[{"publisher":"European Mathematical Society Publishing House","month":"01","_id":"1313","doi":"10.4171/IFB/331","type":"journal_article","publication_status":"published","title":"Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach","acknowledgement":"This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No.  CH-SMM-01/0.","date_published":"2015-01-01T00:00:00Z","author":[{"last_name":"Fischer","first_name":"Julian L","full_name":"Julian Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}],"publication":"Interfaces and Free Boundaries","issue":"1","publist_id":"5956","date_updated":"2021-01-12T06:49:48Z","year":"2015","date_created":"2018-12-11T11:51:19Z","quality_controlled":0,"page":"1 - 20","extern":1,"abstract":[{"text":"We present an algorithm for the derivation of lower bounds on support propagation for a certain class of nonlinear parabolic equations. We proceed by combining the ideas in some recent papers by the author with the algorithmic construction of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination problem. Due to its complexity, the quantifier elimination problem cannot be solved by present exact algorithms. However, by tackling the quantifier elimination problem numerically, in the case of the thin-film equation we are able to improve recent results by the author in the regime of strong slippage n ∈ (1, 2). For certain second-order doubly nonlinear parabolic equations, we are able to extend the known lower bounds on free boundary propagation to the case of irregular oscillatory initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion equation, resulting in an upper bound on the time which it takes for the support to reach every point in the domain.","lang":"eng"}],"volume":17,"status":"public","day":"01","intvolume":"        17","citation":{"chicago":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” <i>Interfaces and Free Boundaries</i>. European Mathematical Society Publishing House, 2015. <a href=\"https://doi.org/10.4171/IFB/331\">https://doi.org/10.4171/IFB/331</a>.","apa":"Fischer, J. L. (2015). Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. <i>Interfaces and Free Boundaries</i>. European Mathematical Society Publishing House. <a href=\"https://doi.org/10.4171/IFB/331\">https://doi.org/10.4171/IFB/331</a>","ista":"Fischer JL. 2015. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 17(1), 1–20.","ieee":"J. L. Fischer, “Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach,” <i>Interfaces and Free Boundaries</i>, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 1–20, 2015.","mla":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” <i>Interfaces and Free Boundaries</i>, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 1–20, doi:<a href=\"https://doi.org/10.4171/IFB/331\">10.4171/IFB/331</a>.","short":"J.L. Fischer, Interfaces and Free Boundaries 17 (2015) 1–20.","ama":"Fischer JL. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. <i>Interfaces and Free Boundaries</i>. 2015;17(1):1-20. doi:<a href=\"https://doi.org/10.4171/IFB/331\">10.4171/IFB/331</a>"}},{"intvolume":"        53","citation":{"ama":"Fischer JL. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. <i>SIAM Journal on Numerical Analysis</i>. 2015;53(5):2178-2205. doi:<a href=\"https://doi.org/10.1137/140966654\">10.1137/140966654</a>","short":"J.L. Fischer, SIAM Journal on Numerical Analysis 53 (2015) 2178–2205.","ieee":"J. L. Fischer, “A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation,” <i>SIAM Journal on Numerical Analysis</i>, vol. 53, no. 5. Society for Industrial and Applied Mathematics , pp. 2178–2205, 2015.","mla":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” <i>SIAM Journal on Numerical Analysis</i>, vol. 53, no. 5, Society for Industrial and Applied Mathematics , 2015, pp. 2178–205, doi:<a href=\"https://doi.org/10.1137/140966654\">10.1137/140966654</a>.","ista":"Fischer JL. 2015. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 53(5), 2178–2205.","chicago":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics , 2015. <a href=\"https://doi.org/10.1137/140966654\">https://doi.org/10.1137/140966654</a>.","apa":"Fischer, J. L. (2015). A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/140966654\">https://doi.org/10.1137/140966654</a>"},"day":"01","status":"public","extern":"1","volume":53,"abstract":[{"lang":"eng","text":"We derive a posteriori estimates for the modeling error caused by the assumption of perfect incompressibility in the incompressible Navier-Stokes equation: Real fluids are never perfectly incompressible but always feature at least some low amount of compressibility. Thus, their behavior is described by the compressible Navier-Stokes equation, the pressure being a steep function of the density. We rigorously estimate the difference between an approximate solution to the incompressible Navier-Stokes equation and any weak solution to the compressible Navier-Stokes equation in the sense of Lions (without assuming any additional regularity of solutions). Heuristics and numerical results suggest that our error estimates are of optimal order in the case of &quot;well-behaved&quot; flows and divergence-free approximations of the velocity field. Thus, we expect our estimates to justify the idealization of fluids as perfectly incompressible also in practical situations."}],"year":"2015","date_created":"2018-12-11T11:51:19Z","page":"2178 - 2205","quality_controlled":"1","date_updated":"2021-01-12T06:49:49Z","issue":"5","publication":"SIAM Journal on Numerical Analysis","publist_id":"5957","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","full_name":"Fischer, Julian L","last_name":"Fischer"}],"oa_version":"None","acknowledgement":"The research of the author was supported by the Lithuanian-Swiss cooperation program under the project agreement CH-SMM-01/0.","date_published":"2015-01-01T00:00:00Z","publication_status":"published","language":[{"iso":"eng"}],"title":"A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation","type":"journal_article","_id":"1314","month":"01","doi":"10.1137/140966654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics "},{"day":"01","citation":{"mla":"Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 218, no. 1, Springer, 2015, pp. 553–87, doi:<a href=\"https://doi.org/10.1007/s00205-015-0866-x\">10.1007/s00205-015-0866-x</a>.","ieee":"J. L. Fischer, “Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 218, no. 1. Springer, pp. 553–587, 2015.","ista":"Fischer JL. 2015. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 218(1), 553–587.","apa":"Fischer, J. L. (2015). Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-015-0866-x\">https://doi.org/10.1007/s00205-015-0866-x</a>","chicago":"Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00205-015-0866-x\">https://doi.org/10.1007/s00205-015-0866-x</a>.","ama":"Fischer JL. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. <i>Archive for Rational Mechanics and Analysis</i>. 2015;218(1):553-587. doi:<a href=\"https://doi.org/10.1007/s00205-015-0866-x\">10.1007/s00205-015-0866-x</a>","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 218 (2015) 553–587."},"intvolume":"       218","date_updated":"2021-01-12T06:49:50Z","date_created":"2018-12-11T11:51:20Z","year":"2015","quality_controlled":0,"page":"553 - 587","extern":1,"abstract":[{"lang":"eng","text":"In the present work we introduce the notion of a renormalized solution for reaction–diffusion systems with entropy-dissipating reactions. We establish the global existence of renormalized solutions. In the case of integrable reaction terms our notion of a renormalized solution reduces to the usual notion of a weak solution. Our existence result in particular covers all reaction–diffusion systems involving a single reversible reaction with mass-action kinetics and (possibly species-dependent) Fick-law diffusion; more generally, it covers the case of systems of reversible reactions with mass-action kinetics which satisfy the detailed balance condition. For such equations the existence of any kind of solution in general was an open problem, thereby motivating the study of renormalized solutions."}],"volume":218,"status":"public","acknowledgement":"This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No. CH-SMM-01/0.","date_published":"2015-10-01T00:00:00Z","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","full_name":"Julian Fischer","last_name":"Fischer"}],"issue":"1","publication":"Archive for Rational Mechanics and Analysis","publist_id":"5955","publisher":"Springer","_id":"1316","month":"10","doi":"10.1007/s00205-015-0866-x","type":"journal_article","publication_status":"published","title":"Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems"},{"issue":"2","publication":"Journal of Allergy and Clinical Immunology","author":[{"full_name":"Einhorn, Lukas","first_name":"Lukas","last_name":"Einhorn"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","last_name":"Fazekas","first_name":"Judit","full_name":"Fazekas, Judit"},{"full_name":"Muhr, Martina","first_name":"Martina","last_name":"Muhr"},{"last_name":"Schoos","full_name":"Schoos, Alexandra","first_name":"Alexandra"},{"full_name":"Oida, Kumiko","first_name":"Kumiko","last_name":"Oida"},{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer"},{"full_name":"Panakova, Lucia","first_name":"Lucia","last_name":"Panakova"},{"last_name":"Manzano-Szalai","full_name":"Manzano-Szalai, Krisztina","first_name":"Krisztina"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"oa_version":"None","date_published":"2015-02-01T00:00:00Z","title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.jaci.2014.12.1263","_id":"8242","month":"02","publisher":"Elsevier","publication_identifier":{"issn":["0091-6749"]},"citation":{"short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. <i>Journal of Allergy and Clinical Immunology</i>. 2015;135(2). doi:<a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">10.1016/j.jaci.2014.12.1263</a>","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101.","apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">https://doi.org/10.1016/j.jaci.2014.12.1263</a>","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">https://doi.org/10.1016/j.jaci.2014.12.1263</a>.","mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 135, no. 2, AB101, Elsevier, 2015, doi:<a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">10.1016/j.jaci.2014.12.1263</a>.","ieee":"L. Einhorn <i>et al.</i>, “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 135, no. 2. Elsevier, 2015."},"intvolume":"       135","day":"01","article_processing_charge":"No","article_number":"AB101","status":"public","volume":135,"extern":"1","quality_controlled":"1","year":"2015","date_created":"2020-08-10T11:54:09Z","date_updated":"2021-01-12T08:17:42Z"},{"day":"20","citation":{"ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. <i>Bio-protocol</i>. 2015;5(8). doi:<a href=\"https://doi.org/10.21769/BioProtoc.1446\">10.21769/BioProtoc.1446</a>","short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015).","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” <i>Bio-Protocol</i>, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:<a href=\"https://doi.org/10.21769/BioProtoc.1446\">10.21769/BioProtoc.1446</a>.","ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” <i>Bio-protocol</i>, vol. 5, no. 8. Bio-protocol LLC, 2015.","apa":"Marhavý, P., &#38; Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. <i>Bio-Protocol</i>. Bio-protocol LLC. <a href=\"https://doi.org/10.21769/BioProtoc.1446\">https://doi.org/10.21769/BioProtoc.1446</a>","ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8).","chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” <i>Bio-Protocol</i>. Bio-protocol LLC, 2015. <a href=\"https://doi.org/10.21769/BioProtoc.1446\">https://doi.org/10.21769/BioProtoc.1446</a>."},"intvolume":"         5","date_updated":"2021-01-12T08:18:07Z","quality_controlled":0,"date_created":"2018-12-11T11:48:44Z","year":"2015","abstract":[{"lang":"eng","text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis."}],"volume":5,"extern":1,"status":"public","date_published":"2015-04-20T00:00:00Z","acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","author":[{"last_name":"Marhavy","first_name":"Peter","full_name":"Peter Marhavy","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","first_name":"Eva","last_name":"Benková"}],"issue":"8","publication":"Bio-protocol","publist_id":"6816","publisher":"Bio-protocol LLC","doi":"10.21769/BioProtoc.1446","_id":"832","month":"04","type":"journal_article","title":"Real time analysis of lateral root organogenesis in arabidopsis","publication_status":"published"},{"article_number":"8361","status":"public","abstract":[{"lang":"eng","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."}],"volume":6,"extern":"1","quality_controlled":"1","date_created":"2020-09-18T10:07:36Z","year":"2015","date_updated":"2021-01-12T08:19:24Z","publication_identifier":{"issn":["2041-1723"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"citation":{"mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” <i>Nature Communications</i>, vol. 6, 8361, Springer Nature, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9361\">10.1038/ncomms9361</a>.","ieee":"P. Ma <i>et al.</i>, “Observing the overall rocking motion of a protein in a crystal,” <i>Nature Communications</i>, vol. 6. Springer Nature, 2015.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms9361\">https://doi.org/10.1038/ncomms9361</a>","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.” <i>Nature Communications</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ncomms9361\">https://doi.org/10.1038/ncomms9361</a>.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9361\">10.1038/ncomms9361</a>","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)."},"intvolume":"         6","day":"05","article_processing_charge":"No","title":"Observing the overall rocking motion of a protein in a crystal","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8456","month":"10","doi":"10.1038/ncomms9361","publisher":"Springer Nature","publication":"Nature Communications","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"first_name":"Yi","full_name":"Xue, Yi","last_name":"Xue"},{"full_name":"Coquelle, Nicolas","first_name":"Nicolas","last_name":"Coquelle"},{"last_name":"Haller","first_name":"Jens D.","full_name":"Haller, Jens D."},{"first_name":"Tairan","full_name":"Yuwen, Tairan","last_name":"Yuwen"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"last_name":"Mikhailovskii","first_name":"Oleg","full_name":"Mikhailovskii, Oleg"},{"first_name":"Dieter","full_name":"Willbold, Dieter","last_name":"Willbold"},{"last_name":"Colletier","first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul"}],"oa_version":"Published Version","date_published":"2015-10-05T00:00:00Z"},{"oa_version":"None","date_published":"2015-09-10T00:00:00Z","publication":"eMagRes","issue":"3","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul"}],"_id":"8457","month":"09","doi":"10.1002/9780470034590.emrstm1418","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","language":[{"iso":"eng"}],"publication_status":"published","title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","type":"journal_article","article_type":"original","day":"10","article_processing_charge":"No","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"citation":{"chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” <i>EMagRes</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">https://doi.org/10.1002/9780470034590.emrstm1418</a>.","apa":"Ma, P., &#38; Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. <i>EMagRes</i>. Wiley. <a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">https://doi.org/10.1002/9780470034590.emrstm1418</a>","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” <i>eMagRes</i>, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” <i>EMagRes</i>, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:<a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">10.1002/9780470034590.emrstm1418</a>.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. <i>eMagRes</i>. 2015;4(3):699-708. doi:<a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">10.1002/9780470034590.emrstm1418</a>"},"intvolume":"         4","year":"2015","date_created":"2020-09-18T10:07:45Z","page":"699-708","quality_controlled":"1","date_updated":"2021-01-12T08:19:24Z","status":"public","extern":"1","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"}],"volume":4},{"citation":{"short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","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>","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>","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>.","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.","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>.","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."},"intvolume":"        32","day":"01","extern":"1","volume":32,"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"}],"status":"public","date_updated":"2021-01-12T08:19:33Z","date_created":"2018-12-11T11:48:49Z","year":"2015","quality_controlled":"1","page":"542 - 554","author":[{"last_name":"Usmanova","full_name":"Usmanova, Dinara","first_name":"Dinara"},{"first_name":"Luca","full_name":"Ferretti, Luca","last_name":"Ferretti"},{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"last_name":"Vlasov","full_name":"Vlasov, Peter","first_name":"Peter"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"issue":"2","publist_id":"6804","publication":"Molecular Biology and Evolution","date_published":"2015-02-01T00:00:00Z","oa_version":"None","type":"journal_article","publication_status":"published","language":[{"iso":"eng"}],"title":"A model of substitution trajectories in sequence space and long-term protein evolution","publisher":"Oxford University Press","_id":"848","doi":"10.1093/molbev/msu318","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"21","article_processing_charge":"No","publication_identifier":{"issn":["0002-9939","1088-6826"]},"intvolume":"       144","citation":{"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>","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","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.","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>","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>."},"page":"1553-1560","quality_controlled":"1","date_created":"2020-09-18T10:46:14Z","year":"2015","date_updated":"2021-01-12T08:19:40Z","status":"public","abstract":[{"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.","lang":"eng"}],"volume":144,"extern":"1","oa_version":"None","date_published":"2015-12-21T00:00:00Z","issue":"4","publication":"Proceedings of the American Mathematical Society","author":[{"last_name":"Bounemoura","full_name":"Bounemoura, Abed","first_name":"Abed"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1090/proc/12796","_id":"8495","month":"12","publisher":"American Mathematical Society","title":"A note on micro-instability for Hamiltonian systems close to integrable","language":[{"iso":"eng"}],"publication_status":"published","article_type":"letter_note","type":"journal_article"},{"article_type":"original","type":"journal_article","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","publication_status":"published","language":[{"iso":"eng"}],"publisher":"IOP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1088/0951-7715/28/8/2699","_id":"8498","month":"06","author":[{"full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"full_name":"Zhang, K","first_name":"K","last_name":"Zhang"}],"publication":"Nonlinearity","issue":"8","date_published":"2015-06-30T00:00:00Z","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]."}],"volume":28,"extern":"1","status":"public","date_updated":"2021-01-12T08:19:41Z","quality_controlled":"1","page":"2699-2720","date_created":"2020-09-18T10:46:43Z","year":"2015","citation":{"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.","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>.","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.” <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>.","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>","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>","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720."},"intvolume":"        28","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"publication_identifier":{"issn":["0951-7715","1361-6544"]},"article_processing_charge":"No","day":"30"},{"volume":17,"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"}],"extern":"1","status":"public","date_updated":"2021-01-12T08:19:41Z","quality_controlled":"1","page":"71-149","year":"2015","date_created":"2020-09-18T10:46:50Z","citation":{"short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","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>","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>.","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>","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.","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>."},"intvolume":"        17","publication_identifier":{"issn":["1435-9855"]},"article_processing_charge":"No","day":"05","article_type":"original","type":"journal_article","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","publication_status":"published","language":[{"iso":"eng"}],"publisher":"European Mathematical Society Publishing House","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8499","month":"02","doi":"10.4171/jems/499","author":[{"first_name":"Marcel","full_name":"Guardia, Marcel","last_name":"Guardia"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim"}],"publication":"Journal of the European Mathematical Society","issue":"1","date_published":"2015-02-05T00:00:00Z","oa_version":"None"},{"extern":1,"abstract":[{"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.","lang":"eng"}],"volume":112,"status":"public","date_updated":"2021-01-12T08:20:26Z","year":"2015","date_created":"2018-12-11T11:48:55Z","quality_controlled":0,"page":"9328 - 9333","intvolume":"       112","citation":{"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>","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.","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>.","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.","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>","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>.","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."},"day":"28","type":"journal_article","publication_status":"published","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","publisher":"National Academy of Sciences","month":"07","_id":"866","doi":"10.1073/pnas.1511328112","author":[{"first_name":"Colin","full_name":"Kretz, Colin A","last_name":"Kretz"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"first_name":"Onuralp","full_name":"Soylemez, Onuralp","last_name":"Soylemez"},{"first_name":"Andrew","full_name":"Yee, 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","first_name":"Kärt","full_name":"Tomberg, Kärt"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov"},{"first_name":"Fan","full_name":"Meng, Fan","last_name":"Meng"},{"first_name":"David","full_name":"Ginsburg, David B","last_name":"Ginsburg"}],"publist_id":"6783","publication":"PNAS","issue":"30","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_published":"2015-07-28T00:00:00Z"},{"abstract":[{"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.","lang":"eng"}],"volume":31,"extern":1,"status":"public","date_updated":"2021-01-12T08:21:16Z","page":"24 - 33","quality_controlled":0,"date_created":"2018-12-11T11:49:01Z","year":"2015","intvolume":"        31","citation":{"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>.","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.","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>.","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.","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>","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33."},"day":"01","type":"journal_article","title":"Topological features of rugged fitness landscapes in sequence space","publication_status":"published","publisher":"Elsevier","_id":"886","month":"01","doi":"10.1016/j.tig.2014.09.009","author":[{"last_name":"Kondrashov","first_name":"Dmitry","full_name":"Kondrashov, Dmitry A"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"}],"publist_id":"6764","publication":"Trends in Genetics","issue":"1","date_published":"2015-01-01T00:00:00Z","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."},{"article_type":"original","publication_status":"published","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","_id":"9017","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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.","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.","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>.","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.","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>","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>."},"intvolume":"        43","day":"18","extern":"1","abstract":[{"lang":"eng","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."}],"status":"public","author":[{"last_name":"Richet","first_name":"Nicolas","full_name":"Richet, Nicolas"},{"last_name":"Liu","first_name":"Danni","full_name":"Liu, Danni"},{"last_name":"Legrand","full_name":"Legrand, Pierre","first_name":"Pierre"},{"last_name":"Velours","full_name":"Velours, Christophe","first_name":"Christophe"},{"first_name":"Armelle","full_name":"Corpet, Armelle","last_name":"Corpet"},{"last_name":"Gaubert","first_name":"Albane","full_name":"Gaubert, Albane"},{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","full_name":"Bakail, May M","last_name":"Bakail"},{"full_name":"Moal-Raisin, Gwenaelle","first_name":"Gwenaelle","last_name":"Moal-Raisin"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"last_name":"Compper","full_name":"Compper, Christel","first_name":"Christel"},{"last_name":"Besle","full_name":"Besle, Arthur","first_name":"Arthur"},{"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"}],"issue":"3","publication":"Nucleic Acids Research","date_published":"2015-02-18T00:00:00Z","oa_version":"Published Version","external_id":{"pmid":["25618846"]},"type":"journal_article","language":[{"iso":"eng"}],"publisher":"Oxford University Press","doi":"10.1093/nar/gkv021","pmid":1,"publication_identifier":{"issn":["1362-4962","0305-1048"]},"article_processing_charge":"No","volume":43,"date_updated":"2023-02-23T13:46:50Z","year":"2015","date_created":"2021-01-19T11:01:01Z","quality_controlled":"1","page":"1905-1917"},{"pmid":1,"scopus_import":"1","publication_identifier":{"issn":["2375-2548"]},"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"article_processing_charge":"No","file":[{"creator":"cziletti","file_size":2416780,"checksum":"b97d62433581875c1b85210c5f6ae370","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2021-02-02T13:22:19Z","date_created":"2021-02-02T13:22:19Z","content_type":"application/pdf","file_id":"9058","file_name":"2015_ScienceAdvances_Palacci.pdf"}],"volume":1,"date_updated":"2023-02-23T13:47:52Z","year":"2015","date_created":"2021-02-02T13:15:02Z","quality_controlled":"1","author":[{"last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"},{"first_name":"Stefano","full_name":"Sacanna, Stefano","last_name":"Sacanna"},{"last_name":"Abramian","first_name":"Anaïs","full_name":"Abramian, Anaïs"},{"full_name":"Barral, Jérémie","first_name":"Jérémie","last_name":"Barral"},{"last_name":"Hanson","first_name":"Kasey","full_name":"Hanson, Kasey"},{"last_name":"Grosberg","full_name":"Grosberg, Alexander Y.","first_name":"Alexander Y."},{"first_name":"David J.","full_name":"Pine, David J.","last_name":"Pine"},{"first_name":"Paul M.","full_name":"Chaikin, Paul M.","last_name":"Chaikin"}],"ddc":["530"],"publication":"Science Advances","issue":"4","date_published":"2015-05-01T00:00:00Z","oa_version":"Published Version","external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"type":"journal_article","file_date_updated":"2021-02-02T13:22:19Z","arxiv":1,"language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science ","doi":"10.1126/sciadv.1400214","citation":{"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>","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>.","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.","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>.","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).","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>"},"intvolume":"         1","has_accepted_license":"1","day":"01","extern":"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"}],"status":"public","article_number":"e1400214","article_type":"original","publication_status":"published","oa":1,"title":"Artificial rheotaxis","month":"05","_id":"9057","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"11","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>","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>","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>.","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)."},"intvolume":"        10","date_updated":"2021-01-12T08:21:48Z","quality_controlled":0,"year":"2015","date_created":"2018-12-11T11:49:08Z","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."}],"volume":10,"extern":1,"status":"public","date_published":"2015-05-11T00:00:00Z","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.","author":[{"last_name":"Arkhipova","first_name":"Oksana","full_name":"Arkhipova, Oksana V"},{"last_name":"Meer","full_name":"Meer, Margarita V","first_name":"Margarita"},{"last_name":"Mikoulinskaia","first_name":"Galina","full_name":"Mikoulinskaia, Galina V"},{"first_name":"Marina","full_name":"Zakharova, Marina V","last_name":"Zakharova"},{"first_name":"Alexander","full_name":"Galushko, Alexander S","last_name":"Galushko"},{"last_name":"Akimenko","first_name":"Vasilii","full_name":"Akimenko, Vasilii K"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov"}],"issue":"5","publication":"PLoS One","publist_id":"6742","publisher":"Public Library of Science","_id":"906","month":"05","doi":"10.1371/journal.pone.0125888","type":"journal_article","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","publication_status":"published"},{"publication_identifier":{"issn":["2169-9275"]},"main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"article_processing_charge":"No","volume":120,"year":"2015","date_created":"2021-02-15T14:21:49Z","page":"4760-4777","quality_controlled":"1","date_updated":"2022-01-24T13:45:41Z","publication":"Journal of Geophysical Research: Oceans","issue":"7","author":[{"last_name":"Lefauve","first_name":"Adrien","full_name":"Lefauve, Adrien"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"first_name":"Angélique","full_name":"Melet, Angélique","last_name":"Melet"}],"oa_version":"Published Version","date_published":"2015-06-08T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1002/2014jc010598","publisher":"American Geophysical Union","intvolume":"       120","citation":{"short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","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>","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>","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>.","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>.","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."},"day":"08","status":"public","extern":"1","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."}],"publication_status":"published","oa":1,"title":"A three-dimensional map of tidal dissipation over abyssal hills","article_type":"original","_id":"9141","month":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"language":[{"iso":"eng"}],"publication_status":"published","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","type":"journal_article","_id":"924","month":"02","doi":"10.1016/j.applthermaleng.2014.10.009","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","publist_id":"6514","publication":"Applied Thermal Engineering","author":[{"last_name":"Boubaker","first_name":"Riadh","full_name":"Boubaker, Riadh"},{"first_name":"Vincent","full_name":"Platel, Vincent","last_name":"Platel"},{"last_name":"Bergès","first_name":"Alexis","full_name":"Bergès, Alexis"},{"full_name":"Bancelin, Mathieu","first_name":"Mathieu","last_name":"Bancelin"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"}],"oa_version":"None","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","date_published":"2015-02-05T00:00:00Z","status":"public","extern":"1","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"}],"volume":76,"date_created":"2018-12-11T11:49:13Z","year":"2015","page":"1 - 8","date_updated":"2021-01-12T08:21:56Z","intvolume":"        76","citation":{"short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","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>","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.","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>.","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>","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>."},"day":"05","article_processing_charge":"No"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":4,"file":[{"file_size":7202224,"creator":"dernst","relation":"main_file","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","date_created":"2018-12-20T15:50:56Z","content_type":"application/pdf","file_id":"5769","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","file_name":"2015_eLife_Sehring.pdf"}],"quality_controlled":"1","date_created":"2018-12-11T11:49:15Z","year":"2015","date_updated":"2021-01-12T08:21:58Z","publist_id":"6512","publication":"eLife","ddc":["539","570"],"author":[{"full_name":"Sehring, Ivonne","first_name":"Ivonne","last_name":"Sehring"},{"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","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"last_name":"Jiang","full_name":"Jiang, Di","first_name":"Di"}],"oa_version":"Published Version","date_published":"2015-10-21T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","doi":"10.7554/eLife.09206","publisher":"eLife Sciences Publications","intvolume":"         4","citation":{"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>","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>.","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.","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>.","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.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (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>"},"day":"21","has_accepted_license":"1","article_number":"e09206","status":"public","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."}],"extern":"1","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"928","month":"10"},{"type":"journal_article","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","publication_status":"published","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"929","doi":"10.1073/pnas.1504762112","month":"07","author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"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"},{"full_name":"Hayashi, Shigeo","first_name":"Shigeo","last_name":"Hayashi"}],"issue":"28","publication":"PNAS","publist_id":"6513","date_published":"2015-07-14T00:00:00Z","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.","oa_version":"None","abstract":[{"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. ","lang":"eng"}],"volume":112,"extern":"1","status":"public","date_updated":"2021-01-12T08:21:59Z","page":"8620 - 8625","year":"2015","date_created":"2018-12-11T11:49:15Z","citation":{"short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","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>","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>.","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>","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>.","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."},"intvolume":"       112","article_processing_charge":"No","day":"14"}]