[{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Usmanova","full_name":"Usmanova, Dinara","first_name":"Dinara"},{"full_name":"Ferretti, Luca","first_name":"Luca","last_name":"Ferretti"},{"full_name":"Povolotskaya, Inna","first_name":"Inna","last_name":"Povolotskaya"},{"last_name":"Vlasov","full_name":"Vlasov, Peter","first_name":"Peter"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"publication_status":"published","date_created":"2018-12-11T11:48:49Z","external_id":{"isi":["000350050700020"]},"date_updated":"2025-09-22T14:32:37Z","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2015-02-01T00:00:00Z","abstract":[{"lang":"eng","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."}],"intvolume":"        32","publist_id":"6804","month":"02","extern":"1","article_processing_charge":"No","publication":"Molecular Biology and Evolution","type":"journal_article","title":"A model of substitution trajectories in sequence space and long-term protein evolution","doi":"10.1093/molbev/msu318","day":"01","publisher":"Oxford University Press","page":"542 - 554","oa_version":"None","volume":32,"issue":"2","_id":"848","citation":{"ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. 2015;32(2):542-554. doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>","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.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>.","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,” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","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.","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., &#38; Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>."},"year":"2015"},{"publication":"Proceedings of the American Mathematical Society","article_processing_charge":"No","extern":"1","month":"12","year":"2015","citation":{"ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>.","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2015. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>.","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. 2015;144(4):1553-1560. doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>"},"_id":"8495","issue":"4","volume":144,"oa_version":"None","page":"1553-1560","doi":"10.1090/proc/12796","publisher":"American Mathematical Society","day":"21","title":"A note on micro-instability for Hamiltonian systems close to integrable","type":"journal_article","date_created":"2020-09-18T10:46:14Z","publication_status":"published","article_type":"letter_note","author":[{"last_name":"Bounemoura","first_name":"Abed","full_name":"Bounemoura, Abed"},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       144","quality_controlled":"1","abstract":[{"lang":"eng","text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting."}],"date_published":"2015-12-21T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-9939","1088-6826"]},"status":"public","date_updated":"2021-01-12T08:19:40Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"last_name":"Zhang","first_name":"K","full_name":"Zhang, K"}],"publication_status":"published","date_created":"2020-09-18T10:46:43Z","article_type":"original","date_updated":"2021-01-12T08:19:41Z","status":"public","publication_identifier":{"issn":["0951-7715","1361-6544"]},"intvolume":"        28","language":[{"iso":"eng"}],"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]."}],"quality_controlled":"1","date_published":"2015-06-30T00:00:00Z","month":"06","extern":"1","article_processing_charge":"No","publication":"Nonlinearity","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"type":"journal_article","page":"2699-2720","day":"30","publisher":"IOP Publishing","doi":"10.1088/0951-7715/28/8/2699","volume":28,"oa_version":"None","year":"2015","issue":"8","_id":"8498","citation":{"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.","mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>.","apa":"Kaloshin, V., &#38; Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” <i>Nonlinearity</i>, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>.","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. 2015;28(8):2699-2720. doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>"}},{"date_updated":"2021-01-12T08:19:41Z","quality_controlled":"1","date_published":"2015-02-05T00:00:00Z","abstract":[{"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 0<T<Kc.","lang":"eng"}],"language":[{"iso":"eng"}],"intvolume":"        17","publication_identifier":{"issn":["1435-9855"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2020-09-18T10:46:50Z","article_type":"original","author":[{"last_name":"Guardia","full_name":"Guardia, Marcel","first_name":"Marcel"},{"first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"}],"day":"05","publisher":"European Mathematical Society Publishing House","doi":"10.4171/jems/499","page":"71-149","type":"journal_article","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","_id":"8499","citation":{"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.","apa":"Guardia, M., &#38; Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>.","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House, 2015. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. 2015;17(1):71-149. doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>"},"issue":"1","year":"2015","oa_version":"None","volume":17,"extern":"1","month":"02","publication":"Journal of the European Mathematical Society","article_processing_charge":"No"},{"author":[{"last_name":"Kretz","first_name":"Colin","full_name":"Kretz, Colin A"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"full_name":"Soylemez, Onuralp","first_name":"Onuralp","last_name":"Soylemez"},{"full_name":"Yee, Andrew","first_name":"Andrew","last_name":"Yee"},{"last_name":"Desch","first_name":"Karl","full_name":"Desch, Karl C"},{"last_name":"Siemieniak","full_name":"Siemieniak, David R","first_name":"David"},{"last_name":"Tomberg","full_name":"Tomberg, Kärt","first_name":"Kärt"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Fan","full_name":"Meng, Fan","last_name":"Meng"},{"first_name":"David","full_name":"Ginsburg, David B","last_name":"Ginsburg"}],"publication_status":"published","date_created":"2018-12-11T11:48:55Z","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","date_updated":"2021-01-12T08:20:26Z","status":"public","intvolume":"       112","date_published":"2015-07-28T00:00:00Z","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"quality_controlled":0,"publist_id":"6783","month":"07","extern":1,"publication":"PNAS","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","type":"journal_article","page":"9328 - 9333","doi":"10.1073/pnas.1511328112","day":"28","publisher":"National Academy of Sciences","volume":112,"year":"2015","issue":"30","_id":"866","citation":{"ieee":"C. Kretz <i>et al.</i>, “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” <i>PNAS</i>, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>.","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>.","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. 2015;112(30):9328-9333. doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>"}},{"publication_status":"published","date_created":"2018-12-11T11:49:01Z","author":[{"last_name":"Kondrashov","first_name":"Dmitry","full_name":"Kondrashov, Dmitry A"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2015-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space."}],"quality_controlled":0,"intvolume":"        31","status":"public","date_updated":"2021-01-12T08:21:16Z","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) 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 BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","publication":"Trends in Genetics","extern":1,"publist_id":"6764","month":"01","issue":"1","_id":"886","citation":{"ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” <i>Trends in Genetics</i>, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>.","apa":"Kondrashov, D., &#38; Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. 2015;31(1):24-33. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>"},"year":"2015","volume":31,"publisher":"Elsevier","day":"01","doi":"10.1016/j.tig.2014.09.009","page":"24 - 33","type":"journal_article","title":"Topological features of rugged fitness landscapes in sequence space"},{"publication_status":"published","article_type":"original","author":[{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"last_name":"Liu","first_name":"Danni","full_name":"Liu, Danni"},{"first_name":"Pierre","full_name":"Legrand, Pierre","last_name":"Legrand"},{"last_name":"Velours","first_name":"Christophe","full_name":"Velours, Christophe"},{"full_name":"Corpet, Armelle","first_name":"Armelle","last_name":"Corpet"},{"first_name":"Albane","full_name":"Gaubert, Albane","last_name":"Gaubert"},{"first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","last_name":"Bakail"},{"full_name":"Moal-Raisin, Gwenaelle","first_name":"Gwenaelle","last_name":"Moal-Raisin"},{"full_name":"Guerois, Raphael","first_name":"Raphael","last_name":"Guerois"},{"last_name":"Compper","first_name":"Christel","full_name":"Compper, Christel"},{"full_name":"Besle, Arthur","first_name":"Arthur","last_name":"Besle"},{"first_name":"Berengère","full_name":"Guichard, Berengère","last_name":"Guichard"},{"last_name":"Almouzni","full_name":"Almouzni, Genevieve","first_name":"Genevieve"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-02-18T00:00:00Z","abstract":[{"text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.","lang":"eng"}],"status":"public","article_processing_charge":"No","pmid":1,"month":"02","issue":"3","_id":"9017","year":"2015","oa_version":"Published Version","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","date_created":"2021-01-19T11:01:01Z","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        43","publication_identifier":{"issn":["1362-4962","0305-1048"]},"date_updated":"2023-02-23T13:46:50Z","external_id":{"pmid":["25618846"]},"publication":"Nucleic Acids Research","extern":"1","citation":{"chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” <i>Nucleic Acids Research</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/nar/gkv021\">https://doi.org/10.1093/nar/gkv021</a>.","ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. <i>Nucleic Acids Research</i>. 2015;43(3):1905-1917. doi:<a href=\"https://doi.org/10.1093/nar/gkv021\">10.1093/nar/gkv021</a>","ieee":"N. Richet <i>et al.</i>, “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” <i>Nucleic Acids Research</i>, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkv021\">https://doi.org/10.1093/nar/gkv021</a>","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” <i>Nucleic Acids Research</i>, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:<a href=\"https://doi.org/10.1093/nar/gkv021\">10.1093/nar/gkv021</a>.","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917."},"volume":43,"day":"18","publisher":"Oxford University Press","doi":"10.1093/nar/gkv021","page":"1905-1917","type":"journal_article"},{"external_id":{"arxiv":["1505.05111"],"pmid":["26601175"]},"date_updated":"2023-02-23T13:47:52Z","has_accepted_license":"1","publication_identifier":{"issn":["2375-2548"]},"intvolume":"         1","language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_number":"e1400214","date_created":"2021-02-02T13:15:02Z","file_date_updated":"2021-02-02T13:22:19Z","type":"journal_article","day":"01","doi":"10.1126/sciadv.1400214","publisher":"American Association for the Advancement of Science ","volume":1,"citation":{"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).","ieee":"J. A. Palacci <i>et al.</i>, “Artificial rheotaxis,” <i>Science Advances</i>, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” <i>Science Advances</i>, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>.","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.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. <i>Science Advances</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. <i>Science Advances</i>. 2015;1(4). doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” <i>Science Advances</i>. American Association for the Advancement of Science , 2015. <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>."},"extern":"1","publication":"Science Advances","ddc":["530"],"arxiv":1,"status":"public","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"}],"scopus_import":"1","date_published":"2015-05-01T00:00:00Z","oa":1,"file":[{"creator":"cziletti","date_created":"2021-02-02T13:22:19Z","access_level":"open_access","content_type":"application/pdf","file_size":2416780,"relation":"main_file","file_id":"9058","checksum":"b97d62433581875c1b85210c5f6ae370","success":1,"file_name":"2015_ScienceAdvances_Palacci.pdf","date_updated":"2021-02-02T13:22:19Z"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","last_name":"Palacci"},{"last_name":"Sacanna","full_name":"Sacanna, Stefano","first_name":"Stefano"},{"first_name":"Anaïs","full_name":"Abramian, Anaïs","last_name":"Abramian"},{"last_name":"Barral","full_name":"Barral, Jérémie","first_name":"Jérémie"},{"first_name":"Kasey","full_name":"Hanson, Kasey","last_name":"Hanson"},{"full_name":"Grosberg, Alexander Y.","first_name":"Alexander Y.","last_name":"Grosberg"},{"full_name":"Pine, David J.","first_name":"David J.","last_name":"Pine"},{"last_name":"Chaikin","full_name":"Chaikin, Paul M.","first_name":"Paul M."}],"publication_status":"published","article_type":"original","title":"Artificial rheotaxis","oa_version":"Published Version","year":"2015","issue":"4","_id":"9057","month":"05","pmid":1,"article_processing_charge":"No"},{"author":[{"full_name":"Arkhipova, Oksana V","first_name":"Oksana","last_name":"Arkhipova"},{"last_name":"Meer","full_name":"Meer, Margarita V","first_name":"Margarita"},{"last_name":"Mikoulinskaia","full_name":"Mikoulinskaia, Galina V","first_name":"Galina"},{"last_name":"Zakharova","full_name":"Zakharova, Marina V","first_name":"Marina"},{"first_name":"Alexander","full_name":"Galushko, Alexander S","last_name":"Galushko"},{"last_name":"Akimenko","full_name":"Akimenko, Vasilii K","first_name":"Vasilii"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"date_created":"2018-12-11T11:49:08Z","publication_status":"published","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)"},"status":"public","intvolume":"        10","quality_controlled":0,"date_published":"2015-05-11T00:00:00Z","abstract":[{"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.","lang":"eng"}],"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_updated":"2021-01-12T08:21:48Z","publication":"PLoS One","month":"05","publist_id":"6742","extern":1,"volume":10,"year":"2015","issue":"5","_id":"906","citation":{"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. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0125888\">10.1371/journal.pone.0125888</a>","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.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0125888\">https://doi.org/10.1371/journal.pone.0125888</a>.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","ieee":"O. Arkhipova <i>et al.</i>, “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0125888\">10.1371/journal.pone.0125888</a>.","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., &#38; Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0125888\">https://doi.org/10.1371/journal.pone.0125888</a>","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)."},"title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","type":"journal_article","doi":"10.1371/journal.pone.0125888","day":"11","publisher":"Public Library of Science"},{"month":"06","article_processing_charge":"No","title":"A three-dimensional map of tidal dissipation over abyssal hills","year":"2015","_id":"9141","issue":"7","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publication_status":"published","article_type":"original","author":[{"first_name":"Adrien","full_name":"Lefauve, Adrien","last_name":"Lefauve"},{"first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"full_name":"Melet, Angélique","first_name":"Angélique","last_name":"Melet"}],"abstract":[{"lang":"eng","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."}],"date_published":"2015-06-08T00:00:00Z","status":"public","extern":"1","main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"publication":"Journal of Geophysical Research: Oceans","page":"4760-4777","day":"08","publisher":"American Geophysical Union","doi":"10.1002/2014jc010598","type":"journal_article","citation":{"ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. 2015;120(7):4760-4777. doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","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.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>.","apa":"Lefauve, A., Muller, C. J., &#38; Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015."},"volume":120,"date_created":"2021-02-15T14:21:49Z","date_updated":"2022-01-24T13:45:41Z","intvolume":"       120","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2169-9275"]}},{"publication":"Applied Thermal Engineering","article_processing_charge":"No","extern":"1","publist_id":"6514","month":"02","year":"2015","citation":{"ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. <i>Applied Thermal Engineering</i>. 2015;76:1-8. doi:<a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">10.1016/j.applthermaleng.2014.10.009</a>","chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” <i>Applied Thermal Engineering</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">https://doi.org/10.1016/j.applthermaleng.2014.10.009</a>.","short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” <i>Applied Thermal Engineering</i>, vol. 76. Elsevier, pp. 1–8, 2015.","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” <i>Applied Thermal Engineering</i>, vol. 76, Elsevier, 2015, pp. 1–8, doi:<a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">10.1016/j.applthermaleng.2014.10.009</a>.","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8.","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., &#38; Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. <i>Applied Thermal Engineering</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">https://doi.org/10.1016/j.applthermaleng.2014.10.009</a>"},"_id":"924","volume":76,"oa_version":"None","page":"1 - 8","day":"05","publisher":"Elsevier","doi":"10.1016/j.applthermaleng.2014.10.009","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","type":"journal_article","publication_status":"published","date_created":"2018-12-11T11:49:13Z","author":[{"last_name":"Boubaker","full_name":"Boubaker, Riadh","first_name":"Riadh"},{"last_name":"Platel","first_name":"Vincent","full_name":"Platel, Vincent"},{"last_name":"Bergès","first_name":"Alexis","full_name":"Bergès, Alexis"},{"last_name":"Bancelin","first_name":"Mathieu","full_name":"Bancelin, Mathieu"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        76","abstract":[{"text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper.","lang":"eng"}],"date_published":"2015-02-05T00:00:00Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2021-01-12T08:21:56Z","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099)."},{"publication":"eLife","extern":"1","publist_id":"6512","citation":{"short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>, vol. 4, e09206, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>.","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>","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.","ieee":"I. Sehring <i>et al.</i>, “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>","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.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>."},"volume":4,"doi":"10.7554/eLife.09206","day":"21","publisher":"eLife Sciences Publications","type":"journal_article","date_created":"2018-12-11T11:49:15Z","file_date_updated":"2020-07-14T12:48:15Z","article_number":"e09206","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)"},"intvolume":"         4","language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2021-01-12T08:21:58Z","has_accepted_license":"1","month":"10","year":"2015","_id":"928","oa_version":"Published Version","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","publication_status":"published","author":[{"last_name":"Sehring","full_name":"Sehring, Ivonne","first_name":"Ivonne"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Denker","full_name":"Denker, Elsa","first_name":"Elsa"},{"full_name":"Kourakis, Matthew","first_name":"Matthew","last_name":"Kourakis"},{"first_name":"Birthe","full_name":"Mathiesen, Birthe","last_name":"Mathiesen"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"last_name":"Jiang","first_name":"Di","full_name":"Jiang, Di"}],"file":[{"file_id":"5769","relation":"main_file","file_size":7202224,"content_type":"application/pdf","creator":"dernst","date_created":"2018-12-20T15:50:56Z","access_level":"open_access","file_name":"2015_eLife_Sehring.pdf","date_updated":"2020-07-14T12:48:15Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"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.","lang":"eng"}],"date_published":"2015-10-21T00:00:00Z","status":"public","ddc":["539","570"]},{"publist_id":"6513","month":"07","extern":"1","article_processing_charge":"No","publication":"PNAS","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","type":"journal_article","page":"8620 - 8625","day":"14","doi":"10.1073/pnas.1504762112","publisher":"National Academy of Sciences","volume":112,"oa_version":"None","year":"2015","citation":{"chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>.","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. 2015;112(28):8620-8625. doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” <i>PNAS</i>, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>.","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., &#38; Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625."},"_id":"929","issue":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Dong","full_name":"Dong, Bo","first_name":"Bo"},{"last_name":"Recho","full_name":"Recho, Pierre","first_name":"Pierre"},{"first_name":"Jean","full_name":"Joanny, Jean","last_name":"Joanny"},{"last_name":"Hayashi","first_name":"Shigeo","full_name":"Hayashi, Shigeo"}],"publication_status":"published","date_created":"2018-12-11T11:49:15Z","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","date_updated":"2021-01-12T08:21:59Z","status":"public","intvolume":"       112","abstract":[{"lang":"eng","text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. "}],"language":[{"iso":"eng"}],"date_published":"2015-07-14T00:00:00Z"},{"date_created":"2018-12-11T11:49:16Z","external_id":{"pmid":["26627719"]},"date_updated":"2021-01-12T08:22:01Z","intvolume":"       112","quality_controlled":"1","language":[{"iso":"eng"}],"publist_id":"6511","extern":"1","main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"publication":"PNAS","type":"journal_article","page":"15314 - 15319","day":"15","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1510973112","volume":112,"citation":{"ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. 2015;112(50):15314-15319. doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” <i>PNAS</i>, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., &#38; Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"García","full_name":"García, Simón","first_name":"Simón"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"},{"first_name":"Jean","full_name":"Joanny, Jean","last_name":"Joanny"},{"last_name":"Silberzan","first_name":"Pascal","full_name":"Silberzan, Pascal"},{"first_name":"Nir","full_name":"Gov, Nir","last_name":"Gov"}],"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data."}],"date_published":"2015-12-15T00:00:00Z","month":"12","pmid":1,"title":"Physics of active jamming during collective cellular motion in a monolayer","oa_version":"None","year":"2015","issue":"50","_id":"933"},{"pmid":1,"month":"12","article_processing_charge":"No","title":"Evolution and function of genomic imprinting in plants","year":"2015","issue":"24","_id":"9532","oa_version":"Published Version","file":[{"success":1,"checksum":"086a88cfca4677646da26ed960cb02e9","date_updated":"2021-06-08T09:55:10Z","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","date_created":"2021-06-08T09:55:10Z","file_id":"9533","file_size":1116846,"relation":"main_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"article_type":"review","publication_status":"published","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"ddc":["570"],"abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"date_published":"2015-12-15T00:00:00Z","scopus_import":"1","status":"public","extern":"1","publication":"Genes and Development","page":"2517–2531","day":"15","publisher":"Cold Spring Harbor Laboratory Press","doi":"10.1101/gad.269902.115","type":"journal_article","citation":{"mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>"},"volume":29,"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_created":"2021-06-08T09:56:24Z","file_date_updated":"2021-06-08T09:55:10Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:58:15Z","has_accepted_license":"1","external_id":{"pmid":["26680300"]},"intvolume":"        29","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"article_type":"original","publication_status":"published","author":[{"first_name":"Michael","full_name":"Krivelevich, Michael","last_name":"Krivelevich"},{"last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"arxiv":1,"abstract":[{"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.","lang":"eng"}],"date_published":"2015-11-01T00:00:00Z","scopus_import":"1","status":"public","month":"11","article_processing_charge":"No","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","year":"2015","_id":"9575","oa_version":"Preprint","date_created":"2021-06-21T06:40:34Z","date_updated":"2023-02-23T14:01:28Z","external_id":{"arxiv":["1501.04816"]},"intvolume":"        49","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1571-0653"]},"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"publication":"Electronic Notes in Discrete Mathematics","page":"181-187","publisher":"Elsevier","day":"01","doi":"10.1016/j.endm.2015.06.027","type":"journal_article","citation":{"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,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49. Elsevier, pp. 181–187, 2015.","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.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49, Elsevier, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. 2015;49:181-187. doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>."},"volume":49},{"year":"2015","citation":{"short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>, vol. 67, Elsevier, 2015, pp. 1–25, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>.","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.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., &#38; Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>","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,” <i>International Journal of Plasticity</i>, vol. 67. Elsevier, pp. 1–25, 2015.","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. <i>International Journal of Plasticity</i>. 2015;67:1-25. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>","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.” <i>International Journal of Plasticity</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>."},"_id":"9673","volume":67,"oa_version":"None","page":"1-25","doi":"10.1016/j.ijplas.2014.09.009","publisher":"Elsevier","day":"01","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","type":"journal_article","publication":"International Journal of Plasticity","article_processing_charge":"No","extern":"1","month":"04","intvolume":"        67","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"date_published":"2015-04-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["0749-6419"]},"date_updated":"2023-02-23T14:04:28Z","date_created":"2021-07-15T14:09:32Z","article_type":"original","publication_status":"published","author":[{"first_name":"H.S.","full_name":"Leung, H.S.","last_name":"Leung"},{"first_name":"P.S.S.","full_name":"Leung, P.S.S.","last_name":"Leung"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"last_name":"Ngan","full_name":"Ngan, A.H.W.","first_name":"A.H.W."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"year":"2015","issue":"3","_id":"9684","citation":{"short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001.","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., &#38; Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>.","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3. IOP Publishing, 2015.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. 2015;23(3). doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>."},"volume":23,"oa_version":"None","publisher":"IOP Publishing","day":"01","doi":"10.1088/0965-0393/23/3/035001","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","type":"journal_article","publication":"Modelling and Simulation in Materials Science and Engineering","article_processing_charge":"No","extern":"1","month":"04","intvolume":"        23","abstract":[{"lang":"eng","text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept."}],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","date_published":"2015-04-01T00:00:00Z","status":"public","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"date_updated":"2023-02-23T14:04:54Z","publication_status":"published","date_created":"2021-07-19T09:11:12Z","article_type":"original","article_number":"035001","author":[{"full_name":"Leung, P S S","first_name":"P S S","last_name":"Leung"},{"last_name":"Leung","first_name":"H S","full_name":"Leung, H S"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"first_name":"A H W","full_name":"Ngan, A H W","last_name":"Ngan"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"arxiv":1,"status":"public","scopus_import":"1","abstract":[{"lang":"eng","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."}],"date_published":"2015-11-01T00:00:00Z","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"article_type":"original","publication_status":"published","title":"Solid-liquid interfacial free energy out of equilibrium","oa_version":"Preprint","year":"2015","_id":"9688","issue":"18","month":"11","article_processing_charge":"No","external_id":{"arxiv":["1511.08668"]},"date_updated":"2021-08-09T12:38:49Z","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"intvolume":"        92","language":[{"iso":"eng"}],"quality_controlled":"1","article_number":"180102","date_created":"2021-07-19T10:07:22Z","type":"journal_article","publisher":"American Physical Society","doi":"10.1103/physrevb.92.180102","day":"01","volume":92,"citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2015;92(18). doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>.","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.","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, 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)."},"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.08668"}],"publication":"Physical Review B - Condensed Matter and Materials Physics"},{"doi":"10.1371/journal.pbio.1002299.s001","day":"18","publisher":"Public Library of Science","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1619"}]},"title":"Excel file containing the raw data for all figures","type":"research_data_reference","year":"2015","citation":{"apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>","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, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","mla":"Chevereau, Guillaume, et al. <i>Excel File Containing the Raw Data for All Figures</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","ieee":"G. Chevereau <i>et al.</i>, “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).","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. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>"},"_id":"9711","oa_version":"Published Version","month":"11","article_processing_charge":"No","date_updated":"2025-09-23T09:58:54Z","date_published":"2015-11-18T00:00:00Z","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-23T11:53:50Z","author":[{"last_name":"Chevereau","first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Batur","first_name":"Tugce","full_name":"Batur, Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan"},{"full_name":"Toprak, Erdal","first_name":"Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"department":[{"_id":"ToBo"}]}]