[{"arxiv":1,"article_processing_charge":"No","issue":"4","file":[{"success":1,"date_created":"2021-02-02T13:22:19Z","content_type":"application/pdf","file_id":"9058","relation":"main_file","date_updated":"2021-02-02T13:22:19Z","access_level":"open_access","checksum":"b97d62433581875c1b85210c5f6ae370","file_name":"2015_ScienceAdvances_Palacci.pdf","file_size":2416780,"creator":"cziletti"}],"article_number":"e1400214","abstract":[{"lang":"eng","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."}],"_id":"9057","date_published":"2015-05-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","oa":1,"file_date_updated":"2021-02-02T13:22:19Z","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"volume":1,"article_type":"original","has_accepted_license":"1","year":"2015","oa_version":"Published Version","scopus_import":"1","external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-02-23T13:47:52Z","publication_identifier":{"issn":["2375-2548"]},"month":"05","extern":"1","date_created":"2021-02-02T13:15:02Z","publisher":"American Association for the Advancement of Science ","publication":"Science Advances","quality_controlled":"1","status":"public","intvolume":" 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).","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214."},"title":"Artificial rheotaxis","day":"01","author":[{"orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci"},{"first_name":"Stefano","full_name":"Sacanna, Stefano","last_name":"Sacanna"},{"full_name":"Abramian, Anaïs","first_name":"Anaïs","last_name":"Abramian"},{"first_name":"Jérémie","full_name":"Barral, Jérémie","last_name":"Barral"},{"first_name":"Kasey","full_name":"Hanson, Kasey","last_name":"Hanson"},{"last_name":"Grosberg","full_name":"Grosberg, Alexander Y.","first_name":"Alexander Y."},{"first_name":"David J.","full_name":"Pine, David J.","last_name":"Pine"},{"last_name":"Chaikin","first_name":"Paul M.","full_name":"Chaikin, Paul M."}],"type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.1400214","ddc":["530"]},{"publication":"PLoS One","quality_controlled":0,"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)"},"status":"public","intvolume":" 10","volume":10,"publication_status":"published","publisher":"Public Library of Science","month":"05","extern":1,"date_created":"2018-12-11T11:49:08Z","_id":"906","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"}],"date_published":"2015-05-11T00:00:00Z","issue":"5","date_updated":"2021-01-12T08:21:48Z","doi":"10.1371/journal.pone.0125888","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.","day":"11","publist_id":"6742","type":"journal_article","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"},{"last_name":"Zakharova","full_name":"Zakharova, Marina V","first_name":"Marina"},{"full_name":"Galushko, Alexander S","first_name":"Alexander","last_name":"Galushko"},{"full_name":"Akimenko, Vasilii K","first_name":"Vasilii","last_name":"Akimenko"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"year":"2015","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. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","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"},{"language":[{"iso":"eng"}],"doi":"10.1002/2014jc010598","day":"08","author":[{"first_name":"Adrien","full_name":"Lefauve, Adrien","last_name":"Lefauve"},{"full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350"},{"first_name":"Angélique","full_name":"Melet, Angélique","last_name":"Melet"}],"type":"journal_article","citation":{"apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598."},"title":"A three-dimensional map of tidal dissipation over abyssal hills","publication":"Journal of Geophysical Research: Oceans","quality_controlled":"1","intvolume":" 120","status":"public","publisher":"American Geophysical Union","month":"06","extern":"1","date_created":"2021-02-15T14:21:49Z","page":"4760-4777","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-24T13:45:41Z","publication_identifier":{"issn":["2169-9275"]},"article_type":"original","year":"2015","oa_version":"Published Version","volume":120,"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"oa":1,"_id":"9141","date_published":"2015-06-08T00:00:00Z","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."}],"article_processing_charge":"No","issue":"7"},{"acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","doi":"10.1016/j.applthermaleng.2014.10.009","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:56Z","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","citation":{"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.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009.","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,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.","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.","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.","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. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009"},"oa_version":"None","year":"2015","type":"journal_article","author":[{"full_name":"Boubaker, Riadh","first_name":"Riadh","last_name":"Boubaker"},{"last_name":"Platel","first_name":"Vincent","full_name":"Platel, Vincent"},{"first_name":"Alexis","full_name":"Bergès, Alexis","last_name":"Bergès"},{"first_name":"Mathieu","full_name":"Bancelin, Mathieu","last_name":"Bancelin"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"publist_id":"6514","day":"05","publication_status":"published","publisher":"Elsevier","volume":76,"status":"public","intvolume":" 76","publication":"Applied Thermal Engineering","article_processing_charge":"No","page":"1 - 8","date_published":"2015-02-05T00:00:00Z","_id":"924","date_created":"2018-12-11T11:49:13Z","abstract":[{"lang":"eng","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."}],"extern":"1","month":"02"},{"file_date_updated":"2020-07-14T12:48:15Z","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,"publication_status":"published","oa":1,"file":[{"date_created":"2018-12-20T15:50:56Z","file_id":"5769","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","creator":"dernst","file_size":7202224,"file_name":"2015_eLife_Sehring.pdf"}],"article_number":"e09206","_id":"928","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:58Z","publist_id":"6512","oa_version":"Published Version","year":"2015","has_accepted_license":"1","publication":"eLife","quality_controlled":"1","status":"public","intvolume":" 4","publisher":"eLife Sciences Publications","month":"10","extern":"1","date_created":"2018-12-11T11:49:15Z","language":[{"iso":"eng"}],"ddc":["539","570"],"doi":"10.7554/eLife.09206","day":"21","type":"journal_article","author":[{"full_name":"Sehring, Ivonne","first_name":"Ivonne","last_name":"Sehring"},{"last_name":"Recho","full_name":"Recho, Pierre","first_name":"Pierre"},{"full_name":"Denker, Elsa","first_name":"Elsa","last_name":"Denker"},{"last_name":"Kourakis","first_name":"Matthew","full_name":"Kourakis, Matthew"},{"last_name":"Mathiesen","full_name":"Mathiesen, Birthe","first_name":"Birthe"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"last_name":"Jiang","full_name":"Jiang, Di","first_name":"Di"}],"citation":{"mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","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 et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, 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. eLife. 2015;4. doi:10.7554/eLife.09206","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015)."},"title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity"},{"article_processing_charge":"No","issue":"28","page":"8620 - 8625","_id":"929","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"}],"date_created":"2018-12-11T11:49:15Z","date_published":"2015-07-14T00:00:00Z","month":"07","extern":"1","publication_status":"published","publisher":"National Academy of Sciences","status":"public","intvolume":" 112","volume":112,"publication":"PNAS","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","citation":{"apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","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.","chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112."},"author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"},{"full_name":"Hayashi, Shigeo","first_name":"Shigeo","last_name":"Hayashi"}],"type":"journal_article","oa_version":"None","year":"2015","publist_id":"6513","day":"14","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.","doi":"10.1073/pnas.1504762112","date_updated":"2021-01-12T08:21:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"page":"15314 - 15319","date_created":"2018-12-11T11:49:16Z","month":"12","extern":"1","publisher":"National Academy of Sciences","status":"public","intvolume":" 112","publication":"PNAS","quality_controlled":"1","title":"Physics of active jamming during collective cellular motion in a monolayer","citation":{"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.","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,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","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.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112"},"type":"journal_article","author":[{"last_name":"García","first_name":"Simón","full_name":"García, Simón"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"last_name":"Joanny","full_name":"Joanny, Jean","first_name":"Jean"},{"first_name":"Pascal","full_name":"Silberzan, Pascal","last_name":"Silberzan"},{"last_name":"Gov","full_name":"Gov, Nir","first_name":"Nir"}],"day":"15","pmid":1,"doi":"10.1073/pnas.1510973112","language":[{"iso":"eng"}],"issue":"50","_id":"933","abstract":[{"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.","lang":"eng"}],"date_published":"2015-12-15T00:00:00Z","main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"oa":1,"publication_status":"published","volume":112,"year":"2015","oa_version":"None","publist_id":"6511","external_id":{"pmid":["26627719"]},"date_updated":"2021-01-12T08:22:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file":[{"creator":"asandaue","file_size":1116846,"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","checksum":"086a88cfca4677646da26ed960cb02e9","access_level":"open_access","date_updated":"2021-06-08T09:55:10Z","relation":"main_file","file_id":"9533","content_type":"application/pdf","date_created":"2021-06-08T09:55:10Z","success":1}],"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"}],"_id":"9532","date_published":"2015-12-15T00:00:00Z","issue":"24","article_processing_charge":"No","file_date_updated":"2021-06-08T09:55:10Z","volume":29,"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publication_status":"published","oa":1,"article_type":"review","oa_version":"Published Version","year":"2015","has_accepted_license":"1","date_updated":"2021-12-14T07:58:15Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","external_id":{"pmid":["26680300"]},"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"extern":"1","month":"12","date_created":"2021-06-08T09:56:24Z","page":"2517–2531","quality_controlled":"1","department":[{"_id":"DaZi"}],"publication":"Genes and Development","intvolume":" 29","status":"public","publisher":"Cold Spring Harbor Laboratory Press","day":"15","author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"type":"journal_article","citation":{"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,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115"},"title":"Evolution and function of genomic imprinting in plants","language":[{"iso":"eng"}],"doi":"10.1101/gad.269902.115","ddc":["570"],"pmid":1},{"publication":"Electronic Notes in Discrete Mathematics","quality_controlled":"1","status":"public","intvolume":" 49","publisher":"Elsevier","month":"11","extern":"1","date_created":"2021-06-21T06:40:34Z","page":"181-187","language":[{"iso":"eng"}],"doi":"10.1016/j.endm.2015.06.027","day":"01","type":"journal_article","author":[{"last_name":"Krivelevich","full_name":"Krivelevich, Michael","first_name":"Michael"},{"last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"citation":{"ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","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."},"title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","volume":49,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"oa":1,"_id":"9575","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","arxiv":1,"article_processing_charge":"No","external_id":{"arxiv":["1501.04816"]},"scopus_import":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T14:01:28Z","publication_identifier":{"issn":["1571-0653"]},"article_type":"original","oa_version":"Preprint","year":"2015"},{"doi":"10.1016/j.ijplas.2014.09.009","publication_identifier":{"issn":["0749-6419"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:04:28Z","scopus_import":"1","year":"2015","oa_version":"None","type":"journal_article","author":[{"last_name":"Leung","full_name":"Leung, H.S.","first_name":"H.S."},{"last_name":"Leung","full_name":"Leung, P.S.S.","first_name":"P.S.S."},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"first_name":"A.H.W.","full_name":"Ngan, A.H.W.","last_name":"Ngan"}],"day":"01","article_type":"original","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","citation":{"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.","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009"},"volume":67,"status":"public","intvolume":" 67","publication":"International Journal of Plasticity","publisher":"Elsevier","publication_status":"published","date_published":"2015-04-01T00:00:00Z","_id":"9673","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}],"date_created":"2021-07-15T14:09:32Z","extern":"1","month":"04","article_processing_charge":"No","page":"1-25"},{"article_processing_charge":"No","issue":"3","_id":"9684","date_published":"2015-04-01T00:00:00Z","date_created":"2021-07-19T09:11:12Z","abstract":[{"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.","lang":"eng"}],"month":"04","extern":"1","article_number":"035001","publisher":"IOP Publishing","publication_status":"published","status":"public","intvolume":" 23","volume":23,"publication":"Modelling and Simulation in Materials Science and Engineering","quality_controlled":"1","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","citation":{"ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.","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.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001.","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.","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,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015."},"type":"journal_article","author":[{"first_name":"P S S","full_name":"Leung, P S S","last_name":"Leung"},{"full_name":"Leung, H S","first_name":"H S","last_name":"Leung"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing"},{"full_name":"Ngan, A H W","first_name":"A H W","last_name":"Ngan"}],"year":"2015","oa_version":"None","article_type":"original","day":"01","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"doi":"10.1088/0965-0393/23/3/035001","scopus_import":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:04:54Z"},{"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"oa":1,"publication_status":"published","volume":92,"issue":"18","article_processing_charge":"No","arxiv":1,"date_published":"2015-11-01T00:00:00Z","_id":"9688","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"article_number":"180102","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2021-08-09T12:38:49Z","scopus_import":"1","external_id":{"arxiv":["1511.08668"]},"year":"2015","oa_version":"Preprint","article_type":"original","publisher":"American Physical Society","intvolume":" 92","status":"public","quality_controlled":"1","publication":"Physical Review B - Condensed Matter and Materials Physics","date_created":"2021-07-19T10:07:22Z","extern":"1","month":"11","doi":"10.1103/physrevb.92.180102","language":[{"iso":"eng"}],"title":"Solid-liquid interfacial free energy out of equilibrium","citation":{"ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","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."},"author":[{"first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"type":"journal_article","day":"01"},{"date_created":"2022-08-12T11:39:40Z","month":"02","extern":"1","page":"90-102","intvolume":" 30","status":"public","publication":"32nd International Symposium on Theoretical Aspects of Computer Science","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Sayan","full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Starnberger","first_name":" Martin","full_name":"Starnberger, Martin"}],"type":"conference","alternative_title":["LIPIcs"],"day":"26","title":"Welfare maximization with friends-of-friends network externalities","conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2015-03-07","start_date":"2015-03-04","location":"Garching, Germany"},"citation":{"ista":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.","ieee":"S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102.","chicago":"Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90.","mla":"Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90.","short":"S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102.","apa":"Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90","ama":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90"},"doi":"10.4230/LIPICS.STACS.2015.90","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"11903","relation":"later_version","status":"public"}]},"date_published":"2015-02-26T00:00:00Z","_id":"11837","abstract":[{"lang":"eng","text":"Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm."}],"article_processing_charge":"No","volume":30,"main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.STACS.2015.90","open_access":"1"}],"oa":1,"publication_status":"published","year":"2015","oa_version":"Published Version","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-939897-78-1"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T16:32:37Z"},{"publication":"Methods in Ecology and Evolution","quality_controlled":"1","intvolume":" 6","status":"public","publisher":"Wiley","month":"01","extern":"1","date_created":"2022-08-16T06:43:49Z","page":"83-91","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1111/2041-210x.12299","pmid":1,"day":"01","author":[{"last_name":"Chernomor","first_name":"Olga","full_name":"Chernomor, Olga"},{"full_name":"Minh, Bui Quang","first_name":"Bui Quang","last_name":"Minh"},{"first_name":"Félix","full_name":"Forest, Félix","last_name":"Forest"},{"first_name":"Steffen","full_name":"Klaere, Steffen","last_name":"Klaere"},{"last_name":"Ingram","full_name":"Ingram, Travis","first_name":"Travis"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"von Haeseler","full_name":"von Haeseler, Arndt","first_name":"Arndt"}],"type":"journal_article","citation":{"mla":"Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:10.1111/2041-210x.12299.","chicago":"Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika H Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution. Wiley, 2015. https://doi.org/10.1111/2041-210x.12299.","ista":"Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger MH, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91.","ieee":"O. Chernomor et al., “Split diversity in constrained conservation prioritization using integer linear programming,” Methods in Ecology and Evolution, vol. 6, no. 1. Wiley, pp. 83–91, 2015.","ama":"Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 2015;6(1):83-91. doi:10.1111/2041-210x.12299","apa":"Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M. H., & von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. Wiley. https://doi.org/10.1111/2041-210x.12299","short":"O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M.H. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91."},"title":"Split diversity in constrained conservation prioritization using integer linear programming","file_date_updated":"2022-08-16T06:52:53Z","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":6,"publication_status":"published","oa":1,"file":[{"creator":"asandaue","file_size":411415,"file_name":"2015_MethodsInEcologyAndEvolutionChernomor.pdf","access_level":"open_access","date_updated":"2022-08-16T06:52:53Z","checksum":"880e78f09f0ac99cb351c48dc97623b6","relation":"main_file","file_id":"11846","content_type":"application/pdf","success":1,"date_created":"2022-08-16T06:52:53Z"}],"_id":"11845","date_published":"2015-01-01T00:00:00Z","abstract":[{"text":"Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda.","lang":"eng"}],"article_processing_charge":"No","issue":"1","scopus_import":"1","external_id":{"pmid":["25893087"]},"date_updated":"2023-02-17T09:30:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-210X"]},"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2015"},{"language":[{"iso":"eng"}],"doi":"10.1145/2746539.2746609","citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015.","ama":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015. doi:10.1145/2746539.2746609","apa":"Henzinger, M. H., Krinninger, S., Nanongkai, D., & Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In 47th Annual ACM Symposium on Theory of Computing. Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746609","chicago":"Henzinger, Monika H, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746609.","ieee":"M. H. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015.","ista":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30.","mla":"Henzinger, Monika H., et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” 47th Annual ACM Symposium on Theory of Computing, 21–30, Association for Computing Machinery, 2015, doi:10.1145/2746539.2746609."},"conference":{"location":"Portland, OR, United States","name":"STOC: Symposium on Theory of Computing","end_date":"2015-06-17","start_date":"2015-06-14"},"title":"Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture","day":"14","type":"conference","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"last_name":"Saranurak","first_name":"Thatchaphol","full_name":"Saranurak, Thatchaphol"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","publication":"47th Annual ACM Symposium on Theory of Computing","status":"public","extern":"1","month":"06","date_created":"2022-08-16T09:31:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T11:09:54Z","scopus_import":"1","external_id":{"arxiv":["1511.06773"]},"publication_identifier":{"issn":["0737.8017"],"isbn":["978-145033536-2"]},"year":"2015","oa_version":"Preprint","publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.06773","open_access":"1"}],"arxiv":1,"article_processing_charge":"No","article_number":"21-30","_id":"11868","abstract":[{"text":"Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems.","lang":"eng"}],"date_published":"2015-06-14T00:00:00Z"},{"day":"01","author":[{"full_name":"Bhattacharya, Sayan","first_name":"Sayan","last_name":"Bhattacharya"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"last_name":"Tsourakakis","full_name":"Tsourakakis, Charalampos","first_name":"Charalampos"}],"type":"conference","citation":{"apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In 47th Annual ACM Symposium on Theory of Computing (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746592","ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015:173-182. doi:10.1145/2746539.2746592","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182.","mla":"Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–82, doi:10.1145/2746539.2746592.","ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182.","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015, pp. 173–182.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In 47th Annual ACM Symposium on Theory of Computing, 173–82. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746592."},"conference":{"location":"Portland, OR, United States","name":"STOC: Symposium on Theory of Computing","end_date":"2015-06-17","start_date":"2015-06-14"},"title":"Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams","language":[{"iso":"eng"}],"doi":"10.1145/2746539.2746592","extern":"1","month":"06","date_created":"2022-08-16T09:36:48Z","page":"173 - 182","quality_controlled":"1","publication":"47th Annual ACM Symposium on Theory of Computing","status":"public","publisher":"Association for Computing Machinery","year":"2015","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T11:17:03Z","external_id":{"arxiv":["1504.02268"]},"scopus_import":"1","publication_identifier":{"isbn":["978-145033536-2"],"issn":["0737-8017"]},"_id":"11869","date_published":"2015-06-01T00:00:00Z","abstract":[{"text":"While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor.","lang":"eng"}],"arxiv":1,"article_processing_charge":"No","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1504.02268","open_access":"1"}],"oa":1},{"year":"2015","oa_version":"None","article_type":"original","publication_identifier":{"issn":["0304-3975"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T14:50:04Z","article_processing_charge":"No","_id":"11901","date_published":"2015-03-30T00:00:00Z","abstract":[{"lang":"eng","text":"We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful."}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.tcs.2015.01.033","open_access":"1"}],"publication_status":"published","volume":573,"title":"Truthful unit-demand auctions with budgets revisited","citation":{"mla":"Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033.","chicago":"Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033.","ieee":"M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015.","ista":"Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15.","ama":"Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033","apa":"Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033","short":"M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15."},"type":"journal_article","author":[{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"day":"30","doi":"10.1016/j.tcs.2015.01.033","language":[{"iso":"eng"}],"page":"1-15","date_created":"2022-08-17T09:06:53Z","month":"03","extern":"1","publisher":"Elsevier","status":"public","intvolume":" 573","publication":"Theoretical Computer Science","quality_controlled":"1"},{"_id":"11962","abstract":[{"lang":"eng","text":"One of the rare alternative reagents for the reduction of carbon–carbon double bonds is diimide (HNNH), which can be generated in situ from hydrazine hydrate (N2H4⋅H2O) and O2. Although this selective method is extremely clean and powerful, it is rarely used, as the rate-determining oxidation of hydrazine in the absence of a catalyst is relatively slow using conventional batch protocols. A continuous high-temperature/high-pressure methodology dramatically enhances the initial oxidation step, at the same time allowing for a safe and scalable processing of the hazardous reaction mixture. Simple alkenes can be selectively reduced within 10–20 min at 100–120 °C and 20 bar O2 pressure. The development of a multi-injection reactor platform for the periodic addition of N2H4⋅H2O enables the reduction of less reactive olefins even at lower reaction temperatures. This concept was utilized for the highly selective reduction of artemisinic acid to dihydroartemisinic acid, the precursor molecule for the semisynthesis of the antimalarial drug artemisinin. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4⋅H2O) and residence time units resulting in a highly selective reduction within approximately 40 min at 60 °C and 20 bar O2 pressure, providing dihydroartemisinic acid in ≥93 % yield and ≥95 % selectivity."}],"date_published":"2015-03-09T00:00:00Z","issue":"11","article_processing_charge":"No","volume":21,"publication_status":"published","article_type":"original","oa_version":"None","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T10:09:30Z","scopus_import":"1","external_id":{"pmid":["25655090"]},"publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"extern":"1","month":"03","date_created":"2022-08-24T11:11:10Z","page":"4368-4376","quality_controlled":"1","publication":"Chemistry - A European Journal","status":"public","intvolume":" 21","publisher":"Wiley","day":"09","type":"journal_article","author":[{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","last_name":"Pieber","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus"},{"last_name":"Glasnov","full_name":"Glasnov, Toma","first_name":"Toma"},{"last_name":"Kappe","full_name":"Kappe, C. Oliver","first_name":"C. Oliver"}],"citation":{"mla":"Pieber, Bartholomäus, et al. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal, vol. 21, no. 11, Wiley, 2015, pp. 4368–76, doi:10.1002/chem.201406439.","ista":"Pieber B, Glasnov T, Kappe CO. 2015. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 21(11), 4368–4376.","ieee":"B. Pieber, T. Glasnov, and C. O. Kappe, “Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs,” Chemistry - A European Journal, vol. 21, no. 11. Wiley, pp. 4368–4376, 2015.","chicago":"Pieber, Bartholomäus, Toma Glasnov, and C. Oliver Kappe. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal. Wiley, 2015. https://doi.org/10.1002/chem.201406439.","apa":"Pieber, B., Glasnov, T., & Kappe, C. O. (2015). Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.201406439","ama":"Pieber B, Glasnov T, Kappe CO. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 2015;21(11):4368-4376. doi:10.1002/chem.201406439","short":"B. Pieber, T. Glasnov, C.O. Kappe, Chemistry - A European Journal 21 (2015) 4368–4376."},"title":"Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs","language":[{"iso":"eng"}],"doi":"10.1002/chem.201406439","pmid":1},{"month":"05","extern":"1","date_created":"2022-08-25T10:52:24Z","page":"4590-4602","publication":"The Journal of Organic Chemistry","quality_controlled":"1","status":"public","intvolume":" 80","publisher":"American Chemical Society","day":"01","type":"journal_article","author":[{"last_name":"Salvador","first_name":"Carlos Eduardo M.","full_name":"Salvador, Carlos Eduardo M."},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","last_name":"Pieber","first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus"},{"full_name":"Neu, Philipp M.","first_name":"Philipp M.","last_name":"Neu"},{"full_name":"Torvisco, Ana","first_name":"Ana","last_name":"Torvisco"},{"last_name":"Kleber Z. Andrade","full_name":"Kleber Z. Andrade, Carlos","first_name":"Carlos"},{"full_name":"Kappe, C. Oliver","first_name":"C. Oliver","last_name":"Kappe"}],"citation":{"short":"C.E.M. Salvador, B. Pieber, P.M. Neu, A. Torvisco, C. Kleber Z. Andrade, C.O. Kappe, The Journal of Organic Chemistry 80 (2015) 4590–4602.","ama":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 2015;80(9):4590-4602. doi:10.1021/acs.joc.5b00445","apa":"Salvador, C. E. M., Pieber, B., Neu, P. M., Torvisco, A., Kleber Z. Andrade, C., & Kappe, C. O. (2015). A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.joc.5b00445","chicago":"Salvador, Carlos Eduardo M., Bartholomäus Pieber, Philipp M. Neu, Ana Torvisco, Carlos Kleber Z. Andrade, and C. Oliver Kappe. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.joc.5b00445.","ista":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. 2015. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 80(9), 4590–4602.","ieee":"C. E. M. Salvador, B. Pieber, P. M. Neu, A. Torvisco, C. Kleber Z. Andrade, and C. O. Kappe, “A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids,” The Journal of Organic Chemistry, vol. 80, no. 9. American Chemical Society, pp. 4590–4602, 2015.","mla":"Salvador, Carlos Eduardo M., et al. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry, vol. 80, no. 9, American Chemical Society, 2015, pp. 4590–602, doi:10.1021/acs.joc.5b00445."},"title":"A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids","language":[{"iso":"eng"}],"doi":"10.1021/acs.joc.5b00445","pmid":1,"_id":"11977","date_published":"2015-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide–alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained."}],"article_processing_charge":"No","issue":"9","volume":80,"publication_status":"published","article_type":"original","year":"2015","oa_version":"None","scopus_import":"1","external_id":{"pmid":["25842982"]},"date_updated":"2023-02-21T10:10:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1520-6904"],"issn":["0022-3263"]}},{"doi":"10.1007/3418_2015_133","language":[{"iso":"eng"}],"alternative_title":["Topics in Organometallic Chemistry"],"type":"book_chapter","author":[{"first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"full_name":"Kappe, C. Oliver","first_name":"C. Oliver","last_name":"Kappe"}],"day":"10","title":"Aerobic oxidations in continuous flow","citation":{"mla":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., vol. 57, Springer Nature, 2015, pp. 97–136, doi:10.1007/3418_2015_133.","ista":"Pieber B, Kappe CO. 2015.Aerobic oxidations in continuous flow. In: Organometallic Flow Chemistry. Topics in Organometallic Chemistry, vol. 57, 97–136.","ieee":"B. Pieber and C. O. Kappe, “Aerobic oxidations in continuous flow,” in Organometallic Flow Chemistry, 1st ed., vol. 57, T. Noël, Ed. Cham: Springer Nature, 2015, pp. 97–136.","chicago":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” In Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., 57:97–136. TOPORGAN. Cham: Springer Nature, 2015. https://doi.org/10.1007/3418_2015_133.","apa":"Pieber, B., & Kappe, C. O. (2015). Aerobic oxidations in continuous flow. In T. Noël (Ed.), Organometallic Flow Chemistry (1st ed., Vol. 57, pp. 97–136). Cham: Springer Nature. https://doi.org/10.1007/3418_2015_133","ama":"Pieber B, Kappe CO. Aerobic oxidations in continuous flow. In: Noël T, ed. Organometallic Flow Chemistry. Vol 57. 1st ed. TOPORGAN. Cham: Springer Nature; 2015:97–136. doi:10.1007/3418_2015_133","short":"B. Pieber, C.O. Kappe, in:, T. Noël (Ed.), Organometallic Flow Chemistry, 1st ed., Springer Nature, Cham, 2015, pp. 97–136."},"status":"public","intvolume":" 57","quality_controlled":"1","publication":"Organometallic Flow Chemistry","publisher":"Springer Nature","series_title":"TOPORGAN","date_created":"2022-08-25T11:58:38Z","place":"Cham","extern":"1","month":"06","page":"97–136","publication_identifier":{"eisbn":["9783319332437"],"eissn":["1616-8534"],"isbn":["9783319332413"],"issn":["1436-6002"]},"date_updated":"2023-02-21T10:10:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","year":"2015","oa_version":"None","editor":[{"full_name":"Noël, Timothy","first_name":"Timothy","last_name":"Noël"}],"volume":57,"edition":"1","publication_status":"published","abstract":[{"lang":"eng","text":"In recent years, the high demand for sustainable processes resulted in the development of highly attractive oxidation protocols utilizing molecular oxygen or even air instead of more uneconomic and often toxic reagents. The application of these sustainable, gaseous oxidants in conventional batch reactors is often associated with severe safety risks and process challenges especially on larger scales. Continuous flow technology offers the possibility to minimize these safety hazards and concurrently allows working in high-temperature/high-pressure regimes to access highly efficient oxidation protocols. This review article critically discusses recent literature examples of flow methodologies for selective aerobic oxidations of organic compounds. Several technologies and reactor designs for biphasic gas/liquid as well as supercritical reaction media are presented in detail. © Springer International Publishing Switzerland 2015."}],"_id":"11989","date_published":"2015-06-10T00:00:00Z","article_processing_charge":"No"}]