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Romatschke P.,Frankfurt Institute for Advanced Studies | Mendoza M.,ETH Zurich | Succi S.,Instituto Per Le Applicazioni Del Calcolo Cnr | Succi S.,Freiburg Institute for Advanced Studies
Physical Review C - Nuclear Physics | Year: 2011

Starting from the Maxwell-Jüttner equilibrium distribution, we develop a relativistic lattice Boltzmann (LB) algorithm capable of handling ultrarelativistic systems with flat, but expanding, spacetimes. The algorithm is validated through simulations of a quark-gluon plasma, yielding excellent agreement with hydrodynamic simulations. The present scheme opens the possibility of transferring the recognized computational advantages of lattice kinetic theory to the context of both weakly and ultrarelativistic systems. © 2011 American Physical Society.

Rao F.,Freiburg Institute for Advanced Studies | Spichty M.,University Claude Bernard Lyon 1
Journal of Computational Chemistry | Year: 2012

Molecular dynamics (MD) simulations provide essential information about the thermodynamics and kinetics of proteins. Technological advances in both hardware and algorithms have seen this method accessing timescales that used to be unreachable only few years ago. The quest to simulate slow, biologically relevant macromolecular conformational changes, is still open. Here, we present an approximate approach to increase the speed of MD simulations by a factor of ∼4.5. This is achieved by using a large integration time step of 7 fs, in combination with frozen covalent bonds and look-up tables for nonbonded interactions of the solvent. Extensive atomistic MD simulations for a flexible peptide in water show that the approach reproduces the peptide's equilibrium conformational changes, preserving the essential properties of both thermodynamics and kinetics. Comparison of this approximate method with state-of-the-art implicit solvation simulations indicates that the former provides a better description of the underlying free-energy surface. Finally, simulations of a 33-residue peptide show that these fast MD settings are readily applicable to investigate biologically relevant systems. Copyright © 2011 Wiley Periodicals, Inc.

Bruckner-Tuderman L.,Albert Ludwigs University of Freiburg | Bruckner-Tuderman L.,Freiburg Institute for Advanced Studies | Has C.,Albert Ludwigs University of Freiburg
Matrix Biology | Year: 2014

The cutaneous basement membrane zone (BMZ) is a highly specialized functional complex that provides the skin with structural adhesion and resistance to shearing forces. Its regulatory functions include control of epithelial-mesenchymal interactions under physiological and pathological conditions. Mutations in genes encoding components of the BMZ are associated with inherited skin disorders of the epidermolysis bullosa (EB) group, characterized by skin fragility, mechanically induced blisters and erosions of the skin and mucous membranes. Although most disease-associated genes are known, the genetic basis of new EB subtypes linked to mutations in genes for focal adhesion proteins was uncovered only recently. The molecular mechanisms leading to blistering, abnormal wound healing, predisposition to skin cancer, and other complications in EB have been elucidated using animal models and disease proteomics. The rapid progress in understanding the molecular basis of EB has enabled the development of strategies for biologically valid causal therapies. © 2013 International Society of Matrix Biology.

Van Agtmael T.,University of Glasgow | Bruckner-Tuderman L.,Albert Ludwigs University of Freiburg | Bruckner-Tuderman L.,Freiburg Institute for Advanced Studies
Cell and Tissue Research | Year: 2010

In 1990, the role of basement membranes in human disease was established by the identification of COL4A5 mutations in Alport's syndrome. Since then, the number of diseases caused by mutations in basement membrane components has steadily increased as has our understanding of the roles of basement membranes in organ development and function. However, many questions remain as to the molecular and cellular consequences of these mutations and the way in which they lead to the observed disease phenotypes. Despite this, exciting progress has recently been made with potential treatment options for some of these so far incurable diseases. © 2009 Springer-Verlag.

News Article | August 29, 2016
Site: phys.org

If implemented, the method could allow researchers to explore quantum energy transport phenomena that are expected to be completely different than what is observed in macroscopic energy transport. In general, understanding energy transport in small-scale devices could lead to the development of methods for reducing the energy dissipation in shrinking computer hardware (however, the researchers note that computer hardware differs from the particular setup proposed here). The scientists, Alejandro Bermudez, at the Institute of Fundamental Physics in Madrid, Spain, and Tobias Schaetz, at the Albert Ludwigs University of Freiburg and the Freiburg Institute for Advanced Studies, both in Freiburg, Germany, have published a paper on their proposed method in a recent issue of the New Journal of Physics. "We have identified a new quantum mechanism that would allow to control the transport of energy/heat at the level of single energy quanta," Bermudez told Phys.org. "This mechanism can be considered as an analogue of Coulomb blockade in electronic nanodevices, and we have proposed to test it using experiments with crystals of self-assembled trapped atomic ions." In the study, the scientists propose building an energy reservoir using trapped magnesium ions. By using a laser to heat and cool the ions, the ions can be made to absorb or release tiny amounts of energy, acting as tiny energy reservoirs. Then to transport the energy, the researchers propose placing a synthetic quantum magnet—which consists of a long line of magnetic spins that form a chain—between two energy reservoirs. When the reservoirs are coupled to the spins in the magnet, they can exchange energy with each other in the form of single phonons. In this way, quantum-scale energy transport occurs across the spin chain. The scientists explain that energy transport at the quantum level can be thought of as analogous to charge (electron) transport at the quantum level, which has already been well-documented. Just as single-electron transport is very different than bulk electron transport, quantum energy transport is expected to be very different than energy transport on a large scale. One particular phenomenon associated with single-electron transport, which is not observed at larger scales, is called the Coulomb-blockade effect. In nanoscale electronic devices, electrons must gain a certain level of charging energy in order to tunnel across a barrier. When one electron manages to gain this energy and tunnel, it blocks the simultaneous tunneling of other electrons because additional electrons would require additional energy. The resulting blockade effect violates Ohm's law of charge transport, and results in only one electron tunneling at a time. In the new study, the physicists theoretically demonstrated that an analogous Coulomb-blockade effect occurs with nanoscale heat transport, which again does not appear at larger scales. The scientists derived a quantum master equation for the transport of energy that shows that there is a "transport window" that defines the energy level needed for energy quanta to travel through a quantum magnet. Similar to the situation with electrons, energy transport is blockaded when the energy quanta do not have sufficient energy. This effect, which the researchers call the Ising blockade effect, violates Fourier's law of heat conduction and results in the transport of only one energy quantum at a time. If the proposed experiment can be realized, the researchers expect to observe the Ising blockade effect along with many other interesting quantum effects in energy transport that so far have been restricted to electronic currents. At this stage, it's difficult to tell what applications quantum energy transport may have. "If the same effect can be shown to be more general, and applicable to other physical setups, it may yield unexpected applications similar to single-electron electronics in Coulomb-blockaded devices," Bermudez said. One of the biggest challenges to realizing the experiment will be to design a device that can directly measure such tiny amounts of heat energy. "We are considering exploring this type of physics in the laboratory of my coauthor, Professor Schätz, at the University of Freiburg," Bermudez said. "Although the experimental requirements to implement the proposed scheme are stringent, Professor Schätz leads a world-class team of fantastic researchers with the required technology to face this challenge." Explore further: Quantum information motion control is now improved More information: Alejandro Bermudez and Tobias Schaetz. "Quantum transport of energy in controlled synthetic quantum magnets." New Journal of Physics. DOI: 10.1088/1367-2630/18/8/083006

Mendoza M.,ETH Zurich | Herrmann H.J.,ETH Zurich | Succi S.,CNR Institute of Neuroscience | Succi S.,Freiburg Institute for Advanced Studies
Physical Review Letters | Year: 2011

We provide numerical evidence that electronic preturbulent phenomena in graphene could be observed, under current experimental conditions, through current fluctuations, echoing the detachment of vortices past localized micron-sized impurities. Vortex generation, due to micron-sized constriction, is also explored with special focus on the effects of relativistic corrections to the normal Navier-Stokes equations. These corrections are found to cause a delay in the stability breakout of the fluid as well as a small shift in the vortex shedding frequency. © 2011 American Physical Society.

Mendoza M.,ETH Zurich | Boghosian B.M.,Tufts University | Herrmann H.J.,ETH Zurich | Succi S.,Instituto Per Le Applicazioni Del Calcolo Cnr | Succi S.,Freiburg Institute for Advanced Studies
Physical Review Letters | Year: 2010

A lattice Boltzmann formulation for relativistic fluids is presented and numerically validated through quantitative comparison with recent hydrodynamic simulations of relativistic fluids. In order to illustrate its capability to handle complex geometries, the scheme is also applied to the case of a three-dimensional relativistic shock wave, generated by a supernova explosion, impacting on a massive interstellar cloud. This formulation opens up the possibility of exporting the proven advantages of lattice Boltzmann methods, namely, computational efficiency and easy handling of complex geometries, to the context of (mildly) relativistic fluid dynamics at large, from quark-gluon plasmas up to supernovae with relativistic outflows. © 2010 The American Physical Society.

Petersen A.M.,IMT Lucca Institute for Advanced Studies | Succi S.,Instituto Applicazioni Calcolo Cnr | Succi S.,Freiburg Institute for Advanced Studies
Journal of Informetrics | Year: 2013

We present a simple generalization of Hirsch's h-index, Z≡h2+C/5, where C is the total number of citations. Z is aimed at correcting the potentially excessive penalty made by h on a scientist's highly cited papers, because for the majority of scientists analyzed, we find the excess citation fraction (C-h2)/C to be distributed closely around the value 0.75, meaning that 75% of the author's impact is neglected. Additionally, Z is less sensitive to local changes in a scientist's citation profile, namely perturbations which increase h while only marginally affecting C. Using real career data for 476 physicists careers and 488 biologist careers, we analyze both the distribution of Z and the rank stability of Z with respect to the Hirsch index h and the Egghe index g. We analyze careers distributed across a wide range of total impact, including top-cited physicists and biologists for benchmark comparison. In practice, the Z-index requires the same information needed to calculate h and could be effortlessly incorporated within career profile databases, such as Google Scholar and ResearcherID. Because Z incorporates information from the entire publication profile while being more robust than h and g to local perturbations, we argue that Z is better suited for ranking comparisons in academic decision-making scenarios comprising a large number of scientists. © 2013 Elsevier Ltd.

Mostarda S.,Freiburg Institute for Advanced Studies | Gfeller D.,Swiss Institute of Bioinformatics | Rao F.,Freiburg Institute for Advanced Studies
PLoS Computational Biology | Year: 2012

A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved β2 - β3 loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the β2 - β3 loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity. © 2012 Mostarda et al.

Sbragaglia M.,University of Rome Tor Vergata | Benzi R.,University of Rome Tor Vergata | Bernaschi M.,CNR Institute of Neuroscience | Succi S.,CNR Institute of Neuroscience | Succi S.,Freiburg Institute for Advanced Studies
Soft Matter | Year: 2012

A systematic study for a single-species lattice Boltzmann model with frustrated-short range attractive and mid/long-range repulsive-interactions is presented. The equilibrium analysis, carried out along the guidelines proposed by [X. Shan, Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2008, 77, 066702], allows us to determine the surface tension density and the resulting disjoining pressure developing in a thin film when two interfaces overlap. Numerical simulations of confined flows are then performed with a multicomponent model and successfully tested against a recent suggestion, motivated by experimental facts, on the existence of a cooperative length underlying the non-local rheology of highly confined soft-glassy materials [Goyon et al., Nature, 2008, 454, 8487; Goyon et al., Soft Matter, 2010, 6, 2668-2678]. © 2012 The Royal Society of Chemistry.

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