[{"ddc":["581"],"type":"journal_article","pubrep_id":"654","intvolume":"         5","article_number":"e19048","month":"09","ec_funded":1,"quality_controlled":"1","citation":{"chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.19048\">https://doi.org/10.7554/eLife.19048</a>.","apa":"Fendrych, M., Leung, J., &#38; Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.19048\">https://doi.org/10.7554/eLife.19048</a>","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. <i>eLife</i>. 2016;5. doi:<a href=\"https://doi.org/10.7554/eLife.19048\">10.7554/eLife.19048</a>","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” <i>ELife</i>, vol. 5, e19048, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.19048\">10.7554/eLife.19048</a>.","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” <i>eLife</i>, vol. 5. eLife Sciences Publications, 2016.","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048."},"publication_status":"published","abstract":[{"lang":"eng","text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms."}],"language":[{"iso":"eng"}],"publist_id":"5908","department":[{"_id":"JiFr"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:44:45Z","publication":"eLife","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-693-v1+1_e19048-download.pdf","file_size":5666343,"date_created":"2018-12-12T10:09:24Z","relation":"main_file","file_id":"4748","access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"9209541fbba00f24daad21a5d568540d"}],"title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","date_updated":"2021-01-12T06:50:01Z","_id":"1344","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","year":"2016","has_accepted_license":"1","oa":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"full_name":"Leung, Jeffrey","first_name":"Jeffrey","last_name":"Leung"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"status":"public","doi":"10.7554/eLife.19048","date_created":"2018-12-11T11:51:29Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":5,"day":"14","date_published":"2016-09-14T00:00:00Z"},{"publisher":"Nature Publishing Group","publication":"Nature Plants","file":[{"file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:12:36Z","file_size":127781,"relation":"main_file","file_id":"4954","creator":"system","access_level":"open_access","checksum":"9ba65f558563b287f875f48fa9f30fb2","content_type":"application/pdf"},{"relation":"main_file","date_created":"2018-12-12T10:12:37Z","file_size":430556,"file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","date_updated":"2020-07-14T12:44:45Z","checksum":"550d252be808d8ca2b43e83dddb4212f","content_type":"application/pdf","creator":"system","access_level":"open_access","file_id":"4955"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:45Z","abstract":[{"text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.","lang":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"5907","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” <i>Nature Plants</i>, vol. 2. Nature Publishing Group, 2016.","mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” <i>Nature Plants</i>, vol. 2, 16102, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/nplants.2016.102\">10.1038/nplants.2016.102</a>.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. <i>Nature Plants</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/nplants.2016.102\">10.1038/nplants.2016.102</a>","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” <i>Nature Plants</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nplants.2016.102\">https://doi.org/10.1038/nplants.2016.102</a>.","apa":"Molnar, G., Fendrych, M., &#38; Friml, J. (2016). Plasma membrane: Negative attraction. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2016.102\">https://doi.org/10.1038/nplants.2016.102</a>"},"quality_controlled":"1","article_number":"16102","intvolume":"         2","pubrep_id":"1007","month":"07","type":"journal_article","ddc":["581"],"day":"01","date_published":"2016-07-01T00:00:00Z","doi":"10.1038/nplants.2016.102","volume":2,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:30Z","oa_version":"Published Version","status":"public","author":[{"first_name":"Gergely","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar"},{"last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"oa":1,"year":"2016","has_accepted_license":"1","_id":"1345","date_updated":"2021-01-12T06:50:02Z","title":"Plasma membrane: Negative attraction"},{"ddc":["570"],"type":"journal_article","pubrep_id":"653","intvolume":"         7","article_number":"11710","month":"06","ec_funded":1,"quality_controlled":"1","citation":{"ieee":"W. Dejonghe <i>et al.</i>, “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>, vol. 7, 11710, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>.","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>."},"publication_status":"published","abstract":[{"text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.","lang":"eng"}],"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publist_id":"5906","publisher":"Nature Publishing Group","scopus_import":1,"file":[{"file_id":"5369","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":3532505,"date_created":"2018-12-12T10:18:47Z","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:45Z","publication":"Nature Communications","title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","date_updated":"2023-09-07T12:54:35Z","_id":"1346","related_material":{"record":[{"id":"7172","status":"public","relation":"dissertation_contains"}]},"project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"year":"2016","acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","has_accepted_license":"1","oa":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Wim","full_name":"Dejonghe, Wim","last_name":"Dejonghe"},{"full_name":"Kuenen, Sabine","first_name":"Sabine","last_name":"Kuenen"},{"last_name":"Mylle","first_name":"Evelien","full_name":"Mylle, Evelien"},{"full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","full_name":"Keech, Olivier","last_name":"Keech"},{"full_name":"Viotti, Corrado","first_name":"Corrado","last_name":"Viotti"},{"full_name":"Swerts, Jef","first_name":"Jef","last_name":"Swerts"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas","orcid":"0000-0002-9767-8699"},{"first_name":"Fausto","full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"full_name":"Delang, Simon","first_name":"Simon","last_name":"Delang"},{"first_name":"Stefan","full_name":"Scholl, Stefan","last_name":"Scholl"},{"last_name":"Zarza","first_name":"Xavier","full_name":"Zarza, Xavier"},{"last_name":"Heilmann","first_name":"Mareike","full_name":"Heilmann, Mareike"},{"last_name":"Kourelis","first_name":"Jiorgos","full_name":"Kourelis, Jiorgos"},{"first_name":"Jaroslaw","full_name":"Kasprowicz, Jaroslaw","last_name":"Kasprowicz"},{"last_name":"Nguyen","first_name":"Le","full_name":"Nguyen, Le"},{"full_name":"Drozdzecki, Andrzej","first_name":"Andrzej","last_name":"Drozdzecki"},{"first_name":"Isabelle","full_name":"Van Houtte, Isabelle","last_name":"Van Houtte"},{"first_name":"Anna","full_name":"Szatmári, Anna","last_name":"Szatmári"},{"first_name":"Mateusz","full_name":"Majda, Mateusz","last_name":"Majda"},{"last_name":"Baisa","first_name":"Gary","full_name":"Baisa, Gary"},{"last_name":"Bednarek","first_name":"Sebastian","full_name":"Bednarek, Sebastian"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"full_name":"Audenaert, Dominique","first_name":"Dominique","last_name":"Audenaert"},{"full_name":"Testerink, Christa","first_name":"Christa","last_name":"Testerink"},{"last_name":"Munnik","first_name":"Teun","full_name":"Munnik, Teun"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"last_name":"Schumacher","first_name":"Karin","full_name":"Schumacher, Karin"},{"first_name":"Johan","full_name":"Winne, Johan","last_name":"Winne"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Verstreken","full_name":"Verstreken, Patrik","first_name":"Patrik"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"status":"public","doi":"10.1038/ncomms11710","date_created":"2018-12-11T11:51:30Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":7,"day":"08","date_published":"2016-06-08T00:00:00Z"},{"doi":"10.1103/PhysRevX.6.011012","volume":6,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:30Z","oa_version":"Published Version","author":[{"last_name":"Schmidt","full_name":"Schmidt, Richard","first_name":"Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","day":"01","date_published":"2016-01-01T00:00:00Z","_id":"1347","date_updated":"2021-01-12T06:50:03Z","title":"Deformation of a quantum many-particle system by a rotating impurity","oa":1,"acknowledgement":"We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory.","year":"2016","has_accepted_license":"1","publication_status":"published","citation":{"ieee":"R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” <i>Physical Review X</i>, vol. 6, no. 1. American Physical Society, 2016.","ista":"Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012.","short":"R. Schmidt, M. Lemeshko, Physical Review X 6 (2016).","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” <i>Physical Review X</i>, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.011012\">10.1103/PhysRevX.6.011012</a>.","ama":"Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. <i>Physical Review X</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.011012\">10.1103/PhysRevX.6.011012</a>","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.011012\">https://doi.org/10.1103/PhysRevX.6.011012</a>.","apa":"Schmidt, R., &#38; Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.011012\">https://doi.org/10.1103/PhysRevX.6.011012</a>"},"quality_controlled":"1","publisher":"American Physical Society","file":[{"file_name":"IST-2016-652-v1+1_PhysRevX.6.011012.pdf","date_updated":"2020-07-14T12:44:45Z","file_size":1165869,"date_created":"2018-12-12T10:15:59Z","relation":"main_file","file_id":"5183","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"6757a164d3c38905e05b2b5a188cb8ff"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:45Z","publication":"Physical Review X","abstract":[{"text":"During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.","lang":"eng"}],"publist_id":"5902","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"type":"journal_article","ddc":["530"],"issue":"1","article_number":"011012","intvolume":"         6","pubrep_id":"652","month":"01"},{"year":"2016","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"oa":1,"title":"Long-term stability of the HR 8799 planetary system without resonant lock","article_processing_charge":"No","date_updated":"2023-08-09T11:09:50Z","_id":"13478","external_id":{"arxiv":["1606.07819"]},"date_published":"2016-08-18T00:00:00Z","day":"18","status":"public","author":[{"orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"last_name":"Davies","full_name":"Davies, Melvyn B.","first_name":"Melvyn B."},{"last_name":"Mustill","full_name":"Mustill, Alexander J.","first_name":"Alexander J."},{"last_name":"Johansen","full_name":"Johansen, Anders","first_name":"Anders"},{"first_name":"Ross P.","full_name":"Church, Ross P.","last_name":"Church"}],"extern":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-03T10:15:28Z","volume":592,"doi":"10.1051/0004-6361/201526309","month":"08","intvolume":"       592","article_number":"A147","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201526309"}],"arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"text":"HR 8799 is a star accompanied by four massive planets on wide orbits. The observed planetary configuration has been shown to be unstable on a timescale much shorter than the estimated age of the system (~30 Myr) unless the planets are locked into mean motion resonances. This condition is characterised by small-amplitude libration of one or more resonant angles that stabilise the system by preventing close encounters. We simulate planetary systems similar to the HR 8799 planetary system, exploring the parameter space in separation between the orbits, planetary masses and distance from the Sun to the star. We find systems that look like HR 8799 and remain stable for longer than the estimated age of HR 8799. None of our systems are forced into resonances. We find, with nominal masses (Mb = 5 MJup and Mc,d,e = 7 MJup) and in a narrow range of orbit separations, that 5 of 100 systems match the observations and lifetime. Considering a broad range of orbit separations, we find 12 of 900 similar systems. The systems survive significantly longer because of their slightly increased initial orbit separations compared to assuming circular orbits from the observed positions. A small increase in separation leads to a significant increase in survival time. The low eccentricity the orbits develop from gravitational interaction is enough for the planets to match the observations. With lower masses, but still comfortably within the estimated planet mass uncertainty, we find 18 of 100 matching and long-lived systems in a narrow orbital separation range. In the broad separation range, we find 82 of 900 matching systems. Our results imply that the planets in the HR 8799 system do not have to be in strong mean motion resonances. We also investigate the future of wide-orbit planetary systems using our HR 8799 analogues. We find that 80% of the systems have two planets left after strong planet-planet scattering and these are on eccentric orbits with semi-major axes of a1 ~ 10 AU and a2 ~ 30−1000 AU. We speculate that other wide-orbit planetary systems, such as AB Pic and HD 106906, are the remnants of HR 8799 analogues that underwent close encounters and dynamical instability.","lang":"eng"}],"publication":"Astronomy & Astrophysics","scopus_import":"1","publisher":"EDP Sciences","quality_controlled":"1","citation":{"ieee":"Y. L. L. Götberg, M. B. Davies, A. J. Mustill, A. Johansen, and R. P. Church, “Long-term stability of the HR 8799 planetary system without resonant lock,” <i>Astronomy &#38; Astrophysics</i>, vol. 592. EDP Sciences, 2016.","ista":"Götberg YLL, Davies MB, Mustill AJ, Johansen A, Church RP. 2016. Long-term stability of the HR 8799 planetary system without resonant lock. Astronomy &#38; Astrophysics. 592, A147.","mla":"Götberg, Ylva Louise Linsdotter, et al. “Long-Term Stability of the HR 8799 Planetary System without Resonant Lock.” <i>Astronomy &#38; Astrophysics</i>, vol. 592, A147, EDP Sciences, 2016, doi:<a href=\"https://doi.org/10.1051/0004-6361/201526309\">10.1051/0004-6361/201526309</a>.","short":"Y.L.L. Götberg, M.B. Davies, A.J. Mustill, A. Johansen, R.P. Church, Astronomy &#38; Astrophysics 592 (2016).","ama":"Götberg YLL, Davies MB, Mustill AJ, Johansen A, Church RP. Long-term stability of the HR 8799 planetary system without resonant lock. <i>Astronomy &#38; Astrophysics</i>. 2016;592. doi:<a href=\"https://doi.org/10.1051/0004-6361/201526309\">10.1051/0004-6361/201526309</a>","apa":"Götberg, Y. L. L., Davies, M. B., Mustill, A. J., Johansen, A., &#38; Church, R. P. (2016). Long-term stability of the HR 8799 planetary system without resonant lock. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201526309\">https://doi.org/10.1051/0004-6361/201526309</a>","chicago":"Götberg, Ylva Louise Linsdotter, Melvyn B. Davies, Alexander J. Mustill, Anders Johansen, and Ross P. Church. “Long-Term Stability of the HR 8799 Planetary System without Resonant Lock.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2016. <a href=\"https://doi.org/10.1051/0004-6361/201526309\">https://doi.org/10.1051/0004-6361/201526309</a>."},"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"publication_status":"published","article_type":"original"},{"main_file_link":[{"url":"https://arxiv.org/abs/1610.07144","open_access":"1"}],"type":"conference","intvolume":"      9843","month":"08","ec_funded":1,"page":"31 - 42","citation":{"ama":"Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:<a href=\"https://doi.org/10.1007/978-3-319-44543-4_3\">10.1007/978-3-319-44543-4_3</a>","apa":"Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-44543-4_3\">https://doi.org/10.1007/978-3-319-44543-4_3</a>","chicago":"Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-44543-4_3\">https://doi.org/10.1007/978-3-319-44543-4_3</a>.","ista":"Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.","ieee":"R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.","mla":"Fulek, Radoslav. <i>Bounded Embeddings of Graphs in the Plane</i>. Vol. 9843, Springer, 2016, pp. 31–42, doi:<a href=\"https://doi.org/10.1007/978-3-319-44543-4_3\">10.1007/978-3-319-44543-4_3</a>.","short":"R. Fulek, in:, Springer, 2016, pp. 31–42."},"quality_controlled":"1","alternative_title":["LNCS"],"publication_status":"published","abstract":[{"text":"A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) &lt; x(v) whenever γ(u) &lt; γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.","lang":"eng"}],"department":[{"_id":"UlWa"}],"publist_id":"5901","language":[{"iso":"eng"}],"publisher":"Springer","scopus_import":1,"title":"Bounded embeddings of graphs in the plane","_id":"1348","date_updated":"2021-01-12T06:50:03Z","conference":{"end_date":"2018-08-19","start_date":"2016-08-17","location":"Helsinki, Finland","name":"IWOCA: International Workshop on Combinatorial Algorithms"},"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"year":"2016","oa":1,"oa_version":"Preprint","author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","full_name":"Fulek, Radoslav"}],"status":"public","doi":"10.1007/978-3-319-44543-4_3","volume":9843,"date_created":"2018-12-11T11:51:31Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"09","date_published":"2016-08-09T00:00:00Z"},{"publication_status":"published","quality_controlled":"1","citation":{"mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, ACM, 2016, pp. 1163–70, doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>.","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, Denver, CO, USA, 2016, pp. 1163–1170.","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 1163–70. ACM, 2016. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>.","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., &#38; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i> (pp. 1163–1170). Denver, CO, USA: ACM. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>. ACM; 2016:1163-1170. doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>"},"file_date_updated":"2020-07-14T12:44:45Z","scopus_import":1,"publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","file_size":979026,"date_created":"2018-12-12T10:16:27Z","access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"a1896e39e4113f2711e46b435d5f3e69","file_id":"5214"}],"publisher":"ACM","language":[{"iso":"eng"}],"publist_id":"5900","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"ddc":["576"],"type":"conference","page":"1163 - 1170","ec_funded":1,"month":"07","pubrep_id":"650","date_created":"2018-12-11T11:51:31Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2908812.2908909","author":[{"full_name":"Oliveto, Pietro","first_name":"Pietro","last_name":"Oliveto"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","date_published":"2016-07-20T00:00:00Z","day":"20","conference":{"name":"GECCO: Genetic and evolutionary computation conference","location":"Denver, CO, USA","start_date":"2016-07-20","end_date":"2016-07-24"},"date_updated":"2021-01-12T06:50:03Z","_id":"1349","title":"When non-elitism outperforms elitism for crossing fitness valleys","oa":1,"has_accepted_license":"1","year":"2016","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"}]},{"oa_version":"Preprint","status":"public","author":[{"first_name":"José","full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán"},{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois"},{"last_name":"Frotscher","full_name":"Frotscher, Michael","first_name":"Michael"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"}],"doi":"10.1126/science.aaf1836","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:31Z","volume":353,"day":"09","date_published":"2016-09-09T00:00:00Z","title":"Synaptic mechanisms of pattern completion in the hippocampal CA3 network","date_updated":"2021-01-12T06:50:04Z","_id":"1350","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","call_identifier":"FP7"},{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","call_identifier":"FWF"}],"year":"2016","has_accepted_license":"1","oa":1,"quality_controlled":"1","citation":{"chicago":"Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf1836\">https://doi.org/10.1126/science.aaf1836</a>.","apa":"Guzmán, J., Schlögl, A., Frotscher, M., &#38; Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf1836\">https://doi.org/10.1126/science.aaf1836</a>","ama":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. <i>Science</i>. 2016;353(6304):1117-1123. doi:<a href=\"https://doi.org/10.1126/science.aaf1836\">10.1126/science.aaf1836</a>","short":"J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.","mla":"Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” <i>Science</i>, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:<a href=\"https://doi.org/10.1126/science.aaf1836\">10.1126/science.aaf1836</a>.","ieee":"J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” <i>Science</i>, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016.","ista":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123."},"publication_status":"published","abstract":[{"text":"The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks.","lang":"eng"}],"publist_id":"5899","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","file":[{"relation":"main_file","date_created":"2018-12-12T10:12:27Z","file_size":19408143,"date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf","content_type":"application/pdf","checksum":"89caefa4e181424cbf0aecc835fcc5ec","access_level":"open_access","creator":"system","file_id":"4945"}],"publication":"Science","scopus_import":1,"file_date_updated":"2020-07-14T12:44:46Z","ddc":["570"],"type":"journal_article","pubrep_id":"823","intvolume":"       353","month":"09","page":"1117 - 1123","acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"issue":"6304"},{"doi":"10.1103/PhysRevB.94.085152","volume":94,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:32Z","oa_version":"Preprint","status":"public","author":[{"last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","first_name":"Jan","full_name":"Kaczmarczyk, Jan"},{"full_name":"Schickling, Tobias","first_name":"Tobias","last_name":"Schickling"},{"last_name":"Bünemann","full_name":"Bünemann, Jörg","first_name":"Jörg"}],"day":"30","date_published":"2016-08-30T00:00:00Z","_id":"1352","date_updated":"2021-01-12T06:50:05Z","title":"Coexistence of nematic order and superconductivity in the Hubbard model","oa":1,"acknowledgement":"The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed.","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"year":"2016","publication_status":"published","citation":{"mla":"Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">10.1103/PhysRevB.94.085152</a>.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 94(8), 085152.","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 8. American Physical Society, 2016.","apa":"Kaczmarczyk, J., Schickling, T., &#38; Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">https://doi.org/10.1103/PhysRevB.94.085152</a>","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">https://doi.org/10.1103/PhysRevB.94.085152</a>.","ama":"Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;94(8). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">10.1103/PhysRevB.94.085152</a>"},"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review B - Condensed Matter and Materials Physics","scopus_import":1,"abstract":[{"text":"We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.","lang":"eng"}],"publist_id":"5897","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1512.06688","open_access":"1"}],"ec_funded":1,"issue":"8","article_number":"085152","intvolume":"        94","month":"08"},{"date_created":"2018-12-11T11:51:32Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":26,"doi":"10.1142/S0218196716500430","author":[{"last_name":"Barto","full_name":"Barto, Libor","first_name":"Libor"},{"full_name":"Kazda, Alexandr","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda"}],"status":"public","oa_version":"Preprint","date_published":"2016-07-20T00:00:00Z","day":"20","date_updated":"2021-01-12T06:50:06Z","_id":"1353","title":"Deciding absorption","oa":1,"year":"2016","acknowledgement":"Libor Barto and Alexandr Kazda were supported by the the Grant Agency of the Czech Republic, grant GACR 13-01832S. ","publication_status":"published","quality_controlled":"1","citation":{"ista":"Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra and Computation. 26(5), 1033–1060.","ieee":"L. Barto and A. Kazda, “Deciding absorption,” <i>International Journal of Algebra and Computation</i>, vol. 26, no. 5. World Scientific Publishing, pp. 1033–1060, 2016.","short":"L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016) 1033–1060.","mla":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” <i>International Journal of Algebra and Computation</i>, vol. 26, no. 5, World Scientific Publishing, 2016, pp. 1033–60, doi:<a href=\"https://doi.org/10.1142/S0218196716500430\">10.1142/S0218196716500430</a>.","ama":"Barto L, Kazda A. Deciding absorption. <i>International Journal of Algebra and Computation</i>. 2016;26(5):1033-1060. doi:<a href=\"https://doi.org/10.1142/S0218196716500430\">10.1142/S0218196716500430</a>","chicago":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” <i>International Journal of Algebra and Computation</i>. World Scientific Publishing, 2016. <a href=\"https://doi.org/10.1142/S0218196716500430\">https://doi.org/10.1142/S0218196716500430</a>.","apa":"Barto, L., &#38; Kazda, A. (2016). Deciding absorption. <i>International Journal of Algebra and Computation</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218196716500430\">https://doi.org/10.1142/S0218196716500430</a>"},"scopus_import":1,"publication":"International Journal of Algebra and Computation","publisher":"World Scientific Publishing","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"publist_id":"5893","abstract":[{"lang":"eng","text":"We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations."}],"type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1512.07009","open_access":"1"}],"issue":"5","page":"1033 - 1060","month":"07","intvolume":"        26"},{"author":[{"first_name":"Paul","full_name":"Dieterle, Paul","last_name":"Dieterle"},{"first_name":"Mahmoud","full_name":"Kalaee, Mahmoud","last_name":"Kalaee"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"}],"status":"public","quality_controlled":"1","citation":{"mla":"Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” <i>Physical Review Applied</i>, vol. 6, no. 1, 014013, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.6.014013\">10.1103/PhysRevApplied.6.014013</a>.","short":"P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6 (2016).","ista":"Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013.","ieee":"P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity electromechanics on a silicon-on-insulator platform,” <i>Physical Review Applied</i>, vol. 6, no. 1. American Physical Society, 2016.","chicago":"Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” <i>Physical Review Applied</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevApplied.6.014013\">https://doi.org/10.1103/PhysRevApplied.6.014013</a>.","apa":"Dieterle, P., Kalaee, M., Fink, J. M., &#38; Painter, O. (2016). Superconducting cavity electromechanics on a silicon-on-insulator platform. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.6.014013\">https://doi.org/10.1103/PhysRevApplied.6.014013</a>","ama":"Dieterle P, Kalaee M, Fink JM, Painter O. Superconducting cavity electromechanics on a silicon-on-insulator platform. <i>Physical Review Applied</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.6.014013\">10.1103/PhysRevApplied.6.014013</a>"},"oa_version":"Preprint","publication_status":"published","date_created":"2018-12-11T11:51:32Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":6,"doi":"10.1103/PhysRevApplied.6.014013","department":[{"_id":"JoFi"}],"publist_id":"5892","language":[{"iso":"eng"}],"abstract":[{"text":"Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11  mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6  Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211  mK.","lang":"eng"}],"date_published":"2016-07-22T00:00:00Z","publication":"Physical Review Applied","scopus_import":1,"publisher":"American Physical Society","day":"22","title":"Superconducting cavity electromechanics on a silicon-on-insulator platform","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.04019"}],"date_updated":"2021-01-12T06:50:06Z","_id":"1354","type":"journal_article","month":"07","intvolume":"         6","year":"2016","article_number":"014013","issue":"1","oa":1},{"ddc":["530"],"type":"journal_article","month":"08","pubrep_id":"629","intvolume":"         7","article_number":"12396","quality_controlled":"1","citation":{"short":"J.M. Fink, M. Kalaee, A. Pitanti, R. Norte, L. Heinzle, M. Davanço, K. Srinivasan, O. Painter, Nature Communications 7 (2016).","mla":"Fink, Johannes M., et al. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” <i>Nature Communications</i>, vol. 7, 12396, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12396\">10.1038/ncomms12396</a>.","ista":"Fink JM, Kalaee M, Pitanti A, Norte R, Heinzle L, Davanço M, Srinivasan K, Painter O. 2016. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 7, 12396.","ieee":"J. M. Fink <i>et al.</i>, “Quantum electromechanics on silicon nitride nanomembranes,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","chicago":"Fink, Johannes M, Mahmoud Kalaee, Alessandro Pitanti, Richard Norte, Lukas Heinzle, Marcelo Davanço, Kartik Srinivasan, and Oskar Painter. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12396\">https://doi.org/10.1038/ncomms12396</a>.","apa":"Fink, J. M., Kalaee, M., Pitanti, A., Norte, R., Heinzle, L., Davanço, M., … Painter, O. (2016). Quantum electromechanics on silicon nitride nanomembranes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12396\">https://doi.org/10.1038/ncomms12396</a>","ama":"Fink JM, Kalaee M, Pitanti A, et al. Quantum electromechanics on silicon nitride nanomembranes. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12396\">10.1038/ncomms12396</a>"},"publication_status":"published","department":[{"_id":"JoFi"}],"publist_id":"5891","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments."}],"scopus_import":1,"publication":"Nature Communications","file_date_updated":"2020-07-14T12:44:46Z","file":[{"file_id":"5014","creator":"system","access_level":"open_access","checksum":"25513bd59d5bda495efa8f5920e91b22","content_type":"application/pdf","file_name":"IST-2016-629-v1+1_ncomms12396.pdf","date_updated":"2020-07-14T12:44:46Z","file_size":2139802,"date_created":"2018-12-12T10:13:30Z","relation":"main_file"}],"publisher":"Nature Publishing Group","title":"Quantum electromechanics on silicon nitride nanomembranes","date_updated":"2021-01-12T06:50:06Z","_id":"1355","has_accepted_license":"1","year":"2016","acknowledgement":"This work was supported by the DARPA MESO programme, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.P. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme, NEMO (GA 298861). Certain commercial equipment and software are identified in this documentation to describe the subject adequately. Such identification does not imply recommendation or endorsement by the NIST, nor does it imply that the equipment identified is necessarily the best available for the purpose.","oa":1,"author":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mahmoud","full_name":"Kalaee, Mahmoud","last_name":"Kalaee"},{"full_name":"Pitanti, Alessandro","first_name":"Alessandro","last_name":"Pitanti"},{"full_name":"Norte, Richard","first_name":"Richard","last_name":"Norte"},{"full_name":"Heinzle, Lukas","first_name":"Lukas","last_name":"Heinzle"},{"last_name":"Davanço","first_name":"Marcelo","full_name":"Davanço, Marcelo"},{"last_name":"Srinivasan","full_name":"Srinivasan, Kartik","first_name":"Kartik"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:51:33Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":7,"doi":"10.1038/ncomms12396","date_published":"2016-08-03T00:00:00Z","day":"03"},{"day":"05","date_published":"2016-01-05T00:00:00Z","doi":"10.1534/genetics.115.184796","volume":202,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:33Z","oa_version":"Submitted Version","status":"public","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"oa":1,"year":"2016","has_accepted_license":"1","_id":"1356","date_updated":"2021-01-12T06:50:07Z","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","publisher":"Genetics Society of America","publication":"Genetics","scopus_import":1,"file_date_updated":"2020-07-14T12:44:46Z","file":[{"file_id":"4687","content_type":"application/pdf","checksum":"3562b89c821a4be84edf2b6ebd870cf5","access_level":"open_access","creator":"system","file_size":112674,"date_created":"2018-12-12T10:08:26Z","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","relation":"main_file"}],"publist_id":"5889","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"publication_status":"published","citation":{"apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>.","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. 2016;202(1):3-4. doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>.","short":"N.H. Barton, Genetics 202 (2016) 3–4.","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” <i>Genetics</i>, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4."},"quality_controlled":"1","page":"3 - 4","issue":"1","intvolume":"       202","pubrep_id":"769","month":"01","type":"journal_article","ddc":["570"]},{"date_published":"2016-03-01T00:00:00Z","day":"01","status":"public","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:51:33Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":202,"doi":"10.1534/genetics.116.187542","has_accepted_license":"1","year":"2016","oa":1,"title":"Richard Hudson and Norman Kaplan on the coalescent process","date_updated":"2021-01-12T06:50:07Z","_id":"1357","department":[{"_id":"NiBa"}],"publist_id":"5888","language":[{"iso":"eng"}],"scopus_import":1,"file":[{"file_id":"5127","checksum":"b2174bab2de1d1142900062a150f35c9","content_type":"application/pdf","creator":"system","access_level":"open_access","file_size":130779,"date_created":"2018-12-12T10:15:09Z","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","date_updated":"2020-07-14T12:44:46Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:46Z","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","citation":{"short":"N.H. Barton, Genetics 202 (2016) 865–866.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>.","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. 2016;202(3):865-866. doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>"},"publication_status":"published","month":"03","pubrep_id":"768","intvolume":"       202","issue":"3","page":"865 - 866","ddc":["576"],"type":"journal_article"},{"volume":7,"date_created":"2018-12-11T11:51:34Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/ncomms12307","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Tamar","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"}],"status":"public","oa_version":"Published Version","date_published":"2016-08-04T00:00:00Z","day":"04","related_material":{"record":[{"id":"6071","relation":"dissertation_contains","status":"public"}]},"_id":"1358","date_updated":"2023-09-07T12:53:49Z","title":"Intrinsic limits to gene regulation by global crosstalk","oa":1,"has_accepted_license":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF"}],"year":"2016","publication_status":"published","citation":{"short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>"},"quality_controlled":"1","publication":"Nature Communications","file_date_updated":"2020-07-14T12:44:46Z","file":[{"date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","file_size":861805,"date_created":"2018-12-12T10:12:01Z","relation":"main_file","file_id":"4919","access_level":"open_access","creator":"system","checksum":"fe3f3a1526d180b29fe691ab11435b78","content_type":"application/pdf"},{"date_created":"2018-12-12T10:12:02Z","file_size":1084703,"date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","relation":"main_file","file_id":"4920","content_type":"application/pdf","checksum":"164864a1a675f3ad80e9917c27aba07f","access_level":"open_access","creator":"system"}],"scopus_import":1,"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publist_id":"5887","abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"type":"journal_article","ddc":["576"],"ec_funded":1,"month":"08","article_number":"12307","intvolume":"         7","pubrep_id":"627"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"type":"journal_article","intvolume":"       113","month":"04","ec_funded":1,"page":"4422 - 4427","issue":"16","citation":{"ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427."},"quality_controlled":"1","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population."}],"language":[{"iso":"eng"}],"publist_id":"5886","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","publication":"PNAS","scopus_import":1,"title":"The effect of gene interactions on the long-term response to selection","article_processing_charge":"No","_id":"1359","date_updated":"2021-01-12T06:50:08Z","year":"2016","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"oa":1,"oa_version":"Published Version","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"status":"public","pmid":1,"doi":"10.1073/pnas.1518830113","volume":113,"date_created":"2018-12-11T11:51:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["27044080"]},"day":"19","date_published":"2016-04-19T00:00:00Z"},{"ec_funded":1,"page":"4501 - 4513","issue":"10","intvolume":"       144","month":"10","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"publisher":"American Mathematical Society","publication":"Proceedings of the American Mathematical Society","scopus_import":1,"abstract":[{"text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. ","lang":"eng"}],"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publist_id":"5885","publication_status":"published","citation":{"ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. 2016;144(10):4501-4513. doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>","apa":"Akopyan, A., Balitskiy, A., Karasev, R., &#38; Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>.","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513.","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016.","mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>.","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513."},"quality_controlled":"1","oa":1,"acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2016","_id":"1360","date_updated":"2021-01-12T06:50:09Z","article_processing_charge":"No","title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","day":"01","date_published":"2016-10-01T00:00:00Z","doi":"10.1090/proc/13062","volume":144,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:34Z","oa_version":"Preprint","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"},{"last_name":"Balitskiy","full_name":"Balitskiy, Alexey","first_name":"Alexey"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"},{"full_name":"Sharipova, Anastasia","first_name":"Anastasia","last_name":"Sharipova"}],"status":"public"},{"day":"11","date_published":"2016-07-11T00:00:00Z","oa_version":"Published Version","status":"public","author":[{"last_name":"Da","full_name":"Da, Fang","first_name":"Fang"},{"first_name":"David","full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn"},{"last_name":"Batty","first_name":"Christopher","full_name":"Batty, Christopher"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eitan","full_name":"Grinspun, Eitan","last_name":"Grinspun"}],"doi":"10.1145/2897824.2925899","volume":35,"date_created":"2018-12-11T11:51:35Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"has_accepted_license":"1","oa":1,"title":"Surface only liquids","_id":"1361","date_updated":"2023-02-21T10:36:07Z","conference":{"end_date":"2016-07-28","start_date":"2016-07-24","name":"ACM SIGGRAPH","location":"Anaheim, CA, USA"},"abstract":[{"lang":"eng","text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes."}],"language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"5881","publisher":"ACM","file_date_updated":"2020-07-14T12:44:46Z","scopus_import":1,"file":[{"relation":"main_file","file_size":10561865,"date_created":"2018-12-12T10:08:01Z","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf","content_type":"application/pdf","checksum":"6d662893bd447d4f575b4961a2247811","access_level":"open_access","creator":"system","file_id":"4660"}],"citation":{"mla":"Da, Fang, et al. <i>Surface Only Liquids</i>. Vol. 35, no. 4, a78, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>.","short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.","ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>.","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., &#38; Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>"},"quality_controlled":"1","alternative_title":["ACM Transactions on Graphics"],"publication_status":"published","article_number":"a78","pubrep_id":"637","intvolume":"        35","month":"07","ec_funded":1,"issue":"4","type":"conference","ddc":["000"]},{"_id":"1362","date_updated":"2023-09-07T12:02:56Z","related_material":{"record":[{"status":"public","id":"839","relation":"dissertation_contains"}]},"conference":{"name":"ACM SIGGRAPH","location":"Anaheim, CA, USA","start_date":"2016-07-24","end_date":"2016-07-28"},"title":"Fast approximations for boundary element based brittle fracture simulation","oa":1,"year":"2016","project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"has_accepted_license":"1","doi":"10.1145/2897824.2925902","volume":35,"date_created":"2018-12-11T11:51:35Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"full_name":"Hahn, David","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","day":"01","date_published":"2016-07-01T00:00:00Z","type":"conference","ddc":["000"],"ec_funded":1,"issue":"4","article_number":"104","pubrep_id":"632","intvolume":"        35","month":"07","publication_status":"published","citation":{"ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>","apa":"Hahn, D., &#38; Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>","chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>.","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","mla":"Hahn, David, and Chris Wojtan. <i>Fast Approximations for Boundary Element Based Brittle Fracture Simulation</i>. Vol. 35, no. 4, 104, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>."},"quality_controlled":"1","alternative_title":["ACM Transactions on Graphics"],"publisher":"ACM","file":[{"access_level":"open_access","creator":"system","checksum":"943712d9c9dc8bb5048d4adc561d7d38","content_type":"application/pdf","file_id":"5121","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-632-v1+2_a104-hahn.pdf","date_created":"2018-12-12T10:15:04Z","file_size":12453704}],"file_date_updated":"2020-07-14T12:44:46Z","abstract":[{"lang":"eng","text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches."}],"department":[{"_id":"ChWo"}],"publist_id":"5880","language":[{"iso":"eng"}]},{"citation":{"chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>","short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. <i>Generalized Non-Reflecting Boundaries for Fluid Re-Simulation</i>. Vol. 35, no. 4, 96, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>.","ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96."},"quality_controlled":"1","alternative_title":["ACM Transactions on Graphics"],"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"5879","department":[{"_id":"ChWo"}],"abstract":[{"lang":"eng","text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special &quot;non-reflecting&quot; boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation."}],"file":[{"content_type":"application/pdf","checksum":"140b5532f0a2a006a0149cab7c73c17c","access_level":"open_access","creator":"system","file_id":"4981","relation":"main_file","date_created":"2018-12-12T10:13:00Z","file_size":12422760,"date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf"}],"file_date_updated":"2020-07-14T12:44:47Z","publisher":"ACM","type":"conference","ddc":["000"],"month":"07","article_number":"96","pubrep_id":"631","intvolume":"        35","issue":"4","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"status":"public","oa_version":"Published Version","volume":35,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:35Z","doi":"10.1145/2897824.2925963","date_published":"2016-07-11T00:00:00Z","day":"11","title":"Generalized non-reflecting boundaries for fluid re-simulation","conference":{"location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","end_date":"2016-07-28","start_date":"2016-07-24"},"_id":"1363","date_updated":"2023-02-21T10:36:12Z","has_accepted_license":"1","acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ","project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"year":"2016","oa":1}]