[{"_id":"8456","article_number":"8361","type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","date_updated":"2021-01-12T08:19:24Z","citation":{"ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015).","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"full_name":"Xue, Yi","last_name":"Xue","first_name":"Yi"},{"first_name":"Nicolas","full_name":"Coquelle, Nicolas","last_name":"Coquelle"},{"first_name":"Jens D.","last_name":"Haller","full_name":"Haller, Jens D."},{"last_name":"Yuwen","full_name":"Yuwen, Tairan","first_name":"Tairan"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"last_name":"Mikhailovskii","full_name":"Mikhailovskii, Oleg","first_name":"Oleg"},{"first_name":"Dieter","full_name":"Willbold, Dieter","last_name":"Willbold"},{"full_name":"Colletier, Jacques-Philippe","last_name":"Colletier","first_name":"Jacques-Philippe"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"title":"Observing the overall rocking motion of a protein in a crystal","abstract":[{"text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.","lang":"eng"}],"oa_version":"Published Version","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 6","month":"10","publication_status":"published","year":"2015","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"publication":"Nature Communications","day":"05","date_created":"2020-09-18T10:07:36Z","date_published":"2015-10-05T00:00:00Z","doi":"10.1038/ncomms9361","volume":6},{"publisher":"Wiley","quality_controlled":"1","intvolume":" 4","month":"09","abstract":[{"text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.","lang":"eng"}],"oa_version":"None","page":"699-708","date_created":"2020-09-18T10:07:45Z","issue":"3","doi":"10.1002/9780470034590.emrstm1418","date_published":"2015-09-10T00:00:00Z","volume":4,"publication_status":"published","year":"2015","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"publication":"eMagRes","language":[{"iso":"eng"}],"day":"10","article_type":"original","type":"journal_article","status":"public","_id":"8457","article_processing_charge":"No","author":[{"first_name":"Peixiang","full_name":"Ma, Peixiang","last_name":"Ma"},{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","date_updated":"2021-01-12T08:19:24Z","citation":{"chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418.","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418","apa":"Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"_id":"848","type":"journal_article","status":"public","citation":{"apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318."},"date_updated":"2021-01-12T08:19:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","author":[{"first_name":"Dinara","last_name":"Usmanova","full_name":"Usmanova, Dinara"},{"last_name":"Ferretti","full_name":"Ferretti, Luca","first_name":"Luca"},{"first_name":"Inna","full_name":"Povolotskaya, Inna","last_name":"Povolotskaya"},{"first_name":"Peter","full_name":"Vlasov, Peter","last_name":"Vlasov"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"publist_id":"6804","title":"A model of substitution trajectories in sequence space and long-term protein evolution","abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"Oxford University Press","intvolume":" 32","month":"02","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Molecular Biology and Evolution","day":"01","page":"542 - 554","date_created":"2018-12-11T11:48:49Z","date_published":"2015-02-01T00:00:00Z","doi":"10.1093/molbev/msu318","volume":32,"issue":"2"},{"_id":"8498","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"status":"public","type":"journal_article","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699","apa":"Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699."},"date_updated":"2021-01-12T08:19:41Z","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","article_processing_charge":"No","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"last_name":"Zhang","full_name":"Zhang, K","first_name":"K"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]."}],"intvolume":" 28","month":"06","quality_controlled":"1","publisher":"IOP Publishing","language":[{"iso":"eng"}],"publication":"Nonlinearity","day":"30","publication_status":"published","year":"2015","publication_identifier":{"issn":["0951-7715","1361-6544"]},"date_created":"2020-09-18T10:46:43Z","date_published":"2015-06-30T00:00:00Z","issue":"8","volume":28,"doi":"10.1088/0951-7715/28/8/2699","page":"2699-2720"},{"author":[{"full_name":"Guardia, Marcel","last_name":"Guardia","first_name":"Marcel"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"}],"article_processing_charge":"No","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","date_updated":"2021-01-12T08:19:41Z","citation":{"chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499","apa":"Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"original","status":"public","_id":"8499","page":"71-149","issue":"1","doi":"10.4171/jems/499","date_published":"2015-02-05T00:00:00Z","volume":17,"date_created":"2020-09-18T10:46:50Z","publication_identifier":{"issn":["1435-9855"]},"year":"2015","publication_status":"published","day":"05","publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"European Mathematical Society Publishing House","month":"02","intvolume":" 17","abstract":[{"lang":"eng","text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214."},"oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science ","date_created":"2021-02-02T13:15:02Z","date_published":"2015-05-01T00:00:00Z","doi":"10.1126/sciadv.1400214","publication":"Science Advances","day":"01","year":"2015","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","_id":"9057","file_date_updated":"2021-02-02T13:22:19Z","ddc":["530"],"extern":"1","date_updated":"2023-02-23T13:47:52Z","intvolume":" 1","month":"05","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"4","volume":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-02-02T13:22:19Z","file_name":"2015_ScienceAdvances_Palacci.pdf","date_updated":"2021-02-02T13:22:19Z","file_size":2416780,"creator":"cziletti","checksum":"b97d62433581875c1b85210c5f6ae370","file_id":"9058","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"906","author":[{"first_name":"Oksana","full_name":"Arkhipova, Oksana V","last_name":"Arkhipova"},{"last_name":"Meer","full_name":"Meer, Margarita V","first_name":"Margarita"},{"first_name":"Galina","last_name":"Mikoulinskaia","full_name":"Mikoulinskaia, Galina V"},{"first_name":"Marina","full_name":"Zakharova, Marina V","last_name":"Zakharova"},{"last_name":"Galushko","full_name":"Galushko, Alexander S","first_name":"Alexander"},{"first_name":"Vasilii","full_name":"Akimenko, Vasilii K","last_name":"Akimenko"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"publist_id":"6742","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","date_updated":"2021-01-12T08:21:48Z","citation":{"mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5)."},"extern":1,"publisher":"Public Library of Science","quality_controlled":0,"intvolume":" 10","month":"05","abstract":[{"lang":"eng","text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1."}],"acknowledgement":"Funding: 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 under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","date_created":"2018-12-11T11:49:08Z","issue":"5","volume":10,"doi":"10.1371/journal.pone.0125888","date_published":"2015-05-11T00:00:00Z","year":"2015","publication_status":"published","publication":"PLoS One","day":"11"},{"page":"4760-4777","doi":"10.1002/2014jc010598","date_published":"2015-06-08T00:00:00Z","date_created":"2021-02-15T14:21:49Z","year":"2015","day":"08","publication":"Journal of Geophysical Research: Oceans","quality_controlled":"1","publisher":"American Geophysical Union","oa":1,"author":[{"first_name":"Adrien","last_name":"Lefauve","full_name":"Lefauve, Adrien"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"Melet, Angélique","last_name":"Melet","first_name":"Angélique"}],"article_processing_charge":"No","title":"A three-dimensional map of tidal dissipation over abyssal hills","citation":{"apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"7","volume":120,"publication_identifier":{"issn":["2169-9275"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"month":"06","intvolume":" 120","abstract":[{"text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.","lang":"eng"}],"oa_version":"Published Version","date_updated":"2022-01-24T13:45:41Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"9141"},{"citation":{"ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ivonne","full_name":"Sehring, Ivonne","last_name":"Sehring"},{"first_name":"Pierre","last_name":"Recho","full_name":"Recho, Pierre"},{"first_name":"Elsa","last_name":"Denker","full_name":"Denker, Elsa"},{"first_name":"Matthew","full_name":"Kourakis, Matthew","last_name":"Kourakis"},{"full_name":"Mathiesen, Birthe","last_name":"Mathiesen","first_name":"Birthe"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Bo","last_name":"Dong","full_name":"Dong, Bo"},{"full_name":"Jiang, Di","last_name":"Jiang","first_name":"Di"}],"publist_id":"6512","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","article_number":"e09206","year":"2015","has_accepted_license":"1","publication":"eLife","day":"21","date_created":"2018-12-11T11:49:15Z","date_published":"2015-10-21T00:00:00Z","doi":"10.7554/eLife.09206","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","date_updated":"2021-01-12T08:21:58Z","ddc":["539","570"],"extern":"1","file_date_updated":"2020-07-14T12:48:15Z","_id":"928","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-20T15:50:56Z","file_name":"2015_eLife_Sehring.pdf","date_updated":"2020-07-14T12:48:15Z","file_size":7202224,"creator":"dernst","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","file_id":"5769","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"volume":4,"abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events."}],"oa_version":"Published Version","intvolume":" 4","month":"10"},{"_id":"9575","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-23T14:01:28Z","extern":"1","abstract":[{"lang":"eng","text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"scopus_import":"1","intvolume":" 49","month":"11","publication_status":"published","publication_identifier":{"issn":["1571-0653"]},"language":[{"iso":"eng"}],"volume":49,"citation":{"apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","external_id":{"arxiv":["1501.04816"]},"author":[{"full_name":"Krivelevich, Michael","last_name":"Krivelevich","first_name":"Michael"},{"last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2015","publication":"Electronic Notes in Discrete Mathematics","day":"01","page":"181-187","date_created":"2021-06-21T06:40:34Z","date_published":"2015-11-01T00:00:00Z","doi":"10.1016/j.endm.2015.06.027"},{"title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","author":[{"full_name":"Leung, H.S.","last_name":"Leung","first_name":"H.S."},{"full_name":"Leung, P.S.S.","last_name":"Leung","first_name":"P.S.S."},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"A.H.W.","full_name":"Ngan, A.H.W.","last_name":"Ngan"}],"article_processing_charge":"No","extern":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009."},"date_updated":"2023-02-23T14:04:28Z","status":"public","type":"journal_article","article_type":"original","_id":"9673","doi":"10.1016/j.ijplas.2014.09.009","date_published":"2015-04-01T00:00:00Z","volume":67,"date_created":"2021-07-15T14:09:32Z","page":"1-25","day":"01","language":[{"iso":"eng"}],"publication":"International Journal of Plasticity","publication_identifier":{"issn":["0749-6419"]},"year":"2015","publication_status":"published","month":"04","intvolume":" 67","publisher":"Elsevier","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}]},{"article_number":"180102","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015)."},"title":"Solid-liquid interfacial free energy out of equilibrium","author":[{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"last_name":"Tribello","full_name":"Tribello, Gareth A.","first_name":"Gareth A."},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"external_id":{"arxiv":["1511.08668"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"01","publication":"Physical Review B - Condensed Matter and Materials Physics","year":"2015","doi":"10.1103/physrevb.92.180102","date_published":"2015-11-01T00:00:00Z","date_created":"2021-07-19T10:07:22Z","_id":"9688","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-08-09T12:38:49Z","oa_version":"Preprint","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"month":"11","intvolume":" 92","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"publication_status":"published","volume":92,"issue":"18"},{"_id":"9711","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001."},"date_updated":"2023-02-23T10:07:02Z","title":"Excel file containing the raw data for all figures","department":[{"_id":"ToBo"}],"author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"first_name":"Aysegul","last_name":"Guvenek","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","oa_version":"Published Version","month":"11","publisher":"Public Library of Science","day":"18","year":"2015","related_material":{"record":[{"status":"public","id":"1619","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.1002299.s001","date_published":"2015-11-18T00:00:00Z","date_created":"2021-07-23T11:53:50Z"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"month":"03","intvolume":" 84","scopus_import":"1","file":[{"date_created":"2018-12-12T10:18:29Z","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1823045,"checksum":"542a0b9b07e78050a81b35f26f0b82da","file_id":"5350","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":84,"issue":"3","related_material":{"record":[{"status":"public","id":"9720","relation":"research_data"}]},"_id":"1855","status":"public","pubrep_id":"460","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-02-23T14:06:09Z","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:45:19Z","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"03","publication":"Journal of Animal Ecology","has_accepted_license":"1","year":"2015","date_published":"2015-03-03T00:00:00Z","doi":"10.1111/1365-2656.12345","date_created":"2018-12-11T11:54:23Z","page":"615 - 624","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624."},"title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"first_name":"Jesicca","full_name":"Caspar, Jesicca","last_name":"Caspar"},{"last_name":"Theodorou","full_name":"Theodorou, Panagiotis","first_name":"Panagiotis"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"publist_id":"5245","external_id":{"pmid":["25646973"]},"article_processing_charge":"No"},{"_id":"1830","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-02-23T14:06:12Z","department":[{"_id":"SyCr"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"intvolume":" 370","month":"05","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"ec_funded":1,"issue":"1669","volume":370,"related_material":{"record":[{"relation":"research_data","id":"9721","status":"public"}]},"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"grant_number":"302004","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"},{"name":"Fellowship of Wissenschaftskolleg zu Berlin","_id":"25E24DB2-B435-11E9-9278-68D0E5697425"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015)."},"title":"Opposing effects of allogrooming on disease transmission in ant societies","external_id":{"pmid":["25870394"]},"article_processing_charge":"No","author":[{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"5273","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","oa":1,"publisher":"Royal Society, The","quality_controlled":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"26","year":"2015","date_created":"2018-12-11T11:54:15Z","doi":"10.1098/rstb.2014.0108","date_published":"2015-05-26T00:00:00Z"},{"article_processing_charge":"No","author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"last_name":"Marr","full_name":"Marr, Carsten","first_name":"Carsten"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","department":[{"_id":"SyCr"}],"citation":{"mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf."},"date_updated":"2023-02-23T10:16:22Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9721","date_created":"2021-07-26T09:38:36Z","date_published":"2015-12-29T00:00:00Z","related_material":{"record":[{"status":"public","id":"1830","relation":"used_in_publication"}]},"doi":"10.5061/dryad.dj2bf","year":"2015","day":"29","main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"oa":1,"publisher":"Dryad","month":"12","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"oa_version":"Published Version"},{"_id":"9718","type":"research_data_reference","status":"public","date_updated":"2023-02-23T10:16:13Z","citation":{"mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"last_name":"Mayo","full_name":"Mayo, Avraham E.","first_name":"Avraham E."},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"last_name":"Alon","full_name":"Alon, Uri","first_name":"Uri"}],"title":"Supporting information text","department":[{"_id":"GaTk"}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"03","year":"2015","day":"23","date_created":"2021-07-26T08:35:23Z","date_published":"2015-03-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1827"}]},"doi":"10.1371/journal.pcbi.1004055.s001"},{"volume":10,"related_material":{"record":[{"id":"9737","status":"public","relation":"research_data"}]},"issue":"6","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:15:30Z","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","creator":"system","date_updated":"2020-07-14T12:45:16Z","file_size":1850825,"checksum":"d20f26461ca575276ad3ed9ce4bfc787","file_id":"5150","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":1,"intvolume":" 10","month":"06","abstract":[{"lang":"eng","text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:16Z","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"date_updated":"2023-02-23T14:06:33Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"454","status":"public","_id":"1793","date_created":"2018-12-11T11:54:02Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657","year":"2015","has_accepted_license":"1","publication":"PLoS One","day":"01","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"},{"last_name":"Topp","full_name":"Topp, Christopher","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"publist_id":"5318","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","citation":{"ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e0127657"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"06","year":"2015","day":"01","doi":"10.1371/journal.pone.0127657.s001","date_published":"2015-06-01T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1793"}]},"date_created":"2021-07-28T06:20:13Z","_id":"9737","type":"research_data_reference","status":"public","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015)."},"date_updated":"2023-02-23T10:14:42Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"article_processing_charge":"No","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"title":"Root traits computed by DynamicRoots for the maize root shown in fig 2"},{"language":[{"iso":"eng"}],"file":[{"file_id":"5161","checksum":"b8aa66f450ff8de393014b87ec7d2efb","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:39Z","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":1811647,"creator":"system"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9718"},{"status":"public","id":"9773","relation":"research_data"}]},"issue":"3","volume":11,"oa_version":"Published Version","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"intvolume":" 11","month":"03","scopus_import":1,"ddc":["576"],"date_updated":"2023-02-23T14:07:51Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1827","pubrep_id":"452","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"PLoS Computational Biology","day":"23","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:14Z","doi":"10.1371/journal.pcbi.1004055","date_published":"2015-03-23T00:00:00Z","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3)."},"title":"Evolution of bow-tie architectures in biology","article_processing_charge":"No","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"last_name":"Alon","full_name":"Alon, Uri","first_name":"Uri"}],"publist_id":"5278","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]}]