientific understanding of this topic and improve the quality of initial research training in Europe. For the first time, these lines of research will be investigated from cross-language and cross-cultural perspectives by bringing together 10 complementary providers of research-training and 12 associated partners from public and private sectors. ITN LCG has four interrelated research objectives: a) deriving indices for selected European languages that reflect the extent to which the features of a language result in gender related representations in speakers/listeners, b) investigating to what extent gender equality in formal standards of language and the use of gender-fair language correlates with higher levels of socio-economic gender equality, c) analysing the impact of language on gender stereotyping in social judgement and decision making, and d) developing and evaluating scientifically-based prototypes of guidelines and training tools for gender-fair communication in European languages. ITN LCG will strengthen the capability of its young fellows to contribute effectively to our knowledge-based economy and society, and will add to their intersectoral and transnational employability.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: FETPROACT-3-2014 | Award Amount: 2.00M | Year: 2015

Quantum simulators promise to provide unprecedented insights into physical phenomena not accessible with classical computers and have the potential to enable radically new technologies. In this proposal, we argue that analog dynamical quantum simulators are currently realisable and constitute a most promising class of architectures to fulfil the ultimate promise to devise quantum machines outperforming classical computers. The approach taken is two-pronged: On the one hand, we devise versatile and practical platforms for dynamical simulators making use of systems of ultra-cold atoms in optical lattices and the continuum, as well as cavity polaritons. We suggest a concerted and interdisciplinary research programme of certifying quantum devices and assess them in their computational capabilities, addressing largely unexplored key questions on the power of quantum simulators. On the other, we make use of those devices to probe important questions in fundamental and applied physics, ranging from technology-relevant problems, concerning transport processes or glassy dynamics, via long-standing challenges in the physics of non-equilibrium and thermalisation phenomena, through puzzles in notions of quantum turbulence, to questions in the study of quantum gravity.


Grant
Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: HEALTH-2009-1.3-1 | Award Amount: 612.80K | Year: 2010

Conventional approaches to toxicity testing and risk assessment are often decades old, costly and low-throughput, and of dubious relevance to humans. These factors have prompted leading scientific bodies to call for a transition to a 21st century paradigm, including a move away from apical outcomes at high doses in whole animals, and toward a mechanistic understanding of the source-to-outcome continuum between xenobiotic exposure and adverse health effects. Such a shift will require a robust understanding of the cellular response/toxicity pathways which that can lead to adverse effects when perturbed; appropriate in vitro systems to study chemical interactions at key targets along a pathway; and computational systems biology models to describe the circuitry underlying each pathway as a basis for creating biologically realistic dose-response models. The AXLR8 project aims to support the transition to a toxicity pathway-based paradigm for quantitative risk assessment, and to this end will: 1) Organise a series of scientific workshops and expert meetings to map and catalogue research progress, gaps and needs in the above areas. 2) Provide a range of tools and opportunities for enhanced interdisciplinary and international communication, coordination and collaboration in order to maximise the impact of available resources. 3) Work to streamline regulatory acceptance procedures to provide for the expeditious uptake of validated 3Rs methods, including a smooth transition to 21st century systems as they become available. 4) Produce an authoritative report on the state of the science, including a practical roadmap detailing priority research and funding targets, in order to ensure a prominent role for European science in this rapidly developing global research area.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2013-IRSES | Award Amount: 196.10K | Year: 2013

This project aims strengthening interdisciplinary and technological collaboration between the scientists working in the topical areas of nanooptics and nanoplasmonics. These subjects investigate unique optical properties of nanoparticles and nanostructured surfaces, which are amazingly useful for improving optical materials, sensing bioorganic molecules, progress in solving of biophysical and biochemical tasks. Exchange by knowledge in such subject matter as giant Raman scattering (SERS), Surface Enhanced Infrared Absorption (SEIRA), metal enhanced fluorescence et al. is planned to organize in form of International Laboratory of Surface Enhanced Spectroscopy(ILSES). It is proposed to organize such laboratory by means of collective access to existing scientific equipment and technological achievements of partners using a system of mutual scientific journeys, meetings and workshops. From the viewpoint of applied science, the proposed partnership contributes to the extremely important and innovatively attractive field: the development of the new complex nanoparticle/bioorganical molecules and development of cheap and effective SEIRA and SERS nanostructured substrates. Since each partner brings its unique and specific expertise to reach the project objectives, the proposed partnership is very important, both for the area of collaboration and for the ERA as a whole. The main expertise of the participating teams cover different areas of present-day physics, biology and chemistry. Thus, the consortium joins scientists from several scientific communities under the common roof of the interdisciplinary research on metal nanoparticle interactions with bioorganic molecules. In addition to the interdisciplinarity of the teams, young scientists are to be widely involved which will allow a sustainable dissemination of knowledge. Thus, besides the scientific results, the project is expected to bring new research experience for young participants unavailable at home institutions.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2009-3.3-2 | Award Amount: 2.03M | Year: 2010

The consumption of alcohol among young people in Europe is rising the last years. Several studies indicate that one quarter to one third of all the students has been drinking alcohol during the last month. Also the problematic drinking is a growing issue. Especially in the age group 12 until 14 year the use of alcohol has increased the last decade. The proposed multilevel research project aims to study the different possible effective strategies for the prevention of alcohol abuse among adolescents in different European countries. It will therefore analyse existing environmental strategies of public and private actors at different governance levels and confront these with outcomes of a study to identify and analyse risk factors that influence the initiation of alcohol use among young people in Europe. The study will build upon a unique dataset from a previous survey of self reported delinquency among 74,000 young people in 33 countries, realised with active involvement of the same research consortium. The (intermediate) outcomes of the study will be largely disseminated through experts and stakeholders conferences in different European regions and a web-based prevention policy guidance book


Haehnel M.,University of Florida | Menzel R.,Free University of Berlin
Journal of Experimental Biology | Year: 2012

Honeybees learn to associate an odor with sucrose reward under conditions that allow the monitoring of neural activity by imaging Ca2 + transients in morphologically identified neurons. Here we report such recordings from mushroom body extrinsic neurons - which belong to a recurrent tract connecting the output of the mushroom body with its input, potentially providing inhibitory feedback -And other extrinsic neurons. The neurons' responses to the learned odor and two novel control odors were measured 24?h after learning. We found that calcium responses to the learned odor and an odor that was strongly generalized with it were enhanced compared with responses to a weakly generalized control. Thus, the physiological responses measured in these extrinsic neurons accurately reflect what is observed in behavior. We conclude that the recorded recurrent neurons feed information back to the mushroom body about the features of learned odor stimuli. Other extrinsic neurons may signal information about learned odors to different brain regions. © 2012. Published by The Company of Biologists Ltd.


Mayr F.,Max Delbrück Center for Molecular Medicine | Mayr F.,Free University of Berlin | Schutz A.,Max Delbrück Center for Molecular Medicine | Doge N.,Max Delbrück Center for Molecular Medicine | And 2 more authors.
Nucleic Acids Research | Year: 2012

The RNA-binding protein Lin28 regulates the processing of a developmentally important group of microRNAs, the let-7 family. Lin28 blocks the biogenesis of let-7 in embryonic stem cells and thereby prevents differentiation. It was shown that both RNA-binding domains (RBDs) of this protein, the cold-shock domain (CSD) and the zinc-knuckle domain (ZKD) are indispensable for pri- or pre-let-7 binding and blocking its maturation. Here, we systematically examined the nucleic acid-binding preferences of the Lin28 RBDs and determined the crystal structure of the Lin28 CSD in the absence and presence of nucleic acids. Both RNA-binding domains bind to single-stranded nucleic acids with the ZKD mediating specific binding to a conserved GGAG motif and the CSD showing only limited sequence specificity. However, only the isolated Lin28 CSD, but not the ZKD, can bind with a reasonable affinity to pre-let-7 and thus is able to remodel the terminal loop of pre-let-7 including the Dicer cleavage site. Further mutagenesis studies reveal that the Lin28 CSD induces a conformational change in the terminal loop of pre-let-7 and thereby facilitates a subsequent specific binding of the Lin28 ZKD to the conserved GGAG motif. © The Author(s) 2012.


Lima A.R.P.,Free University of Berlin | Pelster A.,University of Duisburg - Essen
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We investigate the influence of quantum fluctuations upon dipolar Bose gases by means of the Bogoliubov-de Gennes theory. Thereby, we make use of the local density approximation to evaluate the dipolar exchange interaction between the condensate and the excited particles. This allows to obtain the Bogoliubov spectrum analytically in the limit of large particle numbers. After discussing the condensate depletion and the ground-state energy correction, we derive quantum-corrected equations of motion for harmonically trapped dipolar Bose gases by using superfluid hydrodynamics. These equations are subsequently applied to analyze the equilibrium configuration, the low-lying oscillation frequencies, and the time-of-flight dynamics. We find that both atomic magnetic and molecular electric dipolar systems offer promising scenarios for detecting beyond mean-field effects. © 2011 American Physical Society.


Gruber C.,Free University of Berlin | Luongo O.,University of Naples Federico II | Luongo O.,National Institute of Nuclear Physics, Italy | Luongo O.,National Autonomous University of Mexico
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2014

Cosmography is used in cosmological data processing in order to constrain the kinematics of the universe in a model-independent way, providing an objective means to evaluate the agreement of a model with observations. In this paper, we extend the conventional methodology of cosmography employing Taylor expansions of observables by an alternative approach using Padé approximations. Due to the superior convergence properties of Padé expansions, it is possible to improve the fitting analysis to obtain numerical values for the parameters of the cosmographic series. From the results, we can derive the equation of state parameter of the universe and its first derivative and thus acquire information about the thermodynamic state of the universe. We carry out statistical analyses using observations of the distance modulus of type 1a supernovae, provided by the union 2.1 compilation of the supernova cosmology project, employing a Markov chain Monte Carlo approach with an implemented Metropolis algorithm. We compare the results of the original Taylor approach to the newly introduced Padé formalism. The analyses show that experimental data constrain the observable universe well, finding an accelerating universe and a positive jerk parameter. We demonstrate that the Padé convergence radii are greater than standard Taylor convergence radii, and infer a lower limit on the acceleration of the universe solely by requiring the positivity of the Padé expansion. We obtain fairly good agreement with the Planck results, confirming the ΛCDM model at small redshifts, although we cannot exclude a dark energy density varying in time with negligible speed of sound. © 2014 American Physical Society.


Adelle C.,University of East Anglia | Weiland S.,Free University of Berlin
Impact Assessment and Project Appraisal | Year: 2012

Policy assessment has spread rapidly around the world in the last few decades providing an opportunity for further innovation and understanding in the way in which assessment is conceived, practised and researched. The extension of assessment from project and programme level to policy level was in part intended to improve its effectiveness by moving the focus of study upstream in the policy-making process. This paper reflects on the state of the art in policy assessment. It illustrates how the diffusion of policy assessment has led not to one standard 'correct' way of conducting policy assessment but to a great deal of diversity in how policy assessment is practised as well as researched and even theorized. Although the 'textbook' concept and everyday practices of policy assessment are based on a traditional rational linear concept of policy-making, policy assessment has become the latest arena for post-positivist conceptions of policy-making and assessment to resurface. This paper suggests that the future agenda for both research and practices could - indeed should - attempt to straddle these two theoretical approaches. © 2012 Copyright IAIA.


Arslan I.,Pamukkale University | Celik A.,Pamukkale University | Melzig M.F.,Free University of Berlin
Bioorganic and Medicinal Chemistry | Year: 2013

A bioassay-guided phytochemical analysis of the triterpene saponins from under ground parts of Gypsophila arrostii var. nebulosa allowed the isolation of two triterpene saponins; nebuloside A, B based on gypsogenin and quillaic acid aglycone. Two new oleanane type triterpenoid saponins (nebuloside A, B) and three known saponins (1-3) were isolated from the root bark of Gypsophila arrostii var. nebulosa. The structures of the two new compounds were elucidated as 3-O-β-d-galactopyranosyl-(1→2)-[β-d-xylopyranosyl-(1→3)]- β-d-glucuronopyranosyl quillaic acid 28-O-β-d-glucopyranosyl- (1→3)-[β-d-xylopyranosyl-(1→3)-β-d-xylopyranosyl-(1→4)] -α-l-rhamnopyranosyl-(1→2)-β-d-fucopyranosyl ester (nebuloside A) and 3-O-β-d-xylopyranosyl-(1→3)-[β-d- galactopyranosyl(1→3)-β-d-galactopyranosyl-(1→2)] -β-d-glucuronopyranosyl gypsogenin 28-O-β-d-glucopyranosyl-(1→3)- [β-d-xylopyranosyl-(1→3)-β-d-xylopyranosyl-(1→4)] -α-l-rhamnopyranosyl-(1→2)-β-d-fucopyranosyl ester (nebuloside B), on the basis of extensive spectral analysis and chemical evidence. Nebuloside A and B showed toxicity enhancing properties on saporin a type-I RIP without causing toxicity by themselves at 15 μg/mL. © 2012 Elsevier Ltd. All rights reserved.


Lima A.R.P.,Free University of Berlin | Pelster A.,Free University of Berlin | Pelster A.,University of Duisburg - Essen
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2010

Recently, a seminal stimulated Raman adiabatic passage (STIRAP) experiment allowed the creation of K40Rb87 molecules in the rovibrational ground state. To describe such a polarized dipolar Fermi gas in the hydrodynamic regime, we work out a variational time-dependent Hartree-Fock approach. With this we calculate dynamical properties of such a system, for instance, the frequencies of the low-lying excitations and the time-of-flight expansion. We find that the dipole-dipole interaction induces anisotropic breathing oscillations in momentum space. In addition, after release from the trap, the momentum distribution becomes asymptotically isotropic, while the particle density becomes anisotropic. © 2010 The American Physical Society.


Lima A.R.P.,Free University of Berlin | Pelster A.,University of Duisburg - Essen | Pelster A.,University of Potsdam
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2010

The quest for quantum degenerate Fermi gases interacting through the anisotropic and long-range dipole-dipole interaction is an exciting and fast developing branch within the cold-atom research program. Recent experimental progress in trapping, cooling, and controlling polar molecules with large electric dipole moments has, therefore, motivated much theoretical effort. In a recent letter, we have briefly discussed the application of a variational time-dependent Hartree-Fock approach to study theoretically both the static and the dynamic properties of such a system in a cylinder-symmetric harmonic trap. We focused on the hydrodynamic regime, where collisions ensure the equilibrium locally. Here we present a detailed theory extended to encompass the general case of a harmonic trap geometry without any symmetry. After deriving the equations of motion for the gas, we explore their static solutions to investigate key properties like the aspect ratios in both real and momentum space as well as the stability diagram. We find that, despite the lack of symmetry of the trap, the momentum distribution remains cylinder symmetric. The equations of motion are then used to study the low-lying hydrodynamic excitations, where, apart from the quadrupole and monopole modes, the radial quadrupole mode is also investigated. Furthermore, we study the time-of-flight dynamics as it represents an important diagnostic tool for quantum gases. We find that the real-space aspect ratios are inverted during the expansion, while that in momentum space becomes asymptotically unity. In addition, anisotropic features of the dipole-dipole interaction are discussed in detail. These results could be particularly useful for future investigations of strongly dipolar heteronuclear polar molecules deep in the quantum degenerate regime. © 2010 The American Physical Society.


Courvoisier D.S.,University of Geneva | Eid M.,Free University of Berlin | Lischetzke T.,Free University of Berlin
Psychological Assessment | Year: 2012

Ecological momentary assessment (EMA) is a method that is now widely used to study behavior and mood in the settings in which they naturally occur. It maximizes ecological validity and avoids the limitations of retrospective self-reports. Compliance patterns across time have not been studied. Consistent compliance patterns could lead to data not missing at random and bias the results of subsequent analyses. In order to use modern statistical approaches for handling missing data, it is important to include variables predicting missing values into the statistical analysis. Therefore, these predictors have to be known and measured. The authors collected data on 3 four-item mood scales measuring well-being, wakefulness, and nervousness on 6 occasions per day for 7 days (N = 305) and examined compliance rate across time, within day, and within week. Results show good global compliance (mean compliance: 74.9% of calls answered). Compliance varied more within day than within week. Within day, it was lower for the first call of the day between 9 p.m. and 11 p.m. and higher for the call between 5 p.m. and 7 p.m. Within week, calls were equally answered across days of the week, but, as the study progressed, there was a slight drop in compliance with a progressive decrease that was stronger for the first 2 calls. Compliance on the person level did not depend on personality or on satisfaction with life. Practical consequences of the results for conducting ambulatory assessment studies are discussed, and some recommendations are given. © 2012 American Psychological Association.


Bourne E.C.,Free University of Berlin | Bourne E.C.,CNRS Alpine Ecology Laboratory
Proceedings. Biological sciences / The Royal Society | Year: 2014

The evolutionary potential of populations is mainly determined by population size and available genetic variance. However, the adaptability of spatially structured populations may also be affected by dispersal: positively by spreading beneficial mutations across sub-populations, but negatively by moving locally adapted alleles between demes. We develop an individual-based, two-patch, allelic model to investigate the balance between these opposing effects on a population's evolutionary response to rapid climate change. Individual fitness is controlled by two polygenic traits coding for local adaptation either to the environment or to climate. Under conditions of selection that favour the evolution of a generalist phenotype (i.e. weak divergent selection between patches) dispersal has an overall positive effect on the persistence of the population. However, when selection favours locally adapted specialists, the beneficial effects of dispersal outweigh the associated increase in maladaptation for a narrow range of parameter space only (intermediate selection strength and low linkage among loci), where the spread of beneficial climate alleles is not strongly hampered by selection against non-specialists. Given that local selection across heterogeneous and fragmented landscapes is common, the complex effect of dispersal that we describe will play an important role in determining the evolutionary dynamics of many species under rapidly changing climate.


Groger G.,University of Duisburg - Essen | Meyer-Zaika W.,University of Duisburg - Essen | Bottcher C.,Free University of Berlin | Grohn F.,The Interdisciplinary Center | And 2 more authors.
Journal of the American Chemical Society | Year: 2011

The low molecular weight heteroditopic monomer 1 forms supramolecular polymers in polar solution as shown, for example, by infrared laser-based dynamic light scattering (DLS), small-angle neutron scattering (SANS), electron microscopy (TEM, cryo-TEM), and viscosity measurements. Self-assembly of 1 is based on two orthogonal binding interactions, the formation of a Fe(II)-terpyridine 1:2 metal-ligand complex and the dimerization of a self-complementary guanidiniocarbonyl pyrrole carboxylate zwitterion. Both binding interactions have a sufficient stability in polar (DMSO) and even aqueous solutions to ensure formation of linear polymers of considerable length (up to 100 nm). The supramolecular polymerization follows a ring-chain mechanism causing a significant increase in the viscosity of the solutions at millimolar concentrations and above. The linear polymers then further aggregate in solution into larger globular aggregates with a densely packed core and a loose shell. Both binding interactions can be furthermore switched on and off either by adding a competing ligand to remove the metal ion and subsequent readdition of Fe(II) or by reversible protonation and deprotonation of the zwitterion upon addition of acid or base. The self-assembly of 1 can therefore be switched back and forth between four different states, the monomer, a metal-complexed dimer or an ion paired dimer, and finally the polymer. © 2011 American Chemical Society.


Handy M.R.,Free University of Berlin | M. Schmid S.,Free University of Berlin | M. Schmid S.,ETH Zurich | Bousquet R.,University of Potsdam | And 2 more authors.
Earth-Science Reviews | Year: 2010

A new reconstruction of Alpine Tethys combines plate-kinematic modelling with a wealth of geological data and seismic tomography to shed light on its evolution, from sea-floor spreading through subduction to collision in the Alps. Unlike previous models, which relate the fate of Alpine Tethys solely to relative motions of Africa, Iberia and Europe during opening of the Atlantic, our reconstruction additionally invokes independent microplates whose motions are constrained primarily by the geological record. The motions of these microplates (Adria, Iberia, Alcapia, Alkapecia, and Tiszia) relative to both Africa and Europe during Late Cretaceous to Cenozoic time involved the subduction of remnant Tethyan basins during the following three stages that are characterized by contrasting plate motions and driving forces: (1) 131-84. Ma intra-oceanic subduction of the Ligurian part of Alpine Tethys attached to Iberia coincided with Eo-alpine orogenesis in the Alcapia microplate, north of Africa. These events were triggered primarily by foundering of the older (170-131. Ma) Neotethyan subduction slab along the NE margin of the composite African-Adriatic plate; subduction was linked by a sinistral transform system to E-W opening of the Valais part of Alpine Tethys; (2) 84-35. Ma subduction of primarily the Piemont and Valais parts of Alpine Tethys which were then attached to the European plate beneath the overriding African and later Adriatic plates. NW translation of Adria with respect to Africa was accommodated primarily by slow widening of the Ionian Sea; (3) 35. Ma-Recent rollback subduction of the Ligurian part of Alpine Tethys coincided with Western Alpine orogenesis and involved the formation of the Gibraltar and Calabrian arcs. Rapid subduction and arc formation were driven primarily by the pull of the gravitationally unstable, retreating Adriatic and African slabs during slow convergence of Africa and Europe. The upper European-Iberian plate stretched to accommodate this slab retreat in a very mobile fashion, while the continental core of the Adriatic microplate acted as a rigid indenter within the Alpine collisional zone. The subducted lithosphere in this reconstruction can be correlated with slab material imaged by seismic tomography beneath the Alps and Apennines, as well as beneath parts of the Pannonian Basin, the Adriatic Sea, the Ligurian Sea, and the Western Mediterranean. The predicted amount of subducted lithosphere exceeds the estimated volume of slab material residing at depth by some 10-30%, indicating that parts of slabs may be superposed within the mantle transition zone and/or that some of this subducted lithosphere became seismically transparent. © 2010 Elsevier B.V.


Zuppinger-Dingley D.,University of Zürich | Schmid B.,University of Zürich | Petermann J.S.,Free University of Berlin | Petermann J.S.,Berlin Brandenburg Institute of Advanced Biodiversity Research BBIB | And 4 more authors.
Nature | Year: 2014

In experimental plant communities, relationships between biodiversity and ecosystem functioning have been found to strengthen over time, a fact often attributed to increased resource complementarity between species in mixtures and negative plant-soil feedbacks in monocultures. Here we show that selection for niche differentiation between species can drive this increasing biodiversity effect. Growing 12 grassland species in test monocultures and mixtures, we found character displacement between species and increased biodiversity effects when plants had been selected over 8 years in species mixtures rather than in monocultures. When grown in mixtures, relative differences in height and specific leaf area between plant species selected in mixtures (mixture types) were greater than between species selected in monocultures (monoculture types). Furthermore, net biodiversity and complementarity effects were greater in mixtures of mixture types than in mixtures of monoculture types. Our study demonstrates a novel mechanism for the increase in biodiversity effects: selection for increased niche differentiation through character displacement. Selection in diverse mixtures may therefore increase species coexistence and ecosystem functioning in natural communities and may also allow increased mixture yields in agriculture or forestry. However, loss of biodiversity and prolonged selection of crops in monoculture may compromise this potential for selection in the longer term. ©2014 Macmillan Publishers Limited. All rights reserved.


Mari A.,Free University of Berlin | Mari A.,University of Potsdam | Eisert J.,Free University of Berlin | Eisert J.,University of Potsdam
Physical Review Letters | Year: 2012

We introduce the idea of actually cooling quantum systems by means of incoherent thermal light, hence giving rise to a counterintuitive mechanism of "cooling by heating." In this effect, the mere incoherent occupation of a quantum mechanical mode serves as a trigger to enhance the coupling between other modes. This notion of effectively rendering states more coherent by driving with incoherent thermal quantum noise is applied here to the optomechanical setting, where this effect occurs most naturally. We discuss two ways of describing this situation, one of them making use of stochastic sampling of Gaussian quantum states with respect to stationary classical stochastic processes. The potential of experimentally demonstrating this counterintuitive effect in optomechanical systems with present technology is sketched. © 2012 American Physical Society.


Riera A.,Free University of Berlin | Riera A.,University of Potsdam | Gogolin C.,Free University of Berlin | Gogolin C.,University of Potsdam | And 2 more authors.
Physical Review Letters | Year: 2012

In this work, we show how Gibbs or thermal states appear dynamically in closed quantum many-body systems, building on the program of dynamical typicality. We introduce a novel perturbation theorem for physically relevant weak system-bath couplings that is applicable even in the thermodynamic limit. We identify conditions under which thermalization happens and discuss the underlying physics. Based on these results, we also present a fully general quantum algorithm for preparing Gibbs states on a quantum computer with a certified runtime and error bound. This complements quantum Metropolis algorithms, which are expected to be efficient but have no known runtime estimates and only work for local Hamiltonians. © 2012 American Physical Society.


Chu V.T.,A Leibniz Institute | Chu V.T.,Max Dellbruck Center | Beller A.,A Leibniz Institute | Rausch S.,Free University of Berlin | And 5 more authors.
Immunity | Year: 2014

Although in normal lamina propria (LP) large numbers of eosinophils are present, little is known about their role in mucosal immunity at steady state. Here we show that eosinophils are needed to maintain immune homeostasis in gut-associated tissues. By using eosinophil-deficient δdblGATA-1 and PHIL mice or an eosinophil-specific depletion model, we found a reduction in immunoglobulin A+ (IgA+) plasma cell numbers and in secreted IgA. Eosinophil-deficient mice also showed defects in the intestinal mucous shield and alterations in microbiota composition in the gut lumen. In addition, TGF-β-dependent events including class switching to IgA in Peyer's patches (PP), the formation of CD103+ Tcells including Foxp3+ regulatory (Treg), and also CD103+ dendritic cells were disturbed. Invitro cultures showed that eosinophils produce factors that promote T-independent IgA class switching. Our findings show that eosinophils are important players for immune homeostasis in gut-associated tissues and add to data suggesting that eosinophils can promote tissue integrity. © 2014 Elsevier Inc.


Dechant A.,University of Augsburg | Dechant A.,Free University of Berlin | Lutz E.,University of Augsburg | Lutz E.,Free University of Berlin
Physical Review Letters | Year: 2012

The transport of cold atoms in shallow optical lattices is characterized by slow, nonstationary momentum relaxation. We develop a projector operator method able to derive, in this case, a generalized Smoluchowski equation for the position variable. We show that this explicitly non-Markovian equation can be written as a systematic expansion involving higher-order derivatives. We use the latter to compute arbitrary moments of the spatial distribution and analyze their multifractal properties. © 2012 American Physical Society.


Barthel T.,Free University of Berlin | Barthel T.,University of Potsdam | Kliesch M.,Free University of Berlin | Kliesch M.,University of Potsdam
Physical Review Letters | Year: 2012

We consider open many-body systems governed by a time-dependent quantum master equation with short-range interactions. With a generalized Lieb-Robinson bound, we show that the evolution in this very generic framework is quasilocal; i.e., the evolution of observables can be approximated by implementing the dynamics only in a vicinity of the observables' support. The precision increases exponentially with the diameter of the considered subsystem. Hence, time evolution can be simulated on classical computers with a cost that is independent of the system size. Providing error bounds for Trotter decompositions, we conclude that the simulation on a quantum computer is additionally efficient in time. For experiments and simulations in the Schrödinger picture, our result can be used to rigorously bound finite-size effects. © 2012 American Physical Society.


Ohliger M.,Free University of Berlin | Ohliger M.,University of Potsdam | Eisert J.,Free University of Berlin
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

We present strictly efficient schemes for scalable measurement-based quantum computing using continuous-variable systems: These schemes are based on suitable non-Gaussian resource states, ones that can be prepared using interactions of light with matter systems or even purely optically. Merely Gaussian measurements such as optical homodyning as well as photon counting measurements are required, on individual sites. These schemes overcome limitations posed by Gaussian cluster states, which are known not to be universal for quantum computations of unbounded length, unless one is willing to scale the degree of squeezing with the total system size. We establish a framework derived from tensor networks and matrix product states with infinite physical dimension and finite auxiliary dimension general enough to provide a framework for such schemes. Since in the discussed schemes the logical encoding is finite dimensional, tools of error correction are applicable. We also identify some further limitations for any continuous-variable computing scheme from which one can argue that no substantially easier ways of continuous-variable measurement-based computing than the presented one can exist. © 2012 American Physical Society.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2013.9.1 | Award Amount: 2.66M | Year: 2013

Randomness has established itself as a vital building block of information processing and represents an integral ingredient for practically any aspect in the field of information processing and technology. The principal objective of this project will be to establish and evaluate the role played by randomness in quantum information processing. We propose to address the main difficulties that arise through the use of randomness, in particular, 1) the use of randomness as a theoretical tool to prove existence and properties of information processing applications; 2) the design of novel quantum information processing applications that exploit randomness; 3) the design and analysis of applications that work with real-world (that is, non-uniform) randomness; 4) the construction of design techniques that produce high-quality randomness, both from a computational and adversarial perspective; and, finally, 5) the use of randomness to analyze and improve the physical processes necessary for the design quantum communication and computation devices.The consortium (composed of 8 research teams) aims to unite the forces of EU expertise in computer science, physics and mathematics to undertake a comprehensive study of randomness and quantum information within their research portfolio. Many of the targeted tasks combine the knowledge of partners. Hence, strong research interactions will be necessary to successfully achieve the objectives of the project.


Grant
Agency: Cordis | Branch: H2020 | Program: RIA | Phase: WATER-2a-2014 | Award Amount: 7.82M | Year: 2015

The water sector needs improved climate prediction and downscaling based on consistent grounds (IPCC 5th Assessment Report, 2013). There is also a need for near future weather scenarios and anticipation of their impacts in the water cycle together with risk management strategies. BINGO will provide demand-driven solutions for a number of specific climate-related challenges in particular for highly vulnerable water resources of strategic importance. Water managers and other stakeholders will then be provided with information on specific climate scenarios at the space/time resolution fitting their needs, enabling them to act at various geographical levels (local, regional and European). BINGO aims at reducing the uncertainty of climate predictions and developing response strategies to help society manage that uncertainty. An innovative approach consists of enrolling end-users from the start, identifying specific vulnerabilities, needs and concerns about future climate. BINGO is built around 7 research sites in Northern and Southern Europe, covering a representative range of climatic conditions as well as combinations of water systems and water pressures. They illustrate a variety of water cycles at local/regional scales in Europe over various timescales, as well as common problems, including floods and droughts; water quality pressured by CSO, agriculture and competing demands for water (urban/tourism; agriculture/food security; hydropower). To guarantee sound management strategies for future weather challenges, BINGO will develop and validate all solutions built by strong dynamic interaction of researchers with end-users and decision makers throughout the project. By creating such knowledge alliances, water managers and other stakeholders can share awareness of climate challenges, thus increasing the possibilities of collaboration in order to manage and better cope with future climate challenges.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2015 | Award Amount: 2.50M | Year: 2016

What exactly are the words which priests recite in the Yasna, the core ritual of one of the most ancient and influential living religions, Zoroastrianism? What is their meaning and how do they relate to the ritual actions? The Yasna is significant for our cultural heritage not only because of its influential thought system which arguably impacted on post-exilic Judaism, nascent Christianity and Islam, but also because with parts of it going back to the 2nd millennium BCE, it is the oldest witness to Iranian languages. Its full appreciation, however, is severely hampered by the presence of outdated editions and translations or by their absence altogether. Moreover, the relationship between the text recited and the action performed during the ritual is unexplored due to a lack of documentary evidence. The Multimedia Yasna proposes to fill these gaps in a methodologically ground-breaking fashion. MUYA combines two different, yet complementary approaches by examining the Yasna both as a ritual performance and as a text attested in manuscripts. The two approaches will be integrated to answer questions about the meaning and function of the Yasna in a historical perspective. The research methods for achieving MUYAs objectives unite cutting edge approaches from Digital Humanities, Philology and Linguistics into four interrelated work-packages. These will involve filming and analyzing the ritual performance and teaching practices in priestly schools, the creation of a suite of electronic tools for editing Avestan texts, a database of transcribed manuscripts of the Yasna and in-depth studies of selected parts of the text by combining datasets produced by electronic processes with philological methods of textual criticism and linguistic analysis. These complementary datasets and methods will be used to produce an online publication of the sub-titled and interactive film of the Yasna ritual, together with print editions, translations and commentaries of the Avestan Yasna.


Mari A.,Free University of Berlin | Mari A.,University of Potsdam | Mari A.,CNR Institute of Neuroscience | Eisert J.,Free University of Berlin
Physical Review Letters | Year: 2012

We show that quantum circuits where the initial state and all the following quantum operations can be represented by positive Wigner functions can be classically efficiently simulated. This is true both for continuous-variable as well as discrete variable systems in odd prime dimensions, two cases which will be treated on entirely the same footing. Noting the fact that Clifford and Gaussian operations preserve the positivity of the Wigner function, our result generalizes the Gottesman-Knill theorem. Our algorithm provides a way of sampling from the output distribution of a computation or a simulation, including the efficient sampling from an approximate output distribution in the case of sampling imperfections for initial states, gates, or measurements. In this sense, this work highlights the role of the positive Wigner function as separating classically efficiently simulable systems from those that are potentially universal for quantum computing and simulation, and it emphasizes the role of negativity of the Wigner function as a computational resource. © 2012 American Physical Society.


Grant
Agency: Cordis | Branch: FP7 | Program: ERC-AG | Phase: ERC-AG-SH4 | Award Amount: 2.37M | Year: 2009

Emotion is a prime example of the complexity of human mind and behaviour, a psychobiological mechanism shaped by language and culture, which has puzzled scholars in the humanities and social sciences over the centuries. In an effort to reconcile conflicting theoretical traditions, we advocate a componential approach which treats event appraisal, motivational shifts, physiological responses, motor expression, and subjective feeling as dynamically interrelated and integrated components during emotion episodes. Using a prediction-generating theoretical model, we will address both production (elicitation and reaction patterns) and perception (observer inference of emotion from expressive cues). Key issues are the cognitive architecture and mental chronometry of appraisal, neurophysiological structures of relevance and valence detection, the emergence of conscious feelings due to the synchronization of brain/body systems, the generating mechanism for motor expression, the dimensionality of affective space, and the role of embodiment and empathy in perceiving and interpreting emotional expressions. Using multiple paradigms in laboratory, game, simulation, virtual reality, and field settings, we will critically test theory-driven hypotheses by examining brain structures and circuits (via neuroimagery), behaviour (via monitoring decisions and actions), psychophysiological responses (via electrographic recording), facial, vocal, and bodily expressions (via micro-coding and image processing), and conscious feeling (via advanced self-report procedures). In this endeavour, we benefit from extensive research experience, access to outstanding infrastructure, advanced analysis and synthesis methods, validated experimental paradigms as well as, most importantly, from the joint competence of an interdisciplinary affective science group involving philosophers, linguists, psychologists, neuroscientists, behavioural economists, anthropologists, and computer scientists.


Grant
Agency: Cordis | Branch: FP7 | Program: ERC-AG | Phase: ERC-AG-PE1 | Award Amount: 894.00K | Year: 2009

From the viewpoint of geometric classification, there are two extreme cases of smooth varieties X defined over an algebraically closed field: those which are hyperbolic, and those which are rationally connected. If k is no longer algebraically closed, a central question of Algebraic Arithmetic Geometry is what properties of k force X to have a rational point in those two opposed cases. It is conjectured (Lang-Manin, extended by Kollr), that rationally connected varieties have a rational point over a C1 field. It has been shown for function fields by Graber-Harris-Starr and by myself over a finite field. There is no relation between their geometric proof relying on the geometry of the moduli of punctured curves and my proof relying on motivic analogies between Hodge level and slopes in l-adic cohomology. The study of the case of the maximal unramified extension of the p-adic numbers might provide a bridge through the use of the inertia. Very little is known on Grothendiecks section conjecture, which predicts that sections of the Galois group of k, assumed to be a finite type over Q, into the arithmetic fundamental group of X, are given by rational points. Our hope goes in two directions, arithmetic and geometric on one side, motivic on the other. With Wittenberg, we hope to use Beilinsons geometric description of the nilpotent completion of the fundamental group, and with Levine, we wish to characterize sections of the motivic groups of mixed Tate motives over k and X and relate this to the section conjecture.


Schulz H.,Free University of Berlin | Salzarulo P.,University of Florence
Sleep Medicine Reviews | Year: 2012

The development of sleep research can be divided into two main periods. The first one was initiated in 1863 by the first systematic measurement of the depth of sleep, the second in 1953 by the discovery of recurrent episodes of rapid eye movements in sleep. The main methodological procedure in the first of these two periods was the measurement of a single physiological variable, while beginning with long-term measurements of the electroencephalogram (EEG) in sleep, multi-channel, polygraphic recording became the method of choice for sleep studies. Although rhythmic changes in the ultradian frequency range of one to 2h were observed early in many variables during sleep (movements, autonomic functions, penile erections), the recognition of the existence of two different states of sleep (rapid eye movement (REM) and non-rapid eye movement (NREM sleep)) was contingent upon a 'synthetic' view, which focus on the coalescence of multiple variables. The dual concept of sleep organization evolved stepwise in parallel to the rapid growth of neurophysiological knowledge and techniques in the first half of the 20th century, culminating in the discovery of REM sleep. © 2011 Elsevier Ltd.


Freund H.-J.,Fritz Haber Institute of the Max Planck Society | Nilius N.,Carl von Ossietzky University | Risse T.,Free University of Berlin | Schauermann S.,Fritz Haber Institute of the Max Planck Society
Physical Chemistry Chemical Physics | Year: 2014

The development of model catalyst systems for heterogeneous catalysis going beyond the metal single crystal approach, including phenomena involving the limited size of metal nanoparticles supported on oxide surfaces, as well as the electronic interaction through the oxide-metal interface, is exemplified on the basis of two case studies from the laboratory of the authors. In the first case study the reactivity of supported Pd nanoparticles is studied in comparison with Pd single crystals. The influence of carbon contaminants on the hydrogenation reaction of unsaturated hydrocarbons is discussed. Carbon contaminants are identified as a key parameter in those reactions as they control the surface and sub-surface concentration of hydrogen on and in the particles. In the second case study, scanning probe techniques are used to determine electronic and structural properties of supported Au particles as a function of the number of Au atoms in the particle. It is demonstrated how charge transfer between the support and the particle determines the shape of nanoparticles and a concept is developed that uses charge transfer control through dopants in the support to understand and design catalytically active materials. © 2014 the Owner Societies.


Muller C.,Free University of Berlin | Usvyat D.,University of Regensburg
Journal of Chemical Theory and Computation | Year: 2013

A method for accurate calculations of the cohesive energy of molecular crystals is presented. The cohesive energy is evaluated as a sum of several components. The major contribution is captured by periodic Hartree-Fock (HF) coupled with the local Møller-Plesset perturbation theory of second order (LMP2) with a triple-ζ basis set. Post-MP2 corrections and corrections for the basis set incompleteness are calculated from inexpensive incremental calculations with finite clusters. This is an essential improvement with respect to the periodic LMP2 method and allows for results of benchmark quality for crystalline systems. The proposed technique is superior to the standard incremental scheme as concerns the cluster size and basis set convergence of the results. In contrast to the total energy or electron correlation energy, which are evaluated in standard incremental calculations, post-MP2 and basis set corrections are rather insensitive to approximations and converge quickly both in terms of the order of the increments and the number of terms at a given order. Evaluation of the incremental corrections within the sub-kJ/mol precision requires computing very few of the most compact two-center and three-center non-embedded clusters, making the whole correction scheme computationally inexpensive. This method as well as alternative routes to compute the cohesive energy via the incremental scheme are tested on two molecular crystals: carbon dioxide (CO2) and hydrogen cyanide (HCN). © 2013 American Chemical Society.


Olias P.,Free University of Berlin | Schade B.,Bavarian Animal Health Service | Mehlhorn H.,Heinrich Heine University Düsseldorf
Infection, Genetics and Evolution | Year: 2011

Until recently, besnoitiosis has been a neglected disease of domestic animals. Now, a geographic expansion of the causing protozoan parasite Besnoitia besnoiti in livestock has been recognized and the disease in cattle is considered emerging in Europe. Bovine besnoitiosis leads to significant economic losses by a decline in milk production, sterility, transient or permanent infertility of bulls, skin lesions and increase of mortality in affected cattle population. Phylogenetically, the Besnoitia genus is closest related to the well studied and medically important protozoans, Toxoplasma gondii and Neospora caninum. In contrast, discriminative molecular markers to type and subtype large mammalian Besnoitia species (B. besnoiti, B. caprae, B. tarandi, B. bennetti) on a relevant level of species and strains are lacking. Similarly, these cyst-forming parasites may use two hosts to fulfill their life cycle, but this has not been proven for all large mammalian Besnoitia species yet. Most important though, the final hosts and transmission routes of these Besnoitia species remain mysterious. Here, we review aspects of parasite's pathology, speciation, phylogeny, epidemiology and transmission with a special focus on recent molecular studies of all to date known Besnoitia species. Using an integrated approach, we have tried to highlight some promising directions for future research. © 2011 Elsevier B.V.


Casiraghi C.,University of Manchester | Casiraghi C.,Free University of Berlin
Physica Status Solidi (B) Basic Research | Year: 2011

The Raman scattering process in graphene is always resonant, i.e. involves real electronic states, and this affects the Raman intensity. Thus, a detailed analysis of the Raman intensity of graphene can provide useful information on the Raman scattering process itself, in particular on the interaction between the fundamental excitations in graphene, such as electron-phonon and electron-defect interactions, which can be studied only by transport or complex techniques. Here a detailed analysis of the dependence of the Raman intensity of graphene on doping and disorder is presented. While the intensity of the G peak, I(G), is not strongly affected by small amount of doping or disorder, the intensity of the 2D peak strongly decreases with increasing doping or disorder. By analyzing the dependence of I(2D) with doping in the framework of a fully resonant process, we measured the total electron-phonon scattering rate. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Schwierz N.,University of California at Berkeley | Horinek D.,University of Regensburg | Netz R.R.,Free University of Berlin
Langmuir | Year: 2015

Ion binding to acidic groups is a central mechanism for ion-specificity of macromolecules and surfaces. Depending on pH, acidic groups are either protonated or deprotonated and thus change not only charge but also chemical structure with crucial implications for their interaction with ions. In a two-step modeling approach, we first determine single-ion surface interaction potentials for a few selected halide and alkali ions at uncharged carboxyl (COOH) and charged carboxylate (COO-) surface groups from atomistic MD simulations with explicit water. Care is taken to subtract the bare Coulomb contribution due to the net charge of the carboxylate group and thereby to extract the nonelectrostatic ion-surface potential. Even at this stage, pronounced ion-specific effects are observed and the ion surface affinity strongly depends on whether the carboxyl group is protonated or not. In the second step, the ion surface interaction potentials are used in a Poisson-Boltzmann model to calculate the surface charge and the potential distribution in the solution depending on salt type, salt concentration, and solution pH in a self-consistent manner. Hofmeister phase diagrams are derived on the basis of the long-ranged forces between two carboxyl-functionalized surfaces. For cations we predict direct, reversed, and altered Hofmeister series as a function of the pH, qualitatively similar to recent experimental results for silica surfaces. The Hofmeister series reversal for cations is rationalized by a reversal of the single-cation affinity to the carboxyl group depending on its protonation state: the deprotonated carboxylate (COO-) surface group interacts most favorably with small cations such as Li+ and Na+, whereas the protonated carboxyl (COOH) surface group interacts most favorably with large cations such as Cs+ and thus acts similarly to a hydrophobic surface group. Our results provide a general mechanism for the pH-dependent reversal of the Hofmeister series due to the different specific ion binding to protonated and deprotonated surface groups. © 2014 American Chemical Society.


Schmidt Am Busch M.,Johannes Kepler University | Muh F.,Free University of Berlin | El-Amine Madjet M.,Free University of Berlin | Renger T.,Johannes Kepler University
Journal of Physical Chemistry Letters | Year: 2011

The Fenna-Matthews-Olson (FMO) light-harvesting protein connects the outer antenna system (chlorosome/baseplate) with the reaction center complex in green sulfur bacteria. Since its first structure determination in the mid-70s, this pigment-protein complex has become an important model system to study excitation energy transfer. Recently, an additional bacteriochlorophyll a (the eighth) pigment was discovered in each subunit of this homotrimer. Our structure-based calculations of the optical properties of the FMO protein demonstrate that the eighth pigment is the linker to the baseplate, confirming recent suggestions from crystallographic studies. © 2010 American Chemical Society.


Bode N.,Free University of Berlin | Kusminskiy S.V.,Free University of Berlin | Egger R.,Heinrich Heine University Düsseldorf | Von Oppen F.,Free University of Berlin
Physical Review Letters | Year: 2011

We develop a scattering theory of current-induced forces exerted by the conduction electrons of a general mesoscopic conductor on slow "mechanical" degrees of freedom. Our theory describes the current-induced forces both in and out of equilibrium in terms of the scattering matrix of the phase-coherent conductor. Under general nonequilibrium conditions, the resulting mechanical Langevin dynamics is subject to both nonconservative and velocity-dependent Lorentz-like forces, in addition to (possibly negative) friction. We illustrate our results with a two-mode model inspired by hydrogen molecules in a break junction which exhibits limit-cycle dynamics of the mechanical modes. © 2011 American Physical Society.


Deffner S.,University of Maryland University College | Lutz E.,Free University of Berlin | Lutz E.,Friedrich - Alexander - University, Erlangen - Nuremberg
Physical Review Letters | Year: 2013

We derive a Margolus-Levitin-type bound on the minimal evolution time of an arbitrarily driven open quantum system. We express this quantum speed limit time in terms of the operator norm of the nonunitary generator of the dynamics. We apply these results to the damped Jaynes-Cummings model and demonstrate that the corresponding bound is tight. We further show that non-Markovian effects can speed up quantum evolution and therefore lead to a smaller quantum speed limit time. © 2013 American Physical Society.


Eckmann A.,University of Manchester | Felten A.,Free University of Berlin | Verzhbitskiy I.,Free University of Berlin | Davey R.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

We present a detailed Raman study of defective graphene samples containing specific types of defects. In particular, we compared sp3 sites, vacancies, and substitutional Boron atoms. We find that the ratio between the D and G peak intensities, I(D)/I(G), does not depend on the geometry of the defect (within the Raman spectrometer resolution). In contrast, in the limit of low defect concentration, the ratio between the D′ and G peak intensities is higher for vacancies than sp3 sites. By using the local activation model, we attribute this difference to the term CS,x, representing the Raman cross section of I(x)/I(G) associated with the distortion of the crystal lattice after defect introduction per unit of damaged area, where x = D or D ′. We observed that CS,D=0 for all the defects analyzed, while CS,D′of vacancies is 2.5 times larger than CS,D′ of sp3 sites. This makes I(D)/I(D′) strongly sensitive to the nature of the defect. We also show that the exact dependence of I(D)/I(D ′) on the excitation energy may be affected by the nature of the defect. These results can be used to obtain further insights into the Raman scattering process (in particular for the D′ peak) in order to improve our understanding and modeling of defects in graphene. © 2013 American Physical Society.


Hofmann J.,Fritz Haber Institute of the Max Planck Society | Hofmann J.,Free University of Berlin | Hahm H.S.,Max Planck Institute of Colloids and Interfaces | Hahm H.S.,Free University of Berlin | And 4 more authors.
Nature | Year: 2015

Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry - a method that separates molecules according to their mass, charge, size, and shape - can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s. © 2015 Macmillan Publishers Limited.


Friesdorf M.,Free University of Berlin | Werner A.H.,Free University of Berlin | Brown W.,University College London | Scholz V.B.,ETH Zurich | Eisert J.,Free University of Berlin
Physical Review Letters | Year: 2015

The phenomenon of many-body localization has received a lot of attention recently, both for its implications in condensed-matter physics of allowing systems to be an insulator even at nonzero temperature as well as in the context of the foundations of quantum statistical mechanics, providing examples of systems showing the absence of thermalization following out-of-equilibrium dynamics. In this work, we establish a novel link between dynamical properties - a vanishing group velocity and the absence of transport - with entanglement properties of individual eigenvectors. For systems with a generic spectrum, we prove that strong dynamical localization implies that all of its many-body eigenvectors have clustering correlations. The same is true for parts of the spectrum, thus allowing for the existence of a mobility edge above which transport is possible. In one dimension these results directly imply an entanglement area law; hence, the eigenvectors can be efficiently approximated by matrix-product states. © 2015 American Physical Society.


Schwierz N.,Free University of Berlin | Schwierz N.,TU Munich | Horinek D.,University of Regensburg | Netz R.R.,Free University of Berlin
Langmuir | Year: 2013

Using a two-step modeling approach, we address the full spectrum of direct, reversed, and altered ionic sequences as the charge of the ion, the charge of the surface, and the surface polarity are varied. From solvent-explicit molecular dynamics simulations, we extract single-ion surface interaction potentials for halide and alkali ions at hydrophilic and hydrophobic surfaces. These are used within Poisson-Boltzmann theory to calculate ion density and electrostatic potential distributions at mixed polar/unpolar surfaces for varying surface charge. The resulting interfacial tension increments agree quantitatively with experimental data and capture the Hofmeister series, especially the anomaly of lithium, which is difficult to obtain using continuum theory. Phase diagrams that feature different Hofmeister series as a function of surface charge, salt concentration, and surface polarity are constructed from the long-range force between two surfaces interacting across electrolyte solutions. Large anions such as iodide have a high hydrophobic surface affinity and increase the effective charge magnitude on negatively charged unpolar surfaces. Large cations such as cesium also have a large hydrophobic surface affinity and thereby compensate an external negative charge surface charge most efficiently, which explains the well-known asymmetry between cations and anions. On the hydrophilic surface, the size-dependence of the ion surface affinity is reversed, explaining the Hofmeister series reversal when comparing hydrophobic with hydrophilic surfaces. © 2013 American Chemical Society.


Zabel J.,Free University of Berlin | Nair R.R.,University of Manchester | Ott A.,Free University of Berlin | Georgiou T.,University of Manchester | And 4 more authors.
Nano Letters | Year: 2012

We use graphene bubbles to study the Raman spectrum of graphene under biaxial (e.g., isotropic) strain. Our Gruneisen parameters are in excellent agreement with the theoretical values. Discrepancy in the previously reported values is attributed to the interaction of graphene with the substrate. Bilayer balloons (intentionally pressurized membranes) have been used to avoid the effect of the substrate and to study the dependence of strain on the interlayer interactions. © 2011 American Chemical Society.


Ibert O.,Leibniz Institute for Regional Development and Structural Planning IRS in Erkner | Ibert O.,Free University of Berlin
Environment and Planning A | Year: 2010

The author discusses and explores empirically how far the notion of relational distance might improve understanding of the geography of innovation processes. Relational distance is regarded (1) as a multidimensional concept which becomes fruitful when used in a heuristic way; (2) as an interactional effect; and (3) as being enacted in practice. The author illustrates this under-standing empirically by presenting an ethnographic case study: the development biography of an analytical device. In this case, relational distance emerged between science and business. The author scrutinizes how relational distance not only induces cultural tensions but also intertwines divergent practical activities unfolding differently in space. Thereby it generates dynamic time-spatial ambiguities: namely, effects of dislocation, ambiguities of knowledge allocation, and opportunity costs. © 2010 Pion Ltd and its Licensors.


Jouvet G.,Free University of Berlin | Funk M.,ETH Zurich
Journal of Glaciology | Year: 2014

In this paper we reconstruct the space-time trajectory beneath the surface of Aletschgletscher, Switzerland, of the corpses of three mountaineers that disappeared in March 1926 and reappeared at the glacier surface in June 2012. Our method integrates the time-dependent velocity field of an existing full-Stokes glacier model, starting at the point where the corpses were found at the glacier surface. Our main result is that we were able to localize the immersion location where the brothers presumably died. As a second result, the upstream end point of the computed trajectory emerges very close to the glacier surface in 1926, giving a new and global validation of the glacier model in space and time. Testing the sensitivity of the immersion location obtained with respect to the model and other uncertainties indicates an area of 0.6% of the entire glacier area where the accident could have occurred. Our result suggests that death was not caused by an avalanche or a fall into a crevasse; instead, it is likely that the mountaineers became disoriented in prolonged severe weather conditions and froze to death.


Barak G.,Harvard University | Steinberg H.,Weizmann Institute of Science | Pfeiffer L.N.,Bell Laboratories | West K.W.,Bell Laboratories | And 3 more authors.
Nature Physics | Year: 2010

Over the past several decades, Luttinger-liquid theory has a framework for interacting electrons in one dimension. However, the validity of the theory is strictly limited to low-energy excitations where the electron dispersion is linear. Interacting electrons in one-dimension beyond the Luttinger-liquid limit, where the underlying dispersion of electrons is no longer linear, exhibit intriguing manifestations of the interactions, which have direct implications on many experimental systems. For example, consider the energy relaxation of particles or holes, the unoccupied states in a Fermi sea. Whereas in Luttinger-liquid theory such energy relaxation is strictly forbidden, in a nonlinearly dispersing one-dimensional electron system energy relaxation is allowed but very different for particles and holes. Here, we use momentum-resolved tunnelling to selectively inject energetic particles and holes into a quantum wire and study their relaxation processes. Our measurements confirm that energetic particles undergo fast relaxation to a thermalized distribution and holes retain their original injection energy, thereby providing a clear demonstration of electron dynamics beyond the Luttinger limit. A model of thermalization derived in the limit of weak interactions shows quantitative agreement with the experimental findings. © 2010 Macmillan Publishers Limited. All rights reserved.


Deffner S.,University of Maryland University College | Lutz E.,Free University of Berlin
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2013

We consider a closed quantum system initially at thermal equilibrium and driven by arbitrary external parameters. We derive a lower bound on the entropy production which we express in terms of the Bures angle between the nonequilibrium and the corresponding equilibrium state of the system. The Bures angle is an angle between mixed quantum states and defines a thermodynamic length valid arbitrarily far from equilibrium. As an illustration, we treat the case of a time-dependent harmonic oscillator for which we obtain analytic expressions for generic driving protocols. © 2013 American Physical Society.


Schneider S.,Free University of Berlin | Hammerschmidt K.,Free University of Berlin | Rosenberg C.L.,University Pierre and Marie Curie
Earth and Planetary Science Letters | Year: 2013

We attempt to improve temporal constraints on the longevity and the termination of ductile shear zones by performing texturally-controlled in situ 40Ar/39Ar analyses of pre-kinematic muscovite, biotite and K-feldspars, of syn-kinematic phengite and K-feldspar, and of post-kinematic phengite within the same samples of sinistral shear zones from the western Tauern Window (Eastern Alps). Additionally two samples were dated by the Rb/Sr method (microsampling). Relative sequences of mineral formation based on microstructural, cross-cutting relationships were confirmed by in situ 40Ar/39Ar analyses, showing that syn-kinematic minerals are, in general, younger than pre-kinematic minerals and older or of equal age than the post-kinematic minerals of the same sample.From the rim to the core of the western Tauern Window syn-kinematic phengite and K-feldspar reveal a set of formation ages varying between 33 and 15Ma for the northernmost and peripheral shear zone (Ahorn Shear Zone), between 24 and 12Ma for the intermediate shear zone network (Tuxer Shear Zones), and between 20 and 7Ma for the southernmost and central shear zone (Greiner Shear Zone). The age variation of syn-kinematic phengite and K-feldspar analyses is larger than the analytical error of each age obtained. In addition, isochron calculations of the syn-kinematic minerals reveal atmospheric-like 40Ar/36Ar intercepts. Therefore, the obtained age values of the syn-kinematic minerals are interpreted as formation ages which date increments of a long lasting deformation period. The time range of deformation of each shear zone system is bracketed by the oldest and youngest formation ages of syn-kinematic phengite and K-feldspar.Post-kinematic phengite laths show the youngest formation ages and overlap with the youngest syn-kinematic formation ages. This relationship indicates that post-kinematic growth occurred immediately after syn-kinematic mineral formation at the end of ductile sinistral shear. Hence, the termination of deformation is dated by the ages of these post-kinematic phengite blasts.Pre-kinematic minerals are characterized by break down and exsolution reactions and their age values are heterogeneous and often affected by the presence of extraneous Ar. These age values are usually older than, but sometimes overlapping with, ages of the syn-kinematic minerals.Using the temporal constraints obtained by the ages of pre-, syn-, and post-kinematic minerals, we could assess partly overlapping time intervals of syn-kinematic mineral formation of 19. Myr (33-15. Ma) in the Ahorn Shear Zone, 13. Myr (24-12. Ma) in the Tuxer Shear Zones and 14. Myr (20-7. Ma) in the Greiner Shear Zone. This indicates successive localization and propagation of ductile shear zones in the western Tauern Window from lower metamorphic sites at the rim towards higher metamorphic sites in the center. © 2013 Elsevier B.V.


Adolphs J.,Free University of Berlin | Muh F.,Free University of Berlin | Madjet M.E.-A.,Free University of Berlin | Am Busch M.S.,Johannes Kepler University | Renger T.,Johannes Kepler University
Journal of the American Chemical Society | Year: 2010

Optical line shape theory is combined with a quantum-chemical/electrostatic calculation of the site energies of the 96 chlorophyll a pigments and their excitonic couplings to simulate optical spectra of photosystem I core complexes from Thermosynechococcus elongatus. The absorbance, linear dichroism and circular dichroism spectra, calculated on the basis of the 2.5 Å crystal structure, match the experimental data semiquantitatively allowing for a detailed analysis of the pigment-protein interaction. The majority of site energies are determined by multiple interactions with a large number (>20) of amino acid residues, a result which demonstrates the importance of long-range electrostatic interactions. The low-energy exciton states of the antenna are found to be located at a nearest distance of about 25 Å from the special pair of the reaction center. The intermediate pigments form a high-energy bridge, the site energies of which are stabilized by a particularly large number (>100) of amino acid residues. The concentration of low energy exciton states in the antenna is larger on the side of the A-branch of the reaction center, implying an asymmetric delivery of excitation energy to the latter. This asymmetry in light-harvesting may provide the key for understanding the asymmetric use of the two branches in primary electron transfer reactions. Experiments are suggested to check for this possibility. © 2010 American Chemical Society.


Heeg S.,Free University of Berlin | Fernandez-Garcia R.,Imperial College London | Oikonomou A.,University of Manchester | Schedin F.,University of Manchester | And 4 more authors.
Nano Letters | Year: 2013

We characterize plasmonic enhancement in a hotspot between two Au nanodisks using Raman scattering of graphene. Single layer graphene is suspended across the dimer cavity and provides an ideal two-dimensional test material for the local near-field distribution. We detect a Raman enhancement of the order of 103 originating from the cavity. Spatially resolved Raman measurements reveal a near-field localization one order of magnitude smaller than the wavelength of the excitation, which can be turned off by rotating the polarization of the excitation. The suspended graphene is under tensile strain. The resulting phonon mode softening allows for a clear identification of the enhanced signal compared to unperturbed graphene. © 2012 American Chemical Society.


Netz R.R.,Free University of Berlin | Horinek D.,University of Regensburg
Annual Review of Physical Chemistry | Year: 2012

The behavior of halide salts at the vapor/water interface has been the focus of a tremendous amount of work in the past ten years. A molecular view of the interface has been introduced with the observation that large anions have some affinity for the interface, but a quantitative description of the driving forces that determine ion adsorption or repulsion at the interface is still missing. This review discusses recent developments that are based on classical and quantum-chemical molecular simulations as well as developments that are based on simple potential models. Copyright ©2012 by Annual Reviews. All rights reserved.


Muh F.,Free University of Berlin | Madjet M.E.-A.,Free University of Berlin | Renger T.,Johannes Kepler University
Journal of Physical Chemistry B | Year: 2010

The local S0 → S1 transition energies (site energies) and corresponding excitonic couplings of chlorophyll a (Chla) and b (Chlb) pigments bound to trimeric, major light-harvesting complex II (LHCII) of higher plants are calculated on the basis of the two crystal structures (Liu et al. Nature 2004, 428, 287-292; Standfuss et al. EMBO J. 2005, 24, 919-928) by using a combined quantum chemical/electrostatic method (Müh et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 16862-16867) that has been modified to cover membrane proteins and to account more realistically for the behavior of protonatable groups under the conditions of low-temperature optical spectroscopy. The obtained exciton levels are in reasonable agreement with experimental information (including linear absorption, linear dichroism, circular dichroism, fluorescence spectra of native as well as wild-type-minus-mutant difference absorption spectra of recombinant LHCII) and differ from earlier treatments based on fitted site energies (Novoderezhkin et al. J. Phys. Chem. B 2005, 109, 10493-10504) mainly by assigning a lower energy level to Chla 604 (in the nomenclature of Liu et al.) and Chlb 608 and a higher energy level to Chlb 605 and 609. The energy sink at cyrogenic temperatures is located at Chla 610 in the stromal layer of pigments, but structural changes at elevated temperatures may change the nature of the terminal emitter domain (including Chla 610/611/612). The site energy red-shift of Chla 610 is calculated to be significantly larger on the basis of the crystal structure of Standfuss et al. compared to that of Liu et al. due to conformational differences in the neighborhood of this pigment. A possible conformational change in the vicinity of Chla 604 involving tyrosine 112 and neoxanthin is found to strongly affect the site energy of this Chla and render it an alternative energy sink in the lumenal layer. A detailed, structure-based analysis of electrostatic pigment-protein interactions is performed to identify amino acid residues that are of interest for future mutagenesis experiments with the aim to further characterize the energy sinks, putative " bottleneck" states for excitation energy transfer, and potential sites of nonphotochemical quenching. © 2010 American Chemical Society.


Muller C.,Free University of Berlin | Usvyat D.,University of Regensburg | Stoll H.,University of Stuttgart
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

The correlation contribution to the cohesive energy of the Ar face-centered cubic (fcc) crystal has been evaluated within periodic and finite cluster models, using wave-function-based correlation techniques. The periodic local second-order Møller-Plesset perturbation (MP2) method is compared, in terms of accuracy and efficiency, to the incremental scheme employing standard MP2, local MP2, and local coupled cluster [CCSD(T)] methods. Three different finite cluster models of increasing complexity have been used in the incremental calculations. The local MP2 treatment is found to be relatively insensitive to the choice of the cluster model, and it is shown that within the LMP2 treatment virtually identical results can be expected from the periodic and different incremental calculations. Moreover, the two approaches can be considered as complementary: The periodic treatment allows for a relatively inexpensive reference, while further improvement of the level of correlation treatment and the size of one-particle basis sets is achieved more easily within the incremental scheme. © 2011 American Physical Society.


Bercioux D.,Donostia International Physics Center | Bercioux D.,Ikerbasque | Bercioux D.,Free University of Berlin | Lucignano P.,CNR Institute of Neuroscience | Lucignano P.,University of Naples Federico II
Reports on Progress in Physics | Year: 2015

In this review article we describe spin-dependent transport in materials with spin-orbit interaction of Rashba type. We mainly focus on semiconductor heterostructures, however we consider topological insulators, graphene and hybrid structures involving superconductors as well. We start from the Rashba Hamiltonian in a two dimensional electron gas and then describe transport properties of two- and quasi-one-dimensional systems. The problem of spin current generation and interference effects in mesoscopic devices is described in detail. We address also the role of Rashba interaction on localisation effects in lattices with nontrivial topology, as well as on the Ahronov-Casher effect in ring structures. A brief section, in the end, describes also some related topics including the spin-Hall effect, the transition from weak localisation to weak anti localisation and the physics of Majorana fermions in hybrid heterostructures involving Rashba materials in the presence of superconductivity. © 2015 IOP Publishing Ltd.


Erbas A.,TU Munich | Erbas A.,Free University of Berlin | Horinek D.,University of Regensburg | Netz R.R.,TU Munich | Netz R.R.,Free University of Berlin
Journal of the American Chemical Society | Year: 2012

Amontons' law successfully describes friction between macroscopic solid bodies for a wide range of velocities and normal forces. For the diffusion and forced sliding of adhering or entangled macromolecules, proteins, and biological complexes, temperature effects are invariably important, and a similarly successful friction law at biological length and velocity scales is missing. Hydrogen bonds (HBs) are key to the specific binding of biomatter. Here we show that friction between hydrogen-bonded matter obeys in the biologically relevant low-velocity viscous regime a simple law: the friction force is proportional to the number of HBs, the sliding velocity, and a friction coefficient γ HB. This law is deduced from atomistic molecular dynamics simulations for short peptide chains that are laterally pulled over planar hydroxylated substrates in the presence of water and holds for widely different peptides, surface polarities, and applied normal forces. The value of γ HB is extrapolated from simulations at sliding velocities in the range from V = 10 -2 to 100 m/s by mapping on a simple stochastic model and turns out to be of the order of γ HB ≲ 10 -8 kg/s. The friction of a single HB thus amounts to the Stokes friction of a sphere with an equivalent radius of roughly 1 μm moving in water. Cooperativity is pronounced: roughly three HBs act collectively. © 2011 American Chemical Society.


Worzewski T.,University of Kiel | Jegen M.,University of Kiel | Kopp H.,University of Kiel | Brasse H.,Free University of Berlin | Taylor Castillo W.,Instituto Costarricense Of Electricidad
Nature Geoscience | Year: 2011

Fluids entering the subduction zone play a key role in the subduction process. They cause changes in the dynamics and thermal structure of the subduction zone1, and trigger earthquakes when released from the subducting plate during metamorphism2,3. Fluids are delivered to the subduction zone by the oceanic crust and also enter the oceanic plate as it bends downwards at the plate boundary. However, the amount of fluids entering subduction zones is not matched by that leaving through volcanic emissions 4 or transfer to the deep mantle2, implying possible storage of fluids in the crust. Here we use magnetotelluric data to map the entire hydration and dehydration cycle of the Costa Rican subduction zone to 120 km depth. Along the incoming plate bend, we detect a conductivity anomaly that we interpret as sea water penetrating down extensional faults and cracks into the upper mantle. Along the subducting plate interface we document the dehydration of sediments, the crust and mantle. We identify an accumulation of fluids at ∼20-30 km depth at a distance of 30 km seaward from the volcanic arc. Comparison with other subduction zones5-14 indicates that such fluid accumulation is a global phenomenon. Although we are unable to test whether these fluid reservoirs grow with time, we suggest that they can account for some of the missing outflow of fluid at subduction zones. © 2011 Macmillan Publishers Limited. All rights reserved.


Grant
Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.1.6 | Award Amount: 2.21M | Year: 2008

OPNEX delivers a first principles approach to the design of architectures and protocols for multi-hop wireless networks. Systems and optimization theory is used as the foundation for algorithms that provably achieve full transport capacity of wireless systems. Subsequently a plan for converting the algorithms termed in abstract network models to protocols and architectures in practical wireless systems is given. Finally a validation methodology through experimental protocol evaluation in real network test-beds is proposed. OPNEX will use recent advances in system theoretic network control, including the back-pressure principle, max-weight scheduling, utility optimization congestion control and primal-dual method for extracting network algorithms. These approaches exhibited already vast potential for achieving maximum capacity and full exploitation of resources in abstract network models and found their way to reality in high performance switching architectures and recent variants of TCP that embody the primal-dual optimization principle. Wireless, the fastest growing component of internet today, is also the least understood for the designer due to mobility, rapidly changing topology, radio link unpredictability and volatile load distribution among others. Current approaches used in practice for multi-hop wireless, the basic communication infrastructure for sensor network extensions of the internet, are mostly empirical and heuristic. Our system optimization approach will provide a rigorous integrated system design framework from physical up to network and transport layer that renders itself to validation and comparison with the theoretically optimal performance in terms of throughput, spectrum and energy utilization. The adopted approach on decentralization, communication and computational complexity reduction as well as autonomous operation will lead to implementable algorithms and architectures to be validated eventually in the proposed test-beds.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 3.84M | Year: 2009

Virus infections are a major cause of diseases and death among men and animals. The recent outbreak of SARS and the danger that an avian influenza virus may become pandemic, have clearly shown that members of any virus family can potentially turn into a pathogen. To combat virus infection and propagation, systematic and comprehensive studies both on viral components mediating virus-cell interactions, and on the cell biology behind virus entry are necessary. Our network, teaming academic and industrial groups, is aimed at undertaking an interdisciplinary effort to reveal the diversity of pathways and associated molecular mechanisms of cell entry of enveloped viruses. Research by experimental and theoretical approaches will be directed towards the identification of cellular receptors and of viral fusion proteins responsible for interaction with host cells. Among topics are folding, three-dimensional structure and conformational changes of viral fusion proteins as well as virus triggered signalling cascades in cells. Biophysical approaches will unravel the relationship between energetics of conformational changes of viral proteins and membrane bending and fusion. Together with industrial partners the project will identify potential targets for designed drug development, and will develop virus protein coated nanoparticles as new biotechnological and medical tools. The groups have complementary expertise at the highest standard in all required techniques of virology, molecular and cellular biology, biochemistry, proteomics, structural biology, theoretical and experimental biophysics. A challenging research and training environment in an international setting will provide young scientists with a network wide research-oriented training devoted to the specific aspects of virus entry and to structuring of industry projects and commercial exploitation of results, and a local training in soft skills and basic complementary education adapted to the personal needs.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.68M | Year: 2013

The SusPhos training network will bring about a paradigm shift in the teaching of sustainable phosphorus chemistry, in the training of multidisciplinary-competent scientists, and in the publics view on chemistry to preserve the essential element phosphorus from depletion. SusPhos represents the first systematic investigation of the eco-friendly production, smart use, recycling and commercial exploitation of phosphorus-based processes and materials that use the precious element phosphorus in a sustainable manner. This approach should lead to fundamental insights into sustainable technologies and create an ideal platform for the training of young, ambitious researchers in a superb collaborative European setting. SusPhos will educate 14 broadly-oriented researchers at the interface of synthetic chemistry, catalysis, materials science, process chemistry, industrial phosphorus chemistry, and technology transfer. SusPhos intense training module combines the complementary strengths of nine academic and three industrial teams to promote intersectoral mobility of top-class multi-skilled researchers to enforce cross-fertilization of enhanced research synergies between the public and private European chemical sector. In its dual-mentor programme each of the ESRs and ERs will be supervised by one mentor from academia and one from industry to ensure an outstanding training in both sectors. The training programme uses highly innovative and timely methodologies to provide comprehensive multidisciplinary training of a new generation of young researchers capable of understanding and applying green chemistry to the conservation of phosphorus by environmentally benign conversions. Our SME Magpie Polymers and leading chemical companies Thermphos, Arkema and DSM will ensure rapid and effective technology transfer. As such the network will facilitate Europes continued global leadership on the sustainable use of phosphorus in an increasingly fierce competition for resources.


Grant
Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.74M | Year: 2013

Subduction zones play a fundamental role in our daily life. Half of the world population lives on top or nearby one of them, in coastal areas repeatedly devastated by large earthquakes, tsunamis or volcanic eruptions. Giant earthquakes occurring on subduction zone mega-thrusts (Mw close to 9 or larger) are indeed amongst the deadliest natural hazards. During the last decade, very large earthquakes took many lives (Sumatra, Chile, Japan) and, according to the World Bank, over 200 billion for the 2011 Japan earthquake. These dramatic phenomena are fundamentally controlled by the mechanical coupling and global material transfer at and across subduction zone inter-plate boundaries, between the down-going subducting plate and the overriding plate. Stresses and energy release via earthquakes together with fluid-mediated mass transfer are indeed highly focused on the plate interface, where they interact on a wide range of spatial and temporal scales, both at short- (10e-4 yr) and longer time-scales (10e6 yr). However, despite its social and economic impact, the nature, structure and properties of this plate interface are still largely unknown, calling for a thorough Zoom In between the Plates (ZIP). ZIP represents a real challenge for a new generation of geoscientists and requires innovative, high-end, cross-disciplinary scientific and technologic training to provide them with the skills and strength to tackle such problems, make major contributions, and undertake an academic or industrial career on managing geohazards. This scientific effort is mandatory for risk assessment, to enhance the reliability of early-warning systems and help reduce human loss and economic costs. Educational outreach in vulnerable countries is also crucial to explain the seismic, tectonic and tsunamic processes both to politics and populations.


Kyba C.C.M.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Kyba C.C.M.,Free University of Berlin | Hanel A.,Museum Am Scholerberg | Holker F.,Leibniz Institute of Freshwater Ecology and Inland Fisheries
Energy and Environmental Science | Year: 2014

Improvements in the luminous efficiency of outdoor lamps might not result in energy savings or reductions in greenhouse gas emissions. The reason for this is a rebound effect: when light becomes cheaper, many users will increase illumination, and some previously unlit areas may become lit. We present three policy recommendations that work together to guarantee major energy reductions in street lighting systems. First, taking advantage of new technologies to use light only when and where it is needed. Second, defining maximum permitted illuminances for roadway lighting. Third, defining street lighting system efficiency in terms of kilowatt hours per kilometer per year. Adoption of these policies would not only save energy, but would greatly reduce the amount of light pollution produced by cities. The goal of lighting policy should be to provide the light needed for any given task while minimizing both the energy use and negative environmental side effects of the light. This journal is © the Partner Organisations 2014.


Bergholtz E.J.,Free University of Berlin | Liu Z.,Princeton University | Trescher M.,Free University of Berlin | Moessner R.,Max Planck Institute For Physik Komplexer Systeme | Udagawa M.,University of Tokyo
Physical Review Letters | Year: 2015

We show that, quite generically, a [111] slab of spin-orbit coupled pyrochlore lattice exhibits surface states whose constant energy curves take the shape of Fermi arcs, localized to different surfaces depending on their quasimomentum. Remarkably, these persist independently of the existence of Weyl points in the bulk. Considering interacting electrons in slabs of finite thickness, we find a plethora of known fractional Chern insulating phases, to which we add the discovery of a new higher Chern number state which is likely a generalization of the Moore-Read fermionic fractional quantum Hall state. By contrast, in the three-dimensional limit, we argue for the absence of gapped states of the flat surface band due to a topologically protected coupling of the surface to gapless states in the bulk. We comment on generalizations as well as experimental perspectives in thin slabs of pyrochlore iridates. © 2015 American Physical Society.


Glockner G.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Glockner G.,Free University of Berlin | Glockner G.,University of Cologne | Noegel A.A.,University of Cologne
Biological Reviews | Year: 2013

Amoeboid life forms can be found throughout the evolutionary tree. The greatest proportion of these life forms is found in the Amoebozoa clade, one of the six major eukaryote evolutionary branches. Despite its common origin this clade exhibits a wide diversity of lifestyles including free-living and parasitic species and species with multicellular and multinucleate life stages. In this group, development, cooperation, and social behaviour can be studied in addition to traits common to unicellular organisms. To date, only a few Amoebozoa genomes have been sequenced completely, however a number of expressed sequence tags (ESTs) and complete and draft genomes have become available recently for several species that represent some of the major evolutionary lineages in this clade. This resource allows us to compare and analyse the evolutionary history and fate of branch-specific genes if properly exploited. Despite the large evolutionary time scale since the emergence of the major groups the genomic organization in Amoebozoa has retained common features. The number of Amoebozoa-specific genetic inventions seems to be rather small. The emergence of subgroups is accompanied by gene and domain losses and acquisitions of bacterial gene material. The sophisticated developmental cycles of Myxogastria and Dictyosteliida likely have a common origin and are deeply rooted in amoebozoan evolution. In this review we describe initial approaches to comparative genomics in Amoebozoa, summarize recent findings, and identify goals for further studies. © 2012 Cambridge Philosophical Society.


Schoneberg J.,Free University of Berlin | Heck M.,Charité - Medical University of Berlin | Hofmann K.P.,Charité - Medical University of Berlin | Noe F.,Free University of Berlin
Biophysical Journal | Year: 2014

Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R*) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein. © 2014 Biophysical Society.


Schuz N.,University of Tasmania | Schuz B.,University of Tasmania | Eid M.,Free University of Berlin
Health Psychology | Year: 2013

Objective: Health promotion often faces the problem that populations with high behavioral risk profiles respond defensively to health promotion messages by negating risk or reactant behavior. self-affirmation theory proposes that defensive reactions are an attempt of the self-system to maintain integrity. in this article, we examine whether a self-affirmation manipulation can mitigate defensive responses to personalized visual risk feedback in the skin cancer prevention context (ultraviolet [uv] photography), and whether the effects pertain to individuals with high behavioral risk status (high personal relevance of tanning). method: we conducted a full-factorial randomized controlled trial (n 292; age 11-71) following a 2 2 design (uv photo yes/no, self-affirmation yes/no). follow-up period was 2 weeks. subsequent tanning behavior, sun avoidance intentions, and risk perception. results: a multivariate analysis of variance (manova) revealed a three-way interaction between risk feedback, the self-affirmation manipulation, and risk status for the three outcome measures. follow-up analyses of variance (anovas) indicated that high-risk individuals receiving only the risk feedback intervention reacted defensively and reported higher exposure. a self-affirmation manipulation mitigates this reactance effect both on the level of cognitions and behavior. conclusion: self-affirmation has influential implications not only for social psychology but also for health prevention measures. the findings support the effectiveness of self-affirmation in reducing reactant and defensive reactions to personalized visual risk feedback. interactions with health risk status indicate that self-affirmation might increase the effectiveness of health promotion messages in high-risk populations. © 2013 American Psychological Association.


Coneus K.,Center for European Economic Research | Spiess C.K.,German Institute for Economic Research | Spiess C.K.,Free University of Berlin
Journal of Health Economics | Year: 2012

This paper examines the impact of outdoor pollution and parental smoking on children's health from birth until the age of three years in Germany. We use representative data from the German Socio-Economic Panel (SOEP), combined with five air pollution levels. These data were provided by the Federal Environment Agency and cover the years 2002-2007. Our work makes two important contributions. First, we use European data to replicate and extend an important US study by following the effects of pollution exposure and parental smoking on child health during the first four years of life. Second, we have health measures not only for infants but for toddlers as well. For infants, as well as for two- to three-year-olds, we are able to account for time-invariant and unobserved neighborhood and maternal characteristics. Our results suggest a significantly negative impact of some pollutants on infant health. High exposure to CO prior to birth causes, on average, a 289g lower birth weight. With respect to toddler health, we find that disorders and in particular those as bronchitis and respiratory illnesses are affected particularly by O 3 levels. © 2011 Elsevier B.V.


Romero O.E.,Instituto Andaluz Of Ciencias Of La Tierra Csic Ugr | Jahn R.,Free University of Berlin
Diatom Research | Year: 2013

The nominate varieties of the monoraphid diatoms Cocconeis lineata Ehrenberg and C. euglypta Ehrenberg are typified. Lectotypes of both taxa are preserved at the Ehrenberg Collection, Museum für Naturkunde, Berlin, Germany. The lectotype of C. lineata is a poorly detailed drawing, showing an ovoid valve (or frustule?) with two to three apical lines on each hemivalve. The lectotype of C. euglypta, contained in a mica, shows a unique, broadly elliptical sternum valve with up to five apical striae on each hemivalve, displaying a zigzag pattern. This is roughly consistent with the current concept of C. lineata and C. euglypta and with their usage over the last 160 years. To ensure stabilization of the names and current concepts for these two taxa, culture-based epitypes of C. lineata and C. euglypta are designated. Light and electron microscopy observations, as well as morphometric data from clones for both taxa, are presented and an amended description for each taxon is provided. © 2013 Copyright The International Society for Diatom Research.


Alicea J.,University of California at Irvine | Oreg Y.,Weizmann Institute of Science | Refael G.,California Institute of Technology | Von Oppen F.,Free University of Berlin | And 2 more authors.
Nature Physics | Year: 2011

The synthesis of a quantum computer remains an ongoing challenge in modern physics. Whereas decoherence stymies most approaches, topological quantum computation schemes evade decoherence at the hardware level by storing quantum information non-locally. Here we establish that a key operation-braiding of non-Abelian anyons-can be implemented using one-dimensional semiconducting wires. Such wires can be driven into a topological phase supporting long-sought particles known as Majorana fermions that can encode topological qubits. We show that in wire networks, Majorana fermions can be meaningfully braided by simply adjusting gate voltages, and that they exhibit non-Abelian statistics like vortices in a p+ip superconductor. We propose experimental set-ups that enable probing of the Majorana fusion rules and the efficient exchange of arbitrary numbers of Majorana fermions. This work should open a new direction in topological quantum computation that benefits from physical transparency and experimental feasibility.


Jiang L.,California Institute of Technology | Pekker D.,California Institute of Technology | Alicea J.,University of California at Irvine | Refael G.,California Institute of Technology | And 2 more authors.
Physical Review Letters | Year: 2011

A junction between two topological superconductors containing a pair of Majorana fermions exhibits a "fractional" Josephson effect, 4π periodic in the superconductors' phase difference. An additional fractional Josephson effect, however, arises when the Majorana fermions are spatially separated by a superconducting barrier. This new term gives rise to a set of Shapiro steps which are essentially absent without Majorana modes and therefore provides a unique signature for these exotic states. © 2011 American Physical Society.


Biedermann S.,Washington State University | Biedermann S.,Free University of Berlin | Hellmann H.,Washington State University
Trends in Plant Science | Year: 2011

The ubiquitin proteasome pathway is one of the major regulatory tools used by eukaryotic cells. E3 ligases, which allow controlled modification of proteins with ubiquitin, are crucial for the specificity of the pathway. Recently, an additional plant cullin-based E3 ligase complex was described which contains cullin 4 (CUL4) and DAMAGED DNA BINDING 1 protein as core subunits. Our knowledge of this E3 ligase has increased tremendously since its first description, and it seems to be involved in many developmental and physiological processes. Here, we review the most recent studies on CUL4 E3 complexes, with a focus on their substrate recognition and the plethora of processes that they regulate in plants, such as photomorphogenesis, flowering and abiotic stress response. © 2010 Elsevier Ltd.


Lieb E.H.,Princeton University | Schrader R.,Free University of Berlin
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

It is well known that any given density ρ(x) can be realized by a determinantal wave function for N particles. The question addressed here is whether any given density ρ(x) and current density j(x) can be simultaneously realized by a (finite kinetic energy) determinantal wave function. In case the velocity field v(x)=j(x)/ρ(x) is curlfree, we provide a solution for all N, and we provide an explicit upper bound for the energy. If the velocity field is not curl-free, there is a finite energy solution for all N≥4, but we do not provide an explicit energy bound in this case. For N=2 we provide an example of a non-curl-free velocity field for which there is a solution and an example for which there is no solution. The case N=3 with a non-curl-free velocity field is left open. © 2013 American Physical Society.


Illenberger E.,Free University of Berlin | Meinke M.C.,Charité - Medical University of Berlin
International Journal of Mass Spectrometry | Year: 2014

Dissociative electron attachment (DEA) to acetone (CH3COCH 3), perfluoroacetone (CF3COCF3) and acetylene (HCCH) is studied in the gas phase under collision-free conditions. The results are compared with those recently obtained from a study on electron attachment to homogeneous clusters of acetone and perfluoroacetone (Martin et al., 2009). Gas phase acetone and perfluoroacetone show a series of DEA resonances extending over a wide energy range and leading to various fragment ions. Perfluoroacetone additionally shows a strong signal due to the formation of the parent anion close to zero energy. In strong contrast to that, the cluster analogues exhibit only a low energy resonance while fragmentation is strongly suppressed. Such behaviour mirrors the intrinsic decomposition mechanisms which proceeds rather via predissociation involving a loose transition state than by direct dissociation along repulsive potential energy surfaces. This picture is confirmed by a time-of-flight (TOF) analysis of the fragment ions from the isolated compounds revealing that all fragment ions are formed with only low translational energy. DEA to acetylene leads to C2H- and C2- arising from different resonance regions, with C 2H- as the prominent signal at 3 eV resulting from predissociation of the π* resonance. © 2014 Elsevier B.V.


Citron F.M.M.,Free University of Berlin | Citron F.M.M.,Princeton University | Goldberg A.E.,Free University of Berlin | Goldberg A.E.,Princeton University
Journal of Cognitive Neuroscience | Year: 2014

Why do people so often use metaphorical expressions when literal paraphrases are readily available? This study focuses on a comparison of metaphorical statements involving the source domain of taste (e.g., “She looked at him sweetly”) and their literal paraphrases (e.g., “She looked at him kindly”). Metaphorical and literal sentences differed only in one word and were normed for length, familiarity, imageability, emotional valence, and arousal. Our findings indicate that conventional metaphorical expressions are more emotionally evocative than literal expressions, as the amygdala and the anterior portion of the hippocampus were more active in the metaphorical sentences. They also support the idea that even conventional metaphors can be grounded in sensorimotor and perceptual representations in that primary and secondary gustatory areas (lateral OFC, frontal operculum, anterior insula) were more active as well. A comparison of the individual words that distinguished the metaphorical and literal sentences revealed greater activation in the lateral OFC and the frontal operculum for the taste-related words, supporting the claim that these areas are relevant to taste. © 2014 Massachusetts Institute of Technology.


Gallego R.,Free University of Berlin | Aolita L.,Free University of Berlin | Aolita L.,Federal University of Rio de Janeiro
Physical Review X | Year: 2015

We present an operational framework for Einstein-Podolsky-Rosen steering as a physical resource. For arbitrary-dimensional bipartite systems composed of a quantum subsystem and a black-box device, we show that local operations assisted by one-way classical communication (1W-LOCCs) from the quantum part to the black box cannot create steering. Based on this, we build a resource theory of steering with 1W-LOCCs as the free operations. We introduce the notion of convex steering monotones as the fundamental axiomatic quantifiers of steering. As a convenient example thereof, we present the relative entropy of steering. In addition, we prove that two previously proposed quantifiers, the steerable weight and the robustness of steering, are also convex steering monotones. To end up with for minimal-dimensional systems, we establish, on the one hand, necessary and sufficient conditions for pure-state steering conversions under stochastic 1W-LOCCs and prove, on the other hand, the nonexistence of steering bits, i.e., measure-independent maximally steerable states from which all states can be obtained by means of the free operations. Our findings reveal unexpected aspects of steering and lay the foundations for further research, with potential implications in Bell nonlocality.


Lange K.M.,Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy | Lange K.M.,Helmholtz Center Berlin | Aziz E.F.,Helmholtz Center Berlin | Aziz E.F.,Free University of Berlin
Chemical Society Reviews | Year: 2013

Soft X-ray spectroscopies are powerful tools for probing the local electronic and molecular orbital structures of materials in different phases and various environments. While modern spectroscopic tools using soft X-ray synchrotron photons perspicuously reveal the molecular orbital (MO) structure in detail, structures remain widely unknown in the liquid phase since many of these techniques could only be applied to solutions very recently. Furthermore, the interactions and dynamics of molecules in the liquid phase are especially complicated compared to those in gas and solid phases and thereby impede the understanding of functional materials in solution. This review presents recent developments using soft X-ray radiation for probing the electronic structure of ions and molecules in solution. The presented X-ray absorption, emission, and photo-electron spectroscopy studies exhibit the powerful contributions of soft X-ray liquid spectroscopies in the last few years. © 2013 The Royal Society of Chemistry.


Sisson A.L.,Charité - Medical University of Berlin | Sisson A.L.,Helmholtz Center Geesthacht | Haag R.,Free University of Berlin
Soft Matter | Year: 2010

Branched polyglycerols (PGs) are a versatile class of functionalisable, hydrophilic, hydroxylated polyethers with ideal properties for numerous applications. Historically, synthetic limitations have restricted the study of such materials to globular hyperbranched polymers (<10 nm) or macroscale biocompatible hydrogels (>1000 nm). In this Emerging Area minireview we describe how we use miniemulsion polymerisation to prepare polyglycerol nanogels on previously unobtainable length scales. Various cases are discussed with particle sizes that are highly tunable between 25 and 350 nm diameter; methods to surface functionalise such particles are also described. Biodegradable polyglycerol based nanogels have also been prepared by incorporating redox active disulfide branching points within the nanogel structure. Cell culture studies show that these nanogels are highly biocompatible. Additionally, dye labelled nanogels are shown by optical microscopy techniques to readily internalise into cells by endocytic mechanisms. We believe that these polyglycerol nanogels will emerge as excellent materials for use in a broad range of biomedical applications. © 2010 The Royal Society of Chemistry.


Meyer J.S.,Joseph Fourier University | Refael G.,California Institute of Technology | Refael G.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

Topological behavior can be masked when disorder is present. A topological insulator, either intrinsic or interaction induced, may turn gapless when sufficiently disordered. Nevertheless, the metallic phase that emerges once a topological gap closes retains several topological characteristics. By considering the self-consistent disorder-averaged Green function of a topological insulator, we derive the condition for gaplessness. We show that the edge states survive in the gapless phase as edge resonances and that, similar to a doped topological insulator, the disordered topological metal also has a finite, but nonquantized topological index. We then consider the disordered Mott topological insulator. We show that within mean-field theory, the disordered Mott topological insulator admits a phase where the symmetry-breaking order parameter remains nonzero but the gap is closed, in complete analogy to "gapless superconductivity" due to magnetic disorder. © 2013 American Physical Society.


Oreg Y.,Weizmann Institute of Science | Refael G.,California Institute of Technology | Von Oppen F.,Free University of Berlin
Physical Review Letters | Year: 2010

We show that the combination of spin-orbit coupling with a Zeeman field or strong interactions may lead to the formation of a helical electron liquid in single-channel quantum wires, with spin and velocity perfectly correlated. We argue that zero-energy Majorana bound states are formed in various situations when such wires are situated in proximity to a conventional s-wave superconductor. This occurs when the external magnetic field, the superconducting gap, or, most simply, the chemical potential vary along the wire. These Majorana states do not require the presence of a vortex in the system. Experimental consequences of the helical liquid and the Majorana states are also discussed. © 2010 The American Physical Society.


Schulze M.S.E.D.,Dana-Farber Cancer Institute | Schulze M.S.E.D.,Free University of Berlin | Wucherpfennig K.W.,Dana-Farber Cancer Institute | Wucherpfennig K.W.,Harvard University
Current Opinion in Immunology | Year: 2012

HLA-DM serves a critical function in the loading and editing of peptides on MHC class II (MHCII) molecules. Recent data showed that the interaction cycle between MHCII molecules and HLA-DM is dependent on the occupancy state of the peptide binding groove. Empty MHCII molecules form stable complexes with HLA-DM, which are disrupted by binding of high-affinity peptide. Interestingly, MHCII molecules with fully engaged peptides cannot interact with HLA-DM, and prior dissociation of the peptide N-terminus from the groove is required for HLA-DM binding. There are significant similarities to the peptide loading process for MHC class I molecules, even though it is executed by a distinct set of proteins in a different cellular compartment. © 2011 Elsevier Ltd.


Koch C.P.,Free University of Berlin | Kosloff R.,Hebrew University of Jerusalem
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2010

Two atoms in an ultracold gas are correlated at short interatomic distances due to threshold effects in which the potential energy of their interaction dominates the kinetic energy. The correlations manifest themselves in a distinct nodal structure of the density matrix at short interatomic distances. Pump-probe spectroscopy has recently been suggested to probe these pair correlations: A suitably chosen, short photoassociation laser pulse depletes the ground-state pair density within the photoassociation window, creating a nonstationary wave packet in the electronic ground state. The dynamics of this nonstationary wave packet is monitored by time-delayed probe and ionization pulses. Here we discuss how the choice of the pulse parameters affects the experimental feasibility of this pump-probe spectroscopy of two-body correlations. © 2010 The American Physical Society.


Karzig T.,California Institute of Technology | Refael G.,California Institute of Technology | Refael G.,Free University of Berlin | von Oppen F.,California Institute of Technology | von Oppen F.,Free University of Berlin
Physical Review X | Year: 2014

One-dimensional topological superconductors are known to host Majorana zero modes at domain walls terminating the topological phase. Their non-Abelian nature allows for processing quantum information by braiding operations that are insensitive to local perturbations, making Majorana zero modes a promising platform for topological quantum computation. Motivated by the ultimate goal of executing quantum-information processing on a finite time scale, we study domain walls moving at a constant velocity. We exploit an effective Lorentz invariance of the Hamiltonian to obtain an exact solution of the associated quasiparticle spectrum and wave functions for arbitrary velocities. Essential features of the solution have a natural interpretation in terms of the familiar relativistic effects of Lorentz contraction and time dilation. We find that the Majorana zero modes remain stable as long as the domain wall moves at subluminal velocities with respect to the effective speed of light of the system. However, the Majorana bound state dissolves into a continuous quasiparticle spectrum after the domain wall propagates at luminal or even superluminal velocities. This relativistic catastrophe implies that there is an upper limit for possible braiding frequencies even in a perfectly clean system with an arbitrarily large topological gap.We also exploit our exact solution to consider domain walls moving past static impurities present in the system.


Petojevic T.,University of California at Berkeley | Petojevic T.,Free University of Berlin | Pesavento J.J.,University of California at Berkeley | Costa A.,London Research Institute | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

DNA replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (Mcm2-7) at origin sites. Cell division control protein 45 (Cdc45) and GINS proteins activate the latent Mcm2-7 helicase by inducing allosteric changes through binding, forming a Cdc45/ Mcm2-7/GINS (CMG) complex that is competent to unwind duplex DNA. The CMG has an active gate between subunits Mcm2 and Mcm5 that opens and closes in response to nucleotide binding. The consequences of inappropriate Mcm2/5 gate actuation and the role of a side channel formed between GINS/Cdc45 and the outer edge of the Mcm2-7 ring for unwinding have remained unexplored. Here we uncover a novel function for Cdc45. Cross-linking studies trace the path of the DNA with the CMG complex at a fork junction between duplex and single strands with the bound CMG in an open or closed gate conformation. In the closed state, the lagging strand does not pass through the side channel, but in the open state, the leading strand surprisingly interacts with Cdc45. Mutations in the recombination protein J fold of Cdc45 that ablate this interaction diminish helicase activity. These data indicate that Cdc45 serves as a shield to guard against occasional slippage of the leading strand from the core channel.


Romito A.,Free University of Berlin | Alicea J.,University of California at Irvine | Refael G.,California Institute of Technology | Von Oppen F.,Free University of Berlin
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Topological insulator edges and spin-orbit-coupled quantum wires in proximity to s-wave superconductors can be tuned through a topological quantum phase transition by a Zeeman field. Here we show that a supercurrent flowing in the s-wave superconductor also drives such a transition. We propose to use this mechanism to generate and manipulate Majorana fermions that localize at domain walls between topological and nontopological regions of an edge or wire. In quantum wires, this method carries the added benefit that a supercurrent reduces the critical Zeeman field at which the topological phase appears. © 2012 American Physical Society.


Powell J.R.,Free University of Berlin | Monaghan M.T.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Opik M.,University of Tartu | Rillig M.C.,Free University of Berlin
Molecular Ecology | Year: 2011

Analyses of the structure and function of microbial communities are highly constrained by the diversity of organisms present within most environmental samples. A common approach is to rely almost entirely on DNA sequence data for estimates of microbial diversity, but to date there is no objective method of clustering sequences into groups that is grounded in evolutionary theory of what constitutes a biological lineage. The general mixed Yule-coalescent (GMYC) model uses a likelihood-based approach to distinguish population-level processes within lineages from processes associated with speciation and extinction, thus identifying a distinct point where extant lineages became independent. Using two independent surveys of DNA sequences associated with a group of ubiquitous plant-symbiotic fungi, we compared estimates of species richness derived using the GMYC model to those based on operational taxonomic units (OTUs) defined by fixed levels of sequence similarity. The model predicted lower species richness in these surveys than did traditional methods of sequence similarity. Here, we show for the first time that groups delineated by the GMYC model better explained variation in the distribution of fungi in relation to putative niche-based variables associated with host species identity, edaphic factors, and aspects of how the sampled ecosystems were managed. Our results suggest the coalescent-based GMYC model successfully groups environmental sequences of fungi into clusters that are ecologically more meaningful than more arbitrary approaches for estimating species richness. © 2010 Blackwell Publishing Ltd.


Bohme M.A.,Free University of Berlin | Bohme M.A.,Charité - Medical University of Berlin | Sigrist S.J.,Free University of Berlin | Sigrist S.J.,Charité - Medical University of Berlin
Neuron | Year: 2015

Neuronal response or adaption to a changing environment relies on the modulation of synaptic function. Howthis modulation is achieved remains controversial. In this issue of Neuron, Sugie etal. (2015) now report that active zones of Drosophila photoreceptors undergo activity-dependent changes in their molecular composition. Neuronal response or adaption to a changing environment relies on the modulation of synaptic function. How this modulation is achieved remains controversial. Sugie etal. (2015) now report that active zones of Drosophila photoreceptors undergo activity-dependent changes in their molecular composition. © 2015 Elsevier Inc.


Biedermann S.,Washington State University | Biedermann S.,Free University of Berlin | Hellmann H.,Washington State University
Plant Journal | Year: 2010

The integrity of the genome is a fundamental prerequisite for the well-being of all living organisms. Critical for the genomic integrity are effective DNA damage detection mechanisms that enable the cell to rapidly activate the necessary repair machinery. Here, we describe Arabidopsis thaliana ATCSA-1, which is an ortholog of the mammalian Cockayne Syndrome type-A protein involved in transcription-coupled DNA repair processes. ATCSA-1 is a critical component for initiating the repair of UV-B-induced DNA lesions, and, together with the damage-specific DNA binding protein 2 (DDB2), is necessary for light-independent repair processes in Arabidopsis. The transcriptional profile of both genes revealed that ATCSA-1 is strongly expressed in most tissues, whereas DDB2 is only weakly expressed, predominantly in the root tips and anthers of flowers. In contrast to ATCSA-1, DDB2 expression is rapidly inducible by UV treatment. Like DDB2, ATCSA-1 is localized to the nucleus, and assembles with DDB1 and CUL4 proteins into a complex. ATCSA-1 is an unstable protein that is degraded in a 26S proteasome-dependent manner. Overall, the results presented here form a functional description of a plant Cockayne syndrome factor A (CSA) ortholog, and demonstrate the importance of ATCSA-1 for UV-B tolerance. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.


Lima A.R.P.,Free University of Berlin | Pelster A.,Hanse Wissenschaftskolleg | Pelster A.,University of Kaiserslautern
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

We theoretically investigate various beyond mean-field effects on Bose gases at zero temperature featuring the anisotropic and long-range dipole-dipole interaction in addition to the isotropic and short-range contact interaction. Within the realm of the Bogoliubov-de Gennes theory, we consider static properties and low-lying excitations of both homogeneous and harmonically trapped dipolar bosonic gases. For the homogeneous system, the condensate depletion, the ground-state energy, the equation of state, and the speed of sound are discussed in detail. Making use of the local density approximation, we extend these results in order to study the properties of a dipolar Bose gas in a harmonic trap and in the regime of large particle numbers. After deriving the equations of motion for the general case of a triaxial trap, we analyze the influence of quantum fluctuations on important properties of the gas, such as the equilibrium configuration and the low-lying excitations in the case of a cylinder-symmetric trap. In addition to the monopole and quadrupole oscillation modes, we also discuss the radial quadrupole mode. We find that the latter acquires a quantum correction exclusively due to the dipole-dipole interaction. As a result, we identify the radial quadrupole as a reasonably accessible source for the signature of dipolar many-body effects and stress the enhancing character that dipolar interactions have for quantum fluctuations in the other oscillation modes. © 2012 American Physical Society.


Grant
Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SiS-2007-3.0.6.1 | Award Amount: 638.58K | Year: 2008

It is proposed to analyse use and gratifications concerning science programmes in Europe comparatively by using already existing data of a collection of European Countries. Additionally focus group discussion are proposed to clarify which factors lead recipients in their judgements concerning different types of science programmes. Such a comparative analysis is only possible by ordering systematically what is currently offered in the field of science programmes. Resting on the principle of relevancy a typology of science programmes is developed, which enables research to classify what is currently offered in the field with regard to formats and recipients.


Grant
Agency: Cordis | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2014-ETN | Award Amount: 2.32M | Year: 2015

This network brings together the major academic players active in Europe on the fundamentals and application of multivalency and cooperativity. The network is complemented by industrial partners ranging in scale from a small spin-off to a large multinational. The main objective of this consortium is to raise a new generation of researchers able to develop complex chemical systems that harness cooperativity for enhanced functional properties. Multivalency is one of Natures governing principles for achieving strong and selective biomolecular recognition. Many biological processes rely on the cooperative effects associated with the occurrence of multivalent interactions. Consequently, there is an enormous interest in the development of chemical multivalent systems that display similar features for innovative applications in fields as various as diagnostics, drug discovery, materials science and nanotechnology. The central theme of multivalency and cooperativity is used to connect partners from academia and industry with a common interest in understanding how multivalency works, but for very different scopes and using very different approaches. This network is thus uniquely positioned to train the next generation of European researchers in all multidisciplinary aspects related to multivalency. A broad training program has been developed that comprises top-level individual research projects, both general and specific network-wide dedicated courses, secondments, personalized scientific training and a broad package of complementary skill training. The industrial partners contribute in the form of training, supervision, technical contributions, and perspectives on the commercialisation of multivalent systems. After completion of the program, the ESRs will be the first generation of researchers able to fully exploit the potential of multivalent chemical systems. Their unrivalled career profiles will enable them to compete successfully for positions in academia or industry.


Zydek M.,Charité - Medical University of Berlin | Zydek M.,Free University of Berlin | Hagemeier C.,Charité - Medical University of Berlin | Wiebusch L.,Charité - Medical University of Berlin
PLoS Pathogens | Year: 2010

The onset of human cytomegalovirus (HCMV) lytic infection is strictly synchronized with the host cell cycle. Infected G0/ G1 cells support viral immediate early (IE) gene expression and proceed to the G1/S boundary where they finally arrest. In contrast, S/G2 cells can be infected but effectively block IE gene expression and this inhibition is not relieved until host cells have divided and reentered G1. During latent infection IE gene expression is also inhibited, and for reactivation to occur this block to IE gene expression must be overcome. It is only poorly understood which viral and/or cellular activities maintain the block to cell cycle or latency-associated viral IE gene repression and whether the two mechanisms may be linked. Here, we show that the block to IE gene expression during S and G2 phase can be overcome by both genotoxic stress and chemical inhibitors of cellular DNA replication, pointing to the involvement of checkpoint-dependent signaling pathways in controlling IE gene repression. Checkpoint-dependent rescue of IE expression strictly requires p53 and in the absence of checkpoint activation is mimicked by proteasomal inhibition in a p53 dependent manner. Requirement for the cyclin dependent kinase (CDK) inhibitor p21 downstream of p53 suggests a pivotal role for CDKs in controlling IE gene repression in S/G2 and treatment of S/G2 cells with the CDK inhibitor roscovitine alleviates IE repression independently of p53. Importantly, CDK inhibiton also overcomes the block to IE expression during quiescent infection of NTera2 (NT2) cells. Thus, a timely block to CDK activity not only secures phase specificity of the cell cycle dependent HCMV IE gene expression program, but in addition plays a hitherto unrecognized role in preventing the establishment of a latent-like state. © 2010 Zydek et al.


Schweigel-Rontgen M.,Leibniz Institute for Farm Animal Biology | Kolisek M.,Free University of Berlin
Current Topics in Membranes | Year: 2014

The solute carrier family 41 (SLC41) encompasses three members A1, A2, and A3. Based on their distant homology to the bacterial Mg2+ channel MgtE, all have been linked to Mg2+ transport. There is only very limited knowledge on the molecular biology and exact functions of SLC41A2 and SLC41A3. SLC41A1 is ubiquitously expressed and data on its functional and molecular properties, regulation, complex-forming ability, and spectrum of binding partners are available. SLC41A1 was recently identified as being the Na+/Mg2+ exchanger (NME)-a predominant Mg2+ efflux system. Mg2+-dependent and hormonal regulation of NME activity is now known to depend on the intracellular N terminus of SLC41A1 that is involved in Mg2+ sensing and contains phosphorylation sites for protein kinase (PK) A and PKC. Data showing a link between SLC41A1 and human disorders such as Parkinson's disease, nephronophthisis (induced by the null mutation c.698G>T in renal SLC41A1), and preeclampsia make the protein a candidate therapeutic target. © 2014 Elsevier Inc.


Plattner N.,Free University of Berlin | Doll J.D.,Brown University | Meuwly M.,University of Basel
Journal of Chemical Theory and Computation | Year: 2013

Infinite swapping (INS) is a recently developed method to address the rare event sampling problem. For INS, an expanded computational ensemble composed of a number of replicas at different temperatures is used, similar to the widely used parallel tempering (PT) method. While the basic concept of PT is to sample various replicas of the system at different temperatures and exchange information between the replicas occasionally, INS uses the symmetrized distribution of configurations in temperature space, which corresponds to the infinite swapping limit of PT. The effect of this symmetrization and the enhanced information exchange between replicas is evaluated for three different biological systems representing different sampling problems in biology: (1) blocked alanine dipeptide, which is a small system and therefore optimal to evaluate sampling efficiency quantitatively, (2) Villin headpiece, which is used as a test case for the protein folding process, and (3) neuroglobin, which is used to evaluate the effects of enhanced information exchange between replicas for sampling the substate space of a folded protein. For these three test systems, PINS is compared to PT, and it is found that in all cases the sampling with PINS is substantially more efficient. © 2013 American Chemical Society.


Leonori D.,Max Planck Institute of Colloids and Interfaces | Seeberger P.H.,Free University of Berlin
Organic Letters | Year: 2012

The cell-surface glycans on bacteria contain many monosaccharides that cannot be obtained by isolation from natural sources. Availability of differentially protected monosaccharides is therefore often limiting access to potential oligosaccharide vaccine antigens. D-Fucosamine, Dbacillosamine, and D-xylo-2,6-deoxy-4-ketohexosamine building blocks were prepared via a divergent de novo synthesis from L-Garner aldehyde. The route relies on a chelation-control assisted organometallic addition and an anti-selective dihydroxylation reaction. © 2012 American Chemical Society.


Peschel I.,Free University of Berlin | Eisler V.,University of Vienna
Journal of Physics A: Mathematical and Theoretical | Year: 2012

We consider fermionic and bosonic quantum chains where a defect separates two subsystems and compare the corresponding entanglement spectra. With these, we calculate their Rényi entanglement entropies and obtain analytical formulae for the continuously varying coefficient of the leading logarithmic term. For the bosonic case we also present numerical results. © 2012 IOP Publishing Ltd.


Kleinert H.,Free University of Berlin | Xue S.-S.,ICRANeT Piazzale della Repubblica | Xue S.-S.,University of Rome La Sapienza
Annals of Physics | Year: 2013

Using semiclassical WKB-methods, we calculate the rate of electron-positron pair-production from the vacuum in the presence of two external fields, a strong (space- or time-dependent) classical field and a monochromatic electromagnetic wave. We discuss the possible medium effects on the rate in the presence of thermal electrons, bosons, and neutral plasma of electrons and protons at a given temperature and chemical potential. Using our rate formula, we calculate the rate enhancement due to a laser beam, and discuss the possibility that a significant enhancement may appear in a plasma of electrons and protons with self-focusing properties. © 2013 Elsevier Inc.


Gilmore K.,Max Planck Institute of Colloids and Interfaces | Seeberger P.H.,Max Planck Institute of Colloids and Interfaces | Seeberger P.H.,Free University of Berlin
Chemical Record | Year: 2014

Due to the narrow width of tubing/reactors used, photochemistry performed in micro- and mesoflow systems is significantly more efficient than when performed in batch due to the Beer-Lambert Law. Owing to the constant removal of product and facility of flow chemical scalability, the degree of degradation observed is generally decreased and the productivity of photochemical processes is increased. In this Personal Account, we describe a wide range of photochemical transformations we have examined using both visible and UV light, covering cyclizations, intermolecular couplings, radical polymerizations, as well as singlet oxygen oxygenations. The efforts of the Seeberger group in continuous photochemical reactions, both visible and UV light, are described. These transformations include cyclizations, intermolecular couplings, radical polymeriztions, as well as a range of singlet oxygen oxygenations. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Buchin K.,TU Eindhoven | Buchin M.,Ruhr University Bochum | Meulemans W.,TU Eindhoven | Mulzer W.,Free University of Berlin
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2014

Given two polygonal curves in the plane, there are many ways to define a notion of similarity between them. One measure that is extremely popular is the Frechet distance. Since it has been proposed by Alt and Godau in 1992, many variants and extensions have been studied. Nonetheless, even more than 20 years later, the original O(n2 log n) algorithm by Alt and Godau for computing the Frechet distance remains the state of the art (here n denotes the number of vertices on each curve). This has led Helmut Alt to conjecture that the associated decision problem is 3SUM-hard. In recent work, Agarwal et al. show how to break the quadratic barrier for the discrete version of the Frechet distance, where one considers sequences of points instead of polygonal curves. Building on their work, we give a randomized algorithm to compute the Frechet distance between two polygonal curves in time O(n2√log n(log log n)3/2) on a pointer machine and in time O(n2(loglogn) 2) on a word RAM. Furthermore, we show that there exists an algebraic decision tree for the decision problem of depth O(n2-ε), for some ε > 0. This provides evidence that the decision problem may not be 3SUM-hard after all and reveals an intriguing new aspect of this well-studied problem. Copyright © 2014 by the Society for Industrial and Applied Mathematics.