[{"article_type":"original","oa_version":"None","intvolume":"       136","citation":{"mla":"Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>.","ama":"Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. 2014;136(51):17852-17860. doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>","chicago":"Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>.","apa":"Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>","ista":"Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860.","short":"P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860.","ieee":"P. Schanda <i>et al.</i>, “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014."},"date_published":"2014-11-27T00:00:00Z","type":"journal_article","volume":136,"status":"public","month":"11","quality_controlled":"1","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis."}],"date_updated":"2021-01-12T08:19:24Z","publisher":"American Chemical Society","title":"Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan","doi":"10.1021/ja5105987","publication":"Journal of the American Chemical Society","_id":"8458","date_created":"2020-09-18T10:07:52Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"day":"27","publication_status":"published","author":[{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"full_name":"Triboulet, Sébastien","first_name":"Sébastien","last_name":"Triboulet"},{"last_name":"Laguri","first_name":"Cédric","full_name":"Laguri, Cédric"},{"last_name":"Bougault","first_name":"Catherine M.","full_name":"Bougault, Catherine M."},{"full_name":"Ayala, Isabel","first_name":"Isabel","last_name":"Ayala"},{"last_name":"Callon","full_name":"Callon, Morgane","first_name":"Morgane"},{"last_name":"Arthur","first_name":"Michel","full_name":"Arthur, Michel"},{"full_name":"Simorre, Jean-Pierre","first_name":"Jean-Pierre","last_name":"Simorre"}],"issue":"51","page":"17852-17860","year":"2014","language":[{"iso":"eng"}]},{"issue":"15","publication_identifier":{"issn":["1367-4803","1460-2059"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.","lang":"eng"}],"title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","_id":"8459","status":"public","intvolume":"        30","citation":{"apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>","ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","ieee":"S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220.","mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. 2014;30(15):2219-2220. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>."},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioinformatics/btz397"}]},"language":[{"iso":"eng"}],"year":"2014","author":[{"last_name":"Morin","full_name":"Morin, Sébastien","first_name":"Sébastien"},{"last_name":"Linnet","full_name":"Linnet, Troels E","first_name":"Troels E"},{"last_name":"Lescanne","full_name":"Lescanne, Mathilde","first_name":"Mathilde"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"first_name":"Gary S","full_name":"Thompson, Gary S","last_name":"Thompson"},{"last_name":"Tollinger","first_name":"Martin","full_name":"Tollinger, Martin"},{"last_name":"Teilum","first_name":"Kaare","full_name":"Teilum, Kaare"},{"first_name":"Stéphane","full_name":"Gagné, Stéphane","last_name":"Gagné"},{"last_name":"Marion","first_name":"Dominique","full_name":"Marion, Dominique"},{"first_name":"Christian","full_name":"Griesinger, Christian","last_name":"Griesinger"},{"first_name":"Martin","full_name":"Blackledge, Martin","last_name":"Blackledge"},{"first_name":"Edward J","full_name":"d’Auvergne, Edward J","last_name":"d’Auvergne"}],"keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"page":"2219-2220","date_created":"2020-09-18T10:08:07Z","day":"01","publication_status":"published","article_processing_charge":"No","publisher":"Oxford University Press","date_updated":"2021-01-12T08:19:25Z","doi":"10.1093/bioinformatics/btu166","publication":"Bioinformatics","month":"08","quality_controlled":"1","extern":"1","date_published":"2014-08-01T00:00:00Z","type":"journal_article","volume":30,"oa_version":"None","article_type":"original"},{"month":"03","quality_controlled":"1","extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states."}],"publisher":"Wiley","doi":"10.1002/anie.201311275","title":"Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy","date_updated":"2021-01-12T08:19:25Z","_id":"8460","publication":"Angewandte Chemie International Edition","oa_version":"None","article_type":"original","citation":{"chicago":"Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>.","mla":"Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>.","ama":"Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. 2014;53(17):4312-4317. doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>","ieee":"P. Ma <i>et al.</i>, “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.","short":"P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.","apa":"Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>","ista":"Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317."},"intvolume":"        53","type":"journal_article","date_published":"2014-03-18T00:00:00Z","volume":53,"status":"public","language":[{"iso":"eng"}],"year":"2014","publication_identifier":{"issn":["1433-7851"]},"date_created":"2020-09-18T10:08:53Z","day":"18","publication_status":"published","author":[{"full_name":"Ma, Peixiang","first_name":"Peixiang","last_name":"Ma"},{"first_name":"Jens D.","full_name":"Haller, Jens D.","last_name":"Haller"},{"full_name":"Zajakala, Jérémy","first_name":"Jérémy","last_name":"Zajakala"},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"first_name":"Astrid C.","full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen"},{"last_name":"Willbold","full_name":"Willbold, Dieter","first_name":"Dieter"},{"last_name":"Boisbouvier","first_name":"Jérôme","full_name":"Boisbouvier, Jérôme"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"issue":"17","page":"4312-4317"},{"intvolume":"        67","citation":{"mla":"Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>.","ama":"Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. 2014;67(5):748-775. doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>","chicago":"Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>.","apa":"Kaloshin, V., Levi, M., &#38; Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>","ista":"Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775.","ieee":"V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5. Wiley, pp. 748–775, 2014.","short":"V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775."},"oa_version":"None","article_type":"original","status":"public","volume":67,"type":"journal_article","date_published":"2014-05-01T00:00:00Z","extern":"1","quality_controlled":"1","month":"05","publication":"Communications on Pure and Applied Mathematics","_id":"8500","title":"Arnol′d diffusion in a pendulum lattice","publisher":"Wiley","date_updated":"2022-08-25T13:58:13Z","doi":"10.1002/cpa.21509","abstract":[{"lang":"eng","text":"The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way."}],"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","day":"01","publication_identifier":{"issn":["0010-3640"]},"date_created":"2020-09-18T10:47:01Z","page":"748-775","issue":"5","author":[{"full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"},{"first_name":"Maria","full_name":"Saprykina, Maria","last_name":"Saprykina"}],"keyword":["Applied Mathematics","General Mathematics"],"language":[{"iso":"eng"}],"year":"2014"},{"arxiv":1,"date_created":"2020-09-18T10:47:09Z","day":"01","publication_status":"published","author":[{"first_name":"Abed","full_name":"Bounemoura, Abed","last_name":"Bounemoura"},{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"keyword":["General Mathematics"],"page":"181-203","year":"2014","language":[{"iso":"eng"}],"external_id":{"arxiv":["1304.3050"]},"oa_version":"Preprint","article_type":"original","type":"journal_article","date_published":"2014-04-01T00:00:00Z","volume":14,"month":"04","quality_controlled":"1","extern":"1","article_processing_charge":"No","doi":"10.17323/1609-4514-2014-14-2-181-203","date_updated":"2021-01-12T08:19:43Z","publisher":"Independent University of Moscow","publication":"Moscow Mathematical Journal","publication_identifier":{"issn":["1609-3321","1609-4514"]},"issue":"2","citation":{"short":"A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.","ieee":"A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>","ista":"Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>.","ama":"Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. 2014;14(2):181-203. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>"},"intvolume":"        14","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation."}],"title":"Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom","_id":"8501"},{"year":"2014","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"8","author":[{"full_name":"Rosello, Oriol P","first_name":"Oriol","last_name":"Rosello"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"page":"1949 - 1955","date_created":"2018-12-11T11:48:51Z","publist_id":"6797","publication_status":"published","day":"01","abstract":[{"text":"Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ","lang":"eng"}],"publication":"Genome Biology and Evolution","_id":"852","date_updated":"2021-01-12T08:19:51Z","title":"Long-Term asymmetrical acceleration of protein evolution after gene duplication","publisher":"Oxford University Press","doi":"10.1093/gbe/evu159","month":"08","extern":1,"quality_controlled":0,"volume":6,"type":"journal_article","date_published":"2014-08-01T00:00:00Z","status":"public","intvolume":"         6","citation":{"apa":"Rosello, O., &#38; Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>","ista":"Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.","short":"O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.","ieee":"O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” <i>Genome Biology and Evolution</i>, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014.","mla":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>.","ama":"Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. 2014;6(8):1949-1955. doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>","chicago":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>."}},{"extern":1,"acknowledgement":"K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","quality_controlled":0,"month":"01","_id":"856","publication":"Nature Communications","title":"Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network","doi":"10.1038/ncomms5868","date_updated":"2021-01-12T08:20:01Z","publisher":"Nature Publishing Group","abstract":[{"text":"The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.","lang":"eng"}],"intvolume":"         5","citation":{"ista":"Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5.","apa":"Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>","ieee":"K. Pougach <i>et al.</i>, “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014.","short":"K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014).","ama":"Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>","mla":"Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>, vol. 5, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>.","chicago":"Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>."},"status":"public","volume":5,"date_published":"2014-01-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2014","publication_status":"published","publist_id":"6790","day":"01","date_created":"2018-12-11T11:48:52Z","author":[{"first_name":"Ksenia","full_name":"Pougach, Ksenia S","last_name":"Pougach"},{"last_name":"Voet","first_name":"Arnout","full_name":"Voet, Arnout R"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Voordeckers, Karin","first_name":"Karin","last_name":"Voordeckers"},{"last_name":"Christiaens","full_name":"Christiaens, Joaquin F","first_name":"Joaquin"},{"last_name":"Baying","first_name":"Bianka","full_name":"Baying, Bianka"},{"first_name":"Vladimı́R","full_name":"Bénès, Vladimı́r","last_name":"Bénès"},{"full_name":"Sakai, Ryo","first_name":"Ryo","last_name":"Sakai"},{"last_name":"Aerts","first_name":"Jan","full_name":"Aerts, Jan A"},{"last_name":"Zhu","full_name":"Zhu, Bo","first_name":"Bo"},{"last_name":"Van Dijck","first_name":"Patrick","full_name":"Van Dijck, Patrick"},{"last_name":"Verstrepen","first_name":"Kevin","full_name":"Verstrepen, Kevin J"}]},{"status":"public","volume":510,"date_published":"2014-01-01T00:00:00Z","type":"journal_article","intvolume":"       510","citation":{"ieee":"L. Moroz <i>et al.</i>, “The ctenophore genome and the evolutionary origins of neural systems,” <i>Nature</i>, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014.","short":"L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.","ista":"Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.","apa":"Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>","chicago":"Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>.","ama":"Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. 2014;510(7503):109-114. doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>","mla":"Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>."},"_id":"863","publication":"Nature","doi":"10.1038/nature13400","date_updated":"2021-01-12T08:20:21Z","title":"The ctenophore genome and the evolutionary origins of neural systems","publisher":"Nature Publishing Group","abstract":[{"lang":"eng","text":"The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals."}],"acknowledgement":"We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22.","extern":1,"quality_controlled":0,"month":"01","page":"109 - 114","issue":"7503","author":[{"last_name":"Moroz","first_name":"Leonid","full_name":"Moroz, Leonid L"},{"full_name":"Kocot, Kevin M","first_name":"Kevin","last_name":"Kocot"},{"full_name":"Citarella, Mathew R","first_name":"Mathew","last_name":"Citarella"},{"last_name":"Dosung","full_name":"Dosung, Sohn","first_name":"Sohn"},{"full_name":"Norekian, Tigran P","first_name":"Tigran","last_name":"Norekian"},{"full_name":"Povolotskaya, Inna","first_name":"Inna","last_name":"Povolotskaya"},{"last_name":"Grigorenko","first_name":"Anastasia","full_name":"Grigorenko, Anastasia P"},{"last_name":"Dailey","full_name":"Dailey, Christopher A","first_name":"Christopher"},{"last_name":"Berezikov","first_name":"Eugene","full_name":"Berezikov, Eugene"},{"first_name":"Katherine","full_name":"Buckley, Katherine M","last_name":"Buckley"},{"full_name":"Ptitsyn, Andrey A","first_name":"Andrey","last_name":"Ptitsyn"},{"last_name":"Reshetov","first_name":"Denis","full_name":"Reshetov, Denis A"},{"full_name":"Mukherjee, Krishanu","first_name":"Krishanu","last_name":"Mukherjee"},{"full_name":"Moroz, Tatiana P","first_name":"Tatiana","last_name":"Moroz"},{"last_name":"Bobkova","full_name":"Bobkova, Yelena V","first_name":"Yelena"},{"last_name":"Yu","first_name":"Fahong","full_name":"Yu, Fahong"},{"first_name":"Vladimir","full_name":"Kapitonov, Vladimir V","last_name":"Kapitonov"},{"full_name":"Jurka, Jerzy W","first_name":"Jerzy","last_name":"Jurka"},{"first_name":"Yuriy","full_name":"Bobkov, Yuriy V","last_name":"Bobkov"},{"first_name":"Joshua","full_name":"Swore, Joshua J","last_name":"Swore"},{"full_name":"Girardo, David O","first_name":"David","last_name":"Girardo"},{"last_name":"Fodor","first_name":"Alexander","full_name":"Fodor, Alexander"},{"last_name":"Gusev","first_name":"Fedor","full_name":"Gusev, Fedor E"},{"last_name":"Sanford","first_name":"Rachel","full_name":"Sanford, Rachel S"},{"last_name":"Bruders","full_name":"Bruders, Rebecca","first_name":"Rebecca"},{"last_name":"Kittler","first_name":"Ellen","full_name":"Kittler, Ellen L"},{"last_name":"Mills","full_name":"Mills, Claudia E","first_name":"Claudia"},{"last_name":"Rast","first_name":"Jonathan","full_name":"Rast, Jonathan P"},{"full_name":"Derelle, Romain","first_name":"Romain","last_name":"Derelle"},{"last_name":"Solovyev","first_name":"Victor","full_name":"Solovyev, Victor"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Billie","full_name":"Swalla, Billie J","last_name":"Swalla"},{"full_name":"Sweedler, Jonathan V","first_name":"Jonathan","last_name":"Sweedler"},{"full_name":"Rogaev, Evgeny I","first_name":"Evgeny","last_name":"Rogaev"},{"last_name":"Halanych","full_name":"Halanych, Kenneth M","first_name":"Kenneth"},{"last_name":"Kohn","full_name":"Kohn, Andrea B","first_name":"Andrea"}],"publist_id":"6785","publication_status":"published","day":"01","date_created":"2018-12-11T11:48:54Z","year":"2014","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"}},{"day":"15","publication_status":"published","publist_id":"6782","date_created":"2018-12-11T11:48:55Z","page":"571 - 578","issue":"4","author":[{"first_name":"Alexey","full_name":"Koval, Alexey V","last_name":"Koval"},{"last_name":"Vlasov","full_name":"Vlasov, Peter K","first_name":"Peter"},{"last_name":"Shichkova","full_name":"Shichkova, Polina","first_name":"Polina"},{"first_name":"S","full_name":"Khunderyakova, S","last_name":"Khunderyakova"},{"first_name":"Yury","full_name":"Markov, Yury","last_name":"Markov"},{"last_name":"Panchenko","first_name":"J","full_name":"Panchenko, J"},{"first_name":"A","full_name":"Volodina, A","last_name":"Volodina"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Katanaev","first_name":"Vladimir","full_name":"Katanaev, Vladimir L"}],"year":"2014","citation":{"chicago":"Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>.","ama":"Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. 2014;87(4):571-578. doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>","mla":"Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>.","ieee":"A. Koval <i>et al.</i>, “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” <i>Biochemical Pharmacology</i>, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.","short":"A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.","ista":"Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578.","apa":"Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>"},"intvolume":"        87","status":"public","date_published":"2014-02-15T00:00:00Z","type":"journal_article","volume":87,"quality_controlled":0,"extern":1,"month":"02","title":"Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling","publisher":"Elsevier","doi":"10.1016/j.bcp.2013.12.007","date_updated":"2021-01-12T08:20:24Z","_id":"865","publication":"Biochemical Pharmacology","abstract":[{"lang":"eng","text":"Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers."}]},{"citation":{"short":"D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112.","ieee":"D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” <i>Current Opinion in Structural Biology</i>, vol. 26, no. 1. Elsevier, pp. 104–112, 2014.","ista":"Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.","apa":"Ivankov, D., Finkelstein, A., &#38; Kondrashov, F. (2014). A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>","chicago":"Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>.","ama":"Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. 2014;26(1):104-112. doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>","mla":"Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>."},"intvolume":"        26","status":"public","type":"journal_article","date_published":"2014-06-01T00:00:00Z","volume":26,"quality_controlled":0,"extern":1,"acknowledgement":"The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.\n","month":"06","title":"A structural perspective of compensatory evolution","date_updated":"2021-01-12T08:21:21Z","doi":"10.1016/j.sbi.2014.05.004","publisher":"Elsevier","_id":"892","publication":"Current Opinion in Structural Biology","abstract":[{"lang":"eng","text":"The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution."}],"day":"01","publication_status":"published","publist_id":"6756","date_created":"2018-12-11T11:49:03Z","page":"104 - 112","issue":"1","author":[{"last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry N"},{"first_name":"Alexei","full_name":"Finkelstein, Alexei V","last_name":"Finkelstein"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"year":"2014"},{"scopus_import":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"issue":"11","pmid":1,"title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","_id":"9050","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"lang":"eng","text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter."}],"intvolume":"        10","citation":{"ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1309.5662","open_access":"1"}],"status":"public","year":"2014","language":[{"iso":"eng"}],"day":"21","publication_status":"published","date_created":"2021-02-01T13:43:31Z","arxiv":1,"keyword":["General Chemistry","Condensed Matter Physics"],"author":[{"last_name":"Takagi","full_name":"Takagi, Daisuke","first_name":"Daisuke"},{"last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"},{"full_name":"Braunschweig, Adam B.","first_name":"Adam B.","last_name":"Braunschweig"},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"first_name":"Jun","full_name":"Zhang, Jun","last_name":"Zhang"}],"oa":1,"quality_controlled":"1","article_number":"1784","extern":"1","month":"03","doi":"10.1039/c3sm52815d","publisher":"Royal Society of Chemistry ","date_updated":"2023-02-23T13:47:35Z","publication":"Soft Matter","article_processing_charge":"No","oa_version":"Preprint","article_type":"original","external_id":{"pmid":["24800268"],"arxiv":["1309.5662"]},"date_published":"2014-03-21T00:00:00Z","type":"journal_article","volume":10},{"issue":"2029","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"scopus_import":"1","status":"public","citation":{"chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2014;372(2029). doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>.","short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029. The Royal Society, 2014.","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., &#38; Chaikin, P. M. (2014). Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>"},"intvolume":"       372","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"title":"Light-activated self-propelled colloids","_id":"9166","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.","lang":"eng"}],"pmid":1,"author":[{"orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"last_name":"Sacanna","first_name":"S.","full_name":"Sacanna, S."},{"first_name":"S.-H.","full_name":"Kim, S.-H.","last_name":"Kim"},{"full_name":"Yi, G.-R.","first_name":"G.-R.","last_name":"Yi"},{"last_name":"Pine","first_name":"D. J.","full_name":"Pine, D. J."},{"full_name":"Chaikin, P. M.","first_name":"P. M.","last_name":"Chaikin"}],"keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"day":"28","publication_status":"published","arxiv":1,"date_created":"2021-02-18T14:31:11Z","year":"2014","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2014-11-28T00:00:00Z","volume":372,"article_type":"original","oa_version":"Published Version","external_id":{"pmid":["25332383"],"arxiv":["1410.7278"]},"publisher":"The Royal Society","doi":"10.1098/rsta.2013.0372","date_updated":"2021-02-22T10:44:16Z","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","article_processing_charge":"No","quality_controlled":"1","oa":1,"extern":"1","article_number":"20130372","month":"11"},{"language":[{"iso":"eng"}],"year":"2014","author":[{"first_name":"Bo","full_name":"Dong, Bo","last_name":"Dong"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Shigeo","full_name":"Hayashi, Shigeo","last_name":"Hayashi"}],"issue":"4","page":"941 - 950","date_created":"2018-12-11T11:49:14Z","publication_status":"published","publist_id":"6515","day":"22","abstract":[{"lang":"eng","text":"The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell Reports","_id":"925","title":"Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape","date_updated":"2021-01-12T08:21:57Z","publisher":"Cell Press","doi":"10.1016/j.celrep.2014.03.066","month":"05","extern":"1","acknowledgement":"We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D.","volume":7,"type":"journal_article","date_published":"2014-05-22T00:00:00Z","status":"public","oa_version":"None","intvolume":"         7","citation":{"chicago":"Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>.","mla":"Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>.","ama":"Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. 2014;7(4):941-950. doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>","short":"B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.","ieee":"B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” <i>Cell Reports</i>, vol. 7, no. 4. Cell Press, pp. 941–950, 2014.","apa":"Dong, B., Hannezo, E. B., &#38; Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>","ista":"Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950."}},{"year":"2014","language":[{"iso":"eng"}],"issue":"93","author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Jacques","full_name":"Prost, Jacques","last_name":"Prost"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"}],"publication_status":"published","publist_id":"6516","day":"06","date_created":"2018-12-11T11:49:14Z","_id":"926","publication":"Journal of the Royal Society Interface","doi":"10.1098/rsif.2013.0895","date_updated":"2021-01-12T08:21:57Z","title":"Growth homeostatic regulation and stem cell dynamics in tissues","publisher":"Royal Society of London","abstract":[{"text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","month":"04","status":"public","volume":11,"type":"journal_article","date_published":"2014-04-06T00:00:00Z","intvolume":"        11","citation":{"ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93. Royal Society of London, 2014.","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. 2014;11(93). doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93, Royal Society of London, 2014, doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2014. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>."},"oa_version":"None"},{"date_created":"2018-12-11T11:49:14Z","day":"01","publication_status":"published","publist_id":"6517","author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Prost","first_name":"Jacques","full_name":"Prost, Jacques"},{"full_name":"Joanny, Jean","first_name":"Jean","last_name":"Joanny"}],"issue":"1","page":"27 - 32","language":[{"iso":"eng"}],"year":"2014","oa_version":"None","citation":{"ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” <i>PNAS</i>, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014.","short":"E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32.","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>.","ama":"Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. 2014;111(1):27-32. doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>","mla":"Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>."},"intvolume":"       111","date_published":"2014-01-01T00:00:00Z","type":"journal_article","volume":111,"status":"public","month":"01","extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions."}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1312076111","date_updated":"2021-01-12T08:21:58Z","title":"Theory of epithelial sheet morphology in three dimensions","publication":"PNAS","_id":"927"},{"file_date_updated":"2020-07-14T12:47:48Z","department":[{"_id":"VlKo"},{"_id":"UlWa"}],"ddc":["510"],"language":[{"iso":"eng"}],"year":"2014","date_created":"2019-11-18T15:57:05Z","day":"30","publication_status":"draft","author":[{"id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf","full_name":"Huszár, Kristóf","last_name":"Huszár","orcid":"0000-0002-5445-5057"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"page":"5","month":"06","oa":1,"file":[{"date_updated":"2020-07-14T12:47:48Z","file_size":511233,"file_name":"2014_Playful_Math_Huszar.pdf","access_level":"open_access","checksum":"2b94e5e1f4c3fe8ab89b12806276fb09","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"7039","date_created":"2019-11-18T15:57:51Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"IST Austria","date_updated":"2020-07-14T23:11:45Z","title":"Playful Math - An introduction to mathematical games","_id":"7038","oa_version":"Published Version","citation":{"chicago":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria, n.d.","ama":"Huszár K, Rolinek M. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria","mla":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria.","short":"K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d.","ieee":"K. Huszár and M. Rolinek, <i>Playful Math - An introduction to mathematical games</i>. IST Austria.","ista":"Huszár K, Rolinek M. Playful Math - An introduction to mathematical games, IST Austria, 5p.","apa":"Huszár, K., &#38; Rolinek, M. (n.d.). <i>Playful Math - An introduction to mathematical games</i>. IST Austria."},"has_accepted_license":"1","type":"working_paper","date_published":"2014-06-30T00:00:00Z","status":"public"},{"author":[{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A","full_name":"Modic, Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147"},{"last_name":"Smidt","full_name":"Smidt, Tess E.","first_name":"Tess E."},{"last_name":"Kimchi","full_name":"Kimchi, Itamar","first_name":"Itamar"},{"full_name":"Breznay, Nicholas P.","first_name":"Nicholas P.","last_name":"Breznay"},{"first_name":"Alun","full_name":"Biffin, Alun","last_name":"Biffin"},{"first_name":"Sungkyun","full_name":"Choi, Sungkyun","last_name":"Choi"},{"last_name":"Johnson","full_name":"Johnson, Roger D.","first_name":"Roger D."},{"last_name":"Coldea","full_name":"Coldea, Radu","first_name":"Radu"},{"full_name":"Watkins-Curry, Pilanda","first_name":"Pilanda","last_name":"Watkins-Curry"},{"full_name":"McCandless, Gregory T.","first_name":"Gregory T.","last_name":"McCandless"},{"last_name":"Chan","first_name":"Julia Y.","full_name":"Chan, Julia Y."},{"last_name":"Gandara","full_name":"Gandara, Felipe","first_name":"Felipe"},{"last_name":"Islam","first_name":"Z.","full_name":"Islam, Z."},{"last_name":"Vishwanath","full_name":"Vishwanath, Ashvin","first_name":"Ashvin"},{"first_name":"Arkady","full_name":"Shekhter, Arkady","last_name":"Shekhter"},{"full_name":"McDonald, Ross D.","first_name":"Ross D.","last_name":"McDonald"},{"full_name":"Analytis, James G.","first_name":"James G.","last_name":"Analytis"}],"date_created":"2019-11-19T13:22:39Z","day":"27","publication_status":"published","language":[{"iso":"eng"}],"year":"2014","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2014-06-27T00:00:00Z","type":"journal_article","volume":5,"article_type":"original","oa_version":"Published Version","article_processing_charge":"No","doi":"10.1038/ncomms5203","date_updated":"2021-01-12T08:11:42Z","publisher":"Springer Science and Business Media LLC","publication":"Nature Communications","month":"06","quality_controlled":"1","oa":1,"file":[{"checksum":"d290f0bfa93c5169cc6c8086874c5a78","file_name":"2014_NatureComm_Modic.pdf","access_level":"open_access","file_size":4832820,"date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-26T12:44:23Z","file_id":"7113","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"extern":"1","article_number":"4203","publication_identifier":{"issn":["2041-1723"]},"file_date_updated":"2020-07-14T12:47:48Z","status":"public","citation":{"ama":"Modic KA, Smidt TE, Kimchi I, et al. Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms5203\">10.1038/ncomms5203</a>","mla":"Modic, Kimberly A., et al. “Realization of a Three-Dimensional Spin–Anisotropic Harmonic Honeycomb Iridate.” <i>Nature Communications</i>, vol. 5, 4203, Springer Science and Business Media LLC, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms5203\">10.1038/ncomms5203</a>.","chicago":"Modic, Kimberly A, Tess E. Smidt, Itamar Kimchi, Nicholas P. Breznay, Alun Biffin, Sungkyun Choi, Roger D. Johnson, et al. “Realization of a Three-Dimensional Spin–Anisotropic Harmonic Honeycomb Iridate.” <i>Nature Communications</i>. Springer Science and Business Media LLC, 2014. <a href=\"https://doi.org/10.1038/ncomms5203\">https://doi.org/10.1038/ncomms5203</a>.","ista":"Modic KA, Smidt TE, Kimchi I, Breznay NP, Biffin A, Choi S, Johnson RD, Coldea R, Watkins-Curry P, McCandless GT, Chan JY, Gandara F, Islam Z, Vishwanath A, Shekhter A, McDonald RD, Analytis JG. 2014. Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. Nature Communications. 5, 4203.","apa":"Modic, K. A., Smidt, T. E., Kimchi, I., Breznay, N. P., Biffin, A., Choi, S., … Analytis, J. G. (2014). Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. <i>Nature Communications</i>. Springer Science and Business Media LLC. <a href=\"https://doi.org/10.1038/ncomms5203\">https://doi.org/10.1038/ncomms5203</a>","short":"K.A. Modic, T.E. Smidt, I. Kimchi, N.P. Breznay, A. Biffin, S. Choi, R.D. Johnson, R. Coldea, P. Watkins-Curry, G.T. McCandless, J.Y. Chan, F. Gandara, Z. Islam, A. Vishwanath, A. Shekhter, R.D. McDonald, J.G. Analytis, Nature Communications 5 (2014).","ieee":"K. A. Modic <i>et al.</i>, “Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate,” <i>Nature Communications</i>, vol. 5. Springer Science and Business Media LLC, 2014."},"intvolume":"         5","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Spin and orbital quantum numbers play a key role in the physics of Mott insulators, but in most systems they are connected only indirectly—via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce strong spin–orbit coupling directly, such that these numbers become entwined together and the Mott physics attains a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin–anisotropic magnetic interactions, coupling the spin to a given spatial direction of exchange and leading to strongly frustrated magnetism. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb and exhibits striking evidence for highly spin–anisotropic exchange. The basic structural units of this material suggest that a new family of three-dimensional structures could exist, the ‘harmonic honeycomb’ iridates, of which the present compound is the first example."}],"title":"Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate","_id":"7071"},{"volume":112,"type":"journal_article","date_published":"2014-05-19T00:00:00Z","status":"public","article_type":"original","oa_version":"None","intvolume":"       112","citation":{"ieee":"T. Lancaster <i>et al.</i>, “Controlling magnetic order and quantum disorder in molecule-based magnets,” <i>Physical Review Letters</i>, vol. 112, no. 20. APS, 2014.","short":"T. Lancaster, P.A. Goddard, S.J. Blundell, F.R. Foronda, S. Ghannadzadeh, J.S. Möller, P.J. Baker, F.L. Pratt, C. Baines, L. Huang, J. Wosnitza, R.D. McDonald, K.A. Modic, J. Singleton, C.V. Topping, T.A.W. Beale, F. Xiao, J.A. Schlueter, A.M. Barton, R.D. Cabrera, K.E. Carreiro, H.E. Tran, J.L. Manson, Physical Review Letters 112 (2014).","ista":"Lancaster T, Goddard PA, Blundell SJ, Foronda FR, Ghannadzadeh S, Möller JS, Baker PJ, Pratt FL, Baines C, Huang L, Wosnitza J, McDonald RD, Modic KA, Singleton J, Topping CV, Beale TAW, Xiao F, Schlueter JA, Barton AM, Cabrera RD, Carreiro KE, Tran HE, Manson JL. 2014. Controlling magnetic order and quantum disorder in molecule-based magnets. Physical Review Letters. 112(20), 207201.","apa":"Lancaster, T., Goddard, P. A., Blundell, S. J., Foronda, F. R., Ghannadzadeh, S., Möller, J. S., … Manson, J. L. (2014). Controlling magnetic order and quantum disorder in molecule-based magnets. <i>Physical Review Letters</i>. APS. <a href=\"https://doi.org/10.1103/physrevlett.112.207201\">https://doi.org/10.1103/physrevlett.112.207201</a>","chicago":"Lancaster, T., P. A. Goddard, S. J. Blundell, F. R. Foronda, S. Ghannadzadeh, J. S. Möller, P. J. Baker, et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based Magnets.” <i>Physical Review Letters</i>. APS, 2014. <a href=\"https://doi.org/10.1103/physrevlett.112.207201\">https://doi.org/10.1103/physrevlett.112.207201</a>.","ama":"Lancaster T, Goddard PA, Blundell SJ, et al. Controlling magnetic order and quantum disorder in molecule-based magnets. <i>Physical Review Letters</i>. 2014;112(20). doi:<a href=\"https://doi.org/10.1103/physrevlett.112.207201\">10.1103/physrevlett.112.207201</a>","mla":"Lancaster, T., et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based Magnets.” <i>Physical Review Letters</i>, vol. 112, no. 20, 207201, APS, 2014, doi:<a href=\"https://doi.org/10.1103/physrevlett.112.207201\">10.1103/physrevlett.112.207201</a>."},"abstract":[{"lang":"eng","text":"We investigate the structural and magnetic properties of two molecule-based magnets synthesized from the same starting components. Their different structural motifs promote contrasting exchange pathways and consequently lead to markedly different magnetic ground states. Through examination of their structural and magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field but shows a field-temperature phase diagram reminiscent of that seen in materials showing a Bose-Einstein condensation of magnons."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7072","publication":"Physical Review Letters","date_updated":"2021-01-12T08:11:42Z","doi":"10.1103/physrevlett.112.207201","title":"Controlling magnetic order and quantum disorder in molecule-based magnets","publisher":"APS","month":"05","extern":"1","article_number":"207201","quality_controlled":"1","issue":"20","author":[{"last_name":"Lancaster","full_name":"Lancaster, T.","first_name":"T."},{"full_name":"Goddard, P. A.","first_name":"P. A.","last_name":"Goddard"},{"full_name":"Blundell, S. J.","first_name":"S. J.","last_name":"Blundell"},{"first_name":"F. R.","full_name":"Foronda, F. R.","last_name":"Foronda"},{"full_name":"Ghannadzadeh, S.","first_name":"S.","last_name":"Ghannadzadeh"},{"last_name":"Möller","full_name":"Möller, J. S.","first_name":"J. S."},{"first_name":"P. J.","full_name":"Baker, P. J.","last_name":"Baker"},{"last_name":"Pratt","full_name":"Pratt, F. L.","first_name":"F. L."},{"last_name":"Baines","full_name":"Baines, C.","first_name":"C."},{"last_name":"Huang","first_name":"L.","full_name":"Huang, L."},{"last_name":"Wosnitza","first_name":"J.","full_name":"Wosnitza, J."},{"first_name":"R. D.","full_name":"McDonald, R. D.","last_name":"McDonald"},{"first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","last_name":"Modic"},{"full_name":"Singleton, J.","first_name":"J.","last_name":"Singleton"},{"last_name":"Topping","full_name":"Topping, C. V.","first_name":"C. V."},{"last_name":"Beale","full_name":"Beale, T. A. W.","first_name":"T. A. W."},{"first_name":"F.","full_name":"Xiao, F.","last_name":"Xiao"},{"full_name":"Schlueter, J. A.","first_name":"J. A.","last_name":"Schlueter"},{"last_name":"Barton","full_name":"Barton, A. M.","first_name":"A. M."},{"last_name":"Cabrera","full_name":"Cabrera, R. D.","first_name":"R. D."},{"full_name":"Carreiro, K. E.","first_name":"K. E.","last_name":"Carreiro"},{"full_name":"Tran, H. E.","first_name":"H. E.","last_name":"Tran"},{"full_name":"Manson, J. L.","first_name":"J. L.","last_name":"Manson"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2019-11-19T13:23:13Z","publication_status":"published","day":"19","language":[{"iso":"eng"}],"year":"2014"},{"volume":86,"date_published":"2014-08-14T00:00:00Z","type":"journal_article","status":"public","article_type":"original","oa_version":"None","citation":{"ama":"Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. <i>Analytical Chemistry</i>. 2014;86(18):9293-9300. doi:<a href=\"https://doi.org/10.1021/ac502513g\">10.1021/ac502513g</a>","mla":"Aigner, Daniel, et al. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” <i>Analytical Chemistry</i>, vol. 86, no. 18, ACS, 2014, pp. 9293–300, doi:<a href=\"https://doi.org/10.1021/ac502513g\">10.1021/ac502513g</a>.","chicago":"Aigner, Daniel, Stefan Alexander Freunberger, Martin Wilkening, Robert Saf, Sergey M. Borisov, and Ingo Klimant. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” <i>Analytical Chemistry</i>. ACS, 2014. <a href=\"https://doi.org/10.1021/ac502513g\">https://doi.org/10.1021/ac502513g</a>.","ista":"Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. 2014. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. 86(18), 9293–9300.","apa":"Aigner, D., Freunberger, S. A., Wilkening, M., Saf, R., Borisov, S. M., &#38; Klimant, I. (2014). Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. <i>Analytical Chemistry</i>. ACS. <a href=\"https://doi.org/10.1021/ac502513g\">https://doi.org/10.1021/ac502513g</a>","short":"D. Aigner, S.A. Freunberger, M. Wilkening, R. Saf, S.M. Borisov, I. Klimant, Analytical Chemistry 86 (2014) 9293–9300.","ieee":"D. Aigner, S. A. Freunberger, M. Wilkening, R. Saf, S. M. Borisov, and I. Klimant, “Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols,” <i>Analytical Chemistry</i>, vol. 86, no. 18. ACS, pp. 9293–9300, 2014."},"intvolume":"        86","abstract":[{"text":"Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Analytical Chemistry","_id":"7300","date_updated":"2021-01-12T08:12:53Z","publisher":"ACS","title":"Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols","doi":"10.1021/ac502513g","month":"08","extern":"1","quality_controlled":"1","author":[{"first_name":"Daniel","full_name":"Aigner, Daniel","last_name":"Aigner"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Wilkening, Martin","first_name":"Martin","last_name":"Wilkening"},{"last_name":"Saf","first_name":"Robert","full_name":"Saf, Robert"},{"first_name":"Sergey M.","full_name":"Borisov, Sergey M.","last_name":"Borisov"},{"first_name":"Ingo","full_name":"Klimant, Ingo","last_name":"Klimant"}],"issue":"18","page":"9293-9300","publication_identifier":{"issn":["0003-2700","1520-6882"]},"date_created":"2020-01-15T12:17:17Z","publication_status":"published","day":"14","year":"2014","language":[{"iso":"eng"}]},{"status":"public","date_published":"2014-01-29T00:00:00Z","type":"journal_article","volume":118,"intvolume":"       118","citation":{"short":"C. Li, O. Fontaine, S.A. Freunberger, L. Johnson, S. Grugeon, S. Laruelle, P.G. Bruce, M. Armand, The Journal of Physical Chemistry C 118 (2014) 3393–3401.","ieee":"C. Li <i>et al.</i>, “Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent,” <i>The Journal of Physical Chemistry C</i>, vol. 118, no. 7. ACS, pp. 3393–3401, 2014.","apa":"Li, C., Fontaine, O., Freunberger, S. A., Johnson, L., Grugeon, S., Laruelle, S., … Armand, M. (2014). Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. <i>The Journal of Physical Chemistry C</i>. ACS. <a href=\"https://doi.org/10.1021/jp4093805\">https://doi.org/10.1021/jp4093805</a>","ista":"Li C, Fontaine O, Freunberger SA, Johnson L, Grugeon S, Laruelle S, Bruce PG, Armand M. 2014. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. 118(7), 3393–3401.","chicago":"Li, Chunmei, Olivier Fontaine, Stefan Alexander Freunberger, Lee Johnson, Sylvie Grugeon, Stéphane Laruelle, Peter G. Bruce, and Michel Armand. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” <i>The Journal of Physical Chemistry C</i>. ACS, 2014. <a href=\"https://doi.org/10.1021/jp4093805\">https://doi.org/10.1021/jp4093805</a>.","mla":"Li, Chunmei, et al. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” <i>The Journal of Physical Chemistry C</i>, vol. 118, no. 7, ACS, 2014, pp. 3393–401, doi:<a href=\"https://doi.org/10.1021/jp4093805\">10.1021/jp4093805</a>.","ama":"Li C, Fontaine O, Freunberger SA, et al. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. <i>The Journal of Physical Chemistry C</i>. 2014;118(7):3393-3401. doi:<a href=\"https://doi.org/10.1021/jp4093805\">10.1021/jp4093805</a>"},"article_type":"original","oa_version":"None","title":"Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent","doi":"10.1021/jp4093805","date_updated":"2021-01-12T08:12:53Z","publisher":"ACS","publication":"The Journal of Physical Chemistry C","_id":"7301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Several problems arise at the O2 (positive) electrode in the Li-air battery, including solvent/electrode decomposition and electrode passivation by insulating Li2O2. Progress partially depends on exploring the basic electrochemistry of O2 reduction. Here we describe the effect of complexing-cations on the electrochemical reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent with their strong interaction with reduced O2. The complexing-cations also increase the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3 to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+, the complexing-cations also promote the reduction of O2•– to O22–. In the presence of Li+ and complexing-cations, and despite the interaction of the reduced O2 with the latter, SERS confirms that the product is still Li2O2."}],"quality_controlled":"1","extern":"1","month":"01","page":"3393-3401","author":[{"last_name":"Li","first_name":"Chunmei","full_name":"Li, Chunmei"},{"full_name":"Fontaine, Olivier","first_name":"Olivier","last_name":"Fontaine"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"last_name":"Johnson","full_name":"Johnson, Lee","first_name":"Lee"},{"full_name":"Grugeon, Sylvie","first_name":"Sylvie","last_name":"Grugeon"},{"first_name":"Stéphane","full_name":"Laruelle, Stéphane","last_name":"Laruelle"},{"first_name":"Peter G.","full_name":"Bruce, Peter G.","last_name":"Bruce"},{"last_name":"Armand","first_name":"Michel","full_name":"Armand, Michel"}],"issue":"7","day":"29","publication_status":"published","date_created":"2020-01-15T12:17:28Z","publication_identifier":{"issn":["1932-7447","1932-7455"]},"language":[{"iso":"eng"}],"year":"2014"}]