The Barcelona Institute of Science and Technology
The Barcelona Institute of Science and Technology
News Article | May 16, 2017
Energy dissipation is a key ingredient in understanding many physical phenomena in thermodynamics, photonics, chemical reactions, nuclear fission, photon emissions, or even electronic circuits, among others. In a vibrating system, the energy dissipation is quantified by the quality factor. If the quality factor of the resonator is high, the mechanical energy will dissipate at a very low rate, and therefore the resonator will be extremely accurate at measuring or sensing objects thus enabling these systems to become very sensitive mass and force sensors, as well as exciting quantum systems. Take, for example, a guitar string and make it vibrate. The vibration created in the string resonates in the body of the guitar. Because the vibrations of the body are strongly coupled to the surrounding air, the energy of the string vibration will dissipate more efficiently into the environment bath, increasing the volume of the sound. The decay is well known to be linear, as it does not depend on the vibrational amplitude. Now, take the guitar string and shrink it down to nano-meter dimensions to obtain a nano-mechanical resonator. In these nano systems, energy dissipation has been observed to depend on the amplitude of the vibration, described as a non-linear phenomenon, and so far no proposed theory has been proven to correctly describe this dissipation process. In a recent study, published in Nature Nanotechnology, ICFO researchers Johannes Güttinger, Adrien Noury, Peter Weber, Camille Lagoin, Joel Moser, led by Prof. at ICFO Adrian Bachtold, in collaboration with researchers from Chalmers University of Technology and ETH Zurich, have found an explanation of the non-linear dissipation process using a nano-mechanical resonator based on multilayer graphene. In their work, the team of researchers used a graphene based nano-mechanical resonator, well suited for observing nonlinear effects in energy decay processes, and measured it with a superconducting microwave cavity. Such a system is capable of detecting the mechanical vibrations in a very short period of time as well as being sensitive enough to detect minimum displacements and over a very broad range of vibrational amplitudes. The team took the system, forced it out-of-equilibrium using a driving force, and subsequently switched the force off to measure the vibrational amplitude as the energy of the system decayed. They carried out over 1000 measurements for every energy decay trace and were able to observe that as the energy of a vibrational mode decays, the rate of decay reaches a point where it changes abruptly to a lower value. The larger energy decay at high amplitude vibrations can be explained by a model where the measured vibration mode "hybridizes" with another mode of the system and they decay in unison. This is equivalent to the coupling of the guitar string to the body although the coupling is nonlinear in the case of the graphene nano resonator. As the vibrational amplitude decreases, the rate suddenly changes and the modes become decoupled, resulting in comparatively low decay rates, thus in very giant quality factors exceeding 1 million. This abrupt change in the decay has never been predicted or measured until now. Therefore, the results achieved in this study have shown that nonlinear effects in graphene nano-mechanical resonators reveal a hybridization effect at high energies that, if controlled, could open up new possibilities to manipulate vibrational states, engineer hybrid states with mechanical modes at completely different frequencies, and to study the collective motion of highly tunable systems. ICFO - The Institute of Photonic Sciences, member of The Barcelona Institute of Science and Technology, is a research center located in a specially designed, 14.000 m2-building situated in the Mediterranean Technology Park in the metropolitan area of Barcelona. It currently hosts 400 people, including research group leaders, post-doctoral researchers, PhD students, research engineers, and staff. ICFOnians are organized in 27 research groups working in 60 state-of-the-art research laboratories, equipped with the latest experimental facilities and supported by a range of cutting-edge facilities for nanofabrication, characterization, imaging and engineering. The Severo Ochoa distinction awarded by the Ministry of Science and Innovation, as well as 14 ICREA Professorships, 25 European Research Council grants and 6 Fundació Cellex Barcelona Nest Fellowships, demonstrate the centre's dedication to research excellence, as does the institute's consistent appearance in top worldwide positions in international rankings. From an industrial standpoint, ICFO participates actively in the European Technological Platform Photonics21 and is also very proactive in fostering entrepreneurial activities and spin-off creation. The center participates in incubator activities and seeks to attract venture capital investment. ICFO hosts an active Corporate Liaison Program that aims at creating collaborations and links between industry and ICFO researchers. To date, ICFO has created 5 successful start-up companies.
Jimenez A.,The Barcelona Institute of Science and Technology |
Jimenez A.,University Pompeu Fabra |
Cotterell J.,The Barcelona Institute of Science and Technology |
Cotterell J.,University Pompeu Fabra |
And 5 more authors.
Molecular Systems Biology | Year: 2017
A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi-functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi-functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono-functional sub-circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi-functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non-intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits. © 2017 The Authors. Published under the terms of the CC BY 4.0 license
Pasini D.,Italian National Cancer Institute |
Di Croce L.,The Barcelona Institute of Science and Technology |
Di Croce L.,University Pompeu Fabra |
Di Croce L.,Catalan Institution for Research and Advanced Studies
Current Opinion in Genetics and Development | Year: 2016
The activities of the heterogeneous Polycomb (PcG) group of proteins ensure that the developmental processes of proliferation and cellular identity establishment are carried out correctly. PcG proteins assemble stable multiprotein complexes that, together with additional factors, maintain their target genes in a transcriptionally repressive state. The biochemical and functional features of PcG proteins have been extensively investigated over the years. Here we analyse the biochemical and mechanistic proprieties of PcG proteins with respect to recent advances that link the genetic alterations of PcG activity to cancer development. © 2016 Elsevier Ltd.
News Article | December 8, 2016
Bacterial resistance does not come just through adaptation to antibiotics, sometimes the bacteria simply go to sleep. An international team of researchers is looking at compounds that attack bacteria's ability to go dormant and have found the first oxygen-sensitive toxin antitoxin system. "Antibiotics can only kill bacteria when they are actively growing and dividing," said Thomas K. Wood, professor of chemical engineering and holder of the Biotechnology Endowed Chair, Penn State. "But, environmental stress factors often turn on a bacterial mechanism that creates a toxin that makes the cell dormant and therefore antibiotic resistant." Bacteria that form biofilms are often difficult to kill. They can react to environmental signals and produce a toxin that makes the cells go dormant. Antibiotics cannot target dormant cells. One type of bacterium that does this lives in the gastrointestinal track. Bile, secreted by the liver and stored in the gall bladder, when released into the GI track can kill bacteria. In the presence of bile, these bacteria produce a protein that is a self-toxin and the bacteria go dormant. When the bile is gone, the bacteria produce another protein that destroys the inhibitor protein and the bacteria come alive. These toxin antitoxin systems are inherent in bacteria and serve to protect them against a variety of external, environmental insults. Wood and his colleagues characterized the first toxin antitoxin system in a biofilm. They report today (Dec. 8) in Nature Communications that this system also is the first known to be oxygen-dependent. The characterization was done at the molecular and atomic level by researchers at the Biomolecular NMR Laboratory at the University of Barcelona, Spain. They found that the E. coli antitoxin's structure had channels that are just large enough for oxygen to pass through. The toxin in this system is Hha and the antitoxin is TomB. However, unlike other toxin antitoxin pairs where the toxin makes the cell dormant and the antitoxin inactivates the toxin by binding, this system needs oxygen in the presence of the antitoxin to oxidize the toxin and wake up the bacteria. "If we understand the toxin antitoxin systems at a molecular or atomic level, we can make better antimicrobials," said Wood. "I would argue that the toxin antitoxin systems are fundamental to the physiology of all bacteria. We hope this will give us insight into how they survive the antibiotics." Free-swimming bacteria are usually easily targeted by antibodies or antibiotics, but bacteria that form biofilms are harder to kill. In tuberculosis, the bacteria have as many as 88 different toxin options to react to environmental stresses. According to Wood, this is one of the reasons that TB patients need to stay on antibiotics for months or years to clear the body of all the bacteria. Biofilms are involved in 80 percent of human infections and are one of the strongest contributors to the pressing antibiotic resistance problem. The researchers found that 10 percent oxygen is sufficient to wake up the bacteria, but in a biofilm, the problem becomes accessibility. The bacteria on the edges of the film can be easily exposed to oxygen, but those further inside the film might not come into contact with the oxygen. The channels that form in the E. coli biofilm allow the oxygen to penetrate into the biofilm, awaken the bacteria, break up the biofilm and disperse it. The researchers suggest that this type of toxin, one that is oxygen-dependent, could become the target for antibacterial treatments to inhibit the formation of biofilms. Also working on this project at Penn State were W.C. Soo, postdoctoral fellow, and Thammajun L. Wood, research associate in chemical engineering. Other researchers included Oriol Marimon, Joáo M.C. Teixeira, Tiago N. Cordeiro, Irene Amata, Jesús Garcia, Ainara Morera and Miquel Pons, all at Biomolecular NMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Spain; Maxim Mayzel, and Vladislave Yu. Orekhov, Swedish NMR Centre, Gothenburg University, Gothenburg, Sweden; and Marina Gay and Marta Vilaseca, Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.
News Article | December 19, 2016
Transparent conductors are one of the key elements of today's electronic and optoelectronic devices such as displays, light emitting diodes, photovoltaic cells, smart phones, etc. Most of the current technology is based on the use of the semiconductor Indium Tin Oxide (ITO) as a transparent conducting material. However, even though ITO presents several exceptional properties, such as a large transmission and low resistance, it still lacks mechanical flexibility, needs to be processed under high temperatures and is expensive to produce. An intensive effort has been devoted to the search of alternative TC materials that could definitively replace ITO, especially in the search for device flexibility. While the scientific community has investigated materials such as Al-doped ZnO (AZO), carbon nanotubes, metal nanowires, ultrathin metals, conducting polymers and most recently graphene, none of these have been able to present optimal properties that would make them the candidate to replace ITO. Today ultrathin metal films (UTMFs) have been shown to present very low resistance although their transmission is also low unless antireflection (AR) undercoat and overcoat layers are added to the structure. ICFO researchers Rinu Abraham Maniyara, Vahagn K. Mkhitaryan, Tong Lai Chen, and Dhriti Sundar Ghosh, led by ICREA Prof at ICFO Valerio Pruneri, have developed a room temperature processed multilayer transparent conductor optimizing the antireflection properties to obtain high optical transmissions and low losses, with large mechanical flexibility properties. They have published their results in a recent paper published in Nature Communications. In their study, ICFO researchers applied an Al doped ZnO overcoat and a TiO2 undercoat layer with precise thicknesses to a highly conductive Ag ultrathin film. By using destructive interference, the researchers showed that the proposed multilayer structure could lead to an optical loss of approximately 1.6% and an optical transmission greater than 98% in the visible. As Prof. Valerio Pruneri states, "we have used a simple design to achieve a transparent conductor with the highest performance to date and at the same time other outstanding attributes required for relevant applications in industry". This result represents a record fourfold improvement in figure of merit over ITO and also presents superior mechanical flexibility in comparison to this material. The results of this study show the potential that this multilayer structure could have in future technologies that aim at more efficient and flexible electronic and optoelectronic devices. ICFO - The Institute of Photonic Sciences, member of The Barcelona Institute of Science and Technology, is a research center located in a specially designed, 14.000 m2-building situated in the Mediterranean Technology Park in the metropolitan area of Barcelona. It currently hosts 400 people, including research group leaders, post-doctoral researchers, PhD students, research engineers, and staff. ICFOnians are organized in 23 research groups working in 60 state-of-the-art research laboratories, equipped with the latest experimental facilities and supported by a range of cutting-edge facilities for nanofabrication, characterization, imaging and engineering. The Severo Ochoa distinction awarded by the Ministry of Science and Innovation, as well as 14 ICREA Professorships, 22 European Research Council grants and 6 Fundació Cellex Barcelona Nest Fellowships, demonstrate the centre's dedication to research excellence, as does the institute's consistent appearance in top worldwide positions in international rankings. From an industrial standpoint, ICFO participates actively in the European Technological Platform Photonics21 and is also very proactive in fostering entrepreneurial activities and spin-off creation. The center participates in incubator activities and seeks to attract venture capital investment. ICFO hosts an active Corporate Liaison Program that aims at creating collaborations and links between industry and ICFO researchers. To date, ICFO has created 5 successful start-up companies.
News Article | October 25, 2016
Home > Press > Physicists use lasers to capture first snapshots of rapid chemical bonds breaking Abstract: Lasers have successfully recorded a chemical reaction that happens as fast as a quadrillionth of a second, which could help scientists understand and control chemical reactions. The idea for using a laser to record a few femtoseconds of a molecule's extremely fast vibrations as it breaks apart came from Kansas State University physicists. Chii-Dong Lin, university distinguished professor of physics, and Anh-Thu Le, research associate professor in James R. Macdonald Laboratory, are part of an international collaborative project published in the Oct. 21 issue of Science. "If you want to see something that happens very, very fast, you need a tool that can measure a very, very tiny time period," Lin said. "The only light available in femtosecond measurements is a laser." A femtosecond is one-millionth of a billionth of a second, which is a million times shorter than a nanosecond. Until recently, there was no way to measure what happens during a chemical reaction in that short of a period. Lin's research group made its first molecular movie of an oxygen molecule using lasers in 2012, but to record a larger molecule -- such as the four-atom acetylene molecule -- they needed a more advanced laser. After five years of collaboration with Jens Biegert's group from ICFO-The Institute of Photonic Sciences, a member of The Barcelona Institute of Science and Technology, Lin's idea became reality. The international team used the molecule's own electrons to scatter the molecule -- a process called mid-infrared laser-induced electron diffraction, or LIED -- and capture snapshots of acetylene as it is breaking apart. An intense laser is used to affectan acetylene molecule -- composed of two hydrogen atoms and two carbon atoms -- to strip out an electron and initiate the breakup of the molecule. After nine femtoseconds, the laser drives the free electron back to the elongated molecule to create an image. "Scientists will eventually be able to apply this tool in chemistry, biology and other physical sciences to look at different types of molecules and processes," Lin said. According to Lin, acetylene's four-atom chemical structure provides multiple possibilities where the bonds could break. Being able to measure where and when those breaks occur can help researchers better understand chemical reactions, which Lin said will lead to better control of a reaction and is applicable to multiple areas of science. "In order to control something, you have to know where it is first," Lin said. "If you throw a ball over a house, you can't see what happens to it, so you can't control it anymore. But if you have a way to see each second of the ball in the air, you can figure out why it ends up where it does and potentially change the way you throw it to control the outcome or to influence it in real time." Lin's research group started working with Kansas State University distinguished professor emeritus Lew Cocke's research group in 2008 to conduct the first LIED experiment, which led to the current development. The initial experiments enabled the researchers to apply their theory to decode signals from electrons that produce the image. By decoding the image, the researchers accurately measured the molecule's new bond distances, which are smaller than one hundred-millionth of a centimeter. "Since the snapshots, which are taken by the electrons, occur in a very strong laser field, it was thought to be nearly impossible to decode the electron information and measure the small distances," said Le, who provided critical decoding of the molecule's structure in the snapshot from Barcelona. "This is the first real-time observation of the breakup of a molecule within nine femtoseconds." ### The international collaborators are from the ICFO-The Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, and Catalan Institution for Research and Advanced Studies, all in Spain; the Leiden University in The Netherlands; The University of Kassel, the Center for Free-Electron Laser Science, Max Planck Institute for Nuclear Physics, Physikalisch-Technische Bundesanstalt and University of Jena, all in Germany; and Aarhus University in Denmark. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.
Pegueroles C.,The Barcelona Institute of Science and Technology |
Pegueroles C.,University Pompeu Fabra |
Gabaldon T.,The Barcelona Institute of Science and Technology |
Gabaldon T.,University Pompeu Fabra |
Gabaldon T.,Catalan Institution for Research and Advanced Studies
BMC Biology | Year: 2016
Background: Metazoans transcribe many long non-coding RNAs (lncRNAs) that are poorly conserved and whose function remains unknown. This has raised the questions of what fraction of the predicted lncRNAs is actually functional, and whether selection can effectively constrain lncRNAs in species with small effective population sizes such as human populations. Results: Here we evaluate signatures of selection in human lncRNAs using inter-specific data and intra-specific comparisons from five major populations, as well as by assessing relationships between sequence variation and predictions of secondary structure. In all analyses we included a reference of functionally characterized lncRNAs. Altogether, our results show compelling evidence of recent purifying selection acting on both characterized and predicted lncRNAs. We found that RNA secondary structure constrains sequence variation in lncRNAs, so that polymorphisms are depleted in paired regions with low accessibility and tend to be neutral with respect to structural stability. Conclusions: Important implications of our results are that secondary structure plays a role in the functionality of lncRNAs, and that the set of predicted lncRNAs contains a large fraction of functional ones that may play key roles that remain to be discovered. © 2016 Pegueroles and Gabaldon.
Bartesaghi R.,University of Bologna |
Haydar T.F.,Boston University |
Delabar J.M.,University Paris Diderot |
Dierssen M.,The Barcelona Institute of Science and Technology |
And 3 more authors.
Journal of Neuroscience | Year: 2015
Down syndrome (DS) is a relatively common genetic condition caused by the triplication of human chromosome 21. No therapies currently exist for the rescue of neurocognitive impairment in DS. This review presents exciting findings showing that it is possible to restore brain development and cognitive performance in mouse models of DS with therapies that can also apply to humans. This knowledge provides a potential breakthrough for the prevention of intellectual disability in DS. © 2015 the authors.
Papasaikas P.,The Barcelona Institute of Science and Technology |
Papasaikas P.,University Pompeu Fabra |
Valcarcel J.,The Barcelona Institute of Science and Technology |
Valcarcel J.,University Pompeu Fabra |
Valcarcel J.,Catalan Institution for Research and Advanced Studies
Trends in Biochemical Sciences | Year: 2016
The spliceosome, one of the most complex machineries of eukaryotic cells, removes intronic sequences from primary transcripts to generate functional messenger and long noncoding RNAs (lncRNA). Genetic, biochemical, and structural data reveal that the spliceosome is an RNA-based enzyme. Striking mechanistic and structural similarities strongly argue that pre-mRNA introns originated from self-catalytic group II ribozymes. However, in the spliceosome, protein components organize and activate the catalytic-site RNAs, and recognize and pair together splice sites at intron boundaries. The spliceosome is a dynamic, reversible, and flexible machine that chaperones small nuclear (sn) RNAs and a variety of pre-mRNA sequences into conformations that enable intron removal. This malleability likely contributes to the regulation of alternative splicing, a prevalent process contributing to cell differentiation, homeostasis, and disease. The spliceosome is a ribonucleoprotein complex that chaperones pre-mRNA and small nuclear (sn)RNAs into conformations resembling the RNA-based catalytic core of group II introns. Proteins such as pre-mRNA-processing-splicing factor 8 (Prp8) organize and regulate the activation of the RNA-based catalytic core of the spliceosome. The catalytic site is open to accommodate different intron lengths and sequences, and to interact with other cellular machineries. Spliceosomal subcomplexes recognize and pair splice-site sequences in a highly dynamic and reversible fashion. This architecture, together with iterative substrate recognition and proofreading, provide opportunities for alternative splicing regulation. © 2015 Elsevier Ltd.
Mas G.,The Barcelona Institute of Science and Technology |
Mas G.,University Pompeu Fabra |
Di Croce L.,The Barcelona Institute of Science and Technology |
Di Croce L.,University Pompeu Fabra |
Di Croce L.,Catalan Institution for Research and Advanced Studies
Current Opinion in Cell Biology | Year: 2016
Polycomb-group proteins maintain embryonic stem cell identity by repressing genes that encode for developmental regulatory factors. Failure to properly control developmental transcription programs by Polycomb proteins is linked to disease and embryonic lethality. Recent technological advances have revealed that developmentally repressed genes tend to cluster in the three-dimensional space of the nucleus. Importantly, spatial clustering of developmental genes is fundamental for the correct regulation of gene expression during early development. Here, we outline novel insights and perspectives regarding the function of Polycomb complexes in shaping the stem cell genome architecture, and discuss how this function might be required to properly orchestrate transcriptional programs during differentiation. © 2016 Elsevier Ltd