[{"date_created":"2018-12-11T11:44:53Z","publication":"Nature","volume":560,"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"year":"2018","quality_controlled":"1","title":"Inositol phosphates are assembly co-factors for HIV-1","date_published":"2018-08-29T00:00:00Z","type":"journal_article","citation":{"ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Dick, Robert","first_name":"Robert","last_name":"Dick"},{"last_name":"Zadrozny","first_name":"Kaneil K","full_name":"Zadrozny, Kaneil K"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian","full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Terri D","full_name":"Lyddon, Terri D","last_name":"Lyddon"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"last_name":"Wagner","first_name":"Jonathan M","full_name":"Wagner, Jonathan M"},{"full_name":"Perilla, Juan R","first_name":"Juan R","last_name":"Perilla"},{"first_name":"Pornillos Barbie K","full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser"},{"full_name":"Johnson, Marc C","first_name":"Marc C","last_name":"Johnson"},{"last_name":"Pornillos","full_name":"Pornillos, Owen","first_name":"Owen"},{"first_name":"Volker","full_name":"Vogt, Volker","last_name":"Vogt"}],"oa":1,"date_updated":"2023-09-12T07:44:37Z","oa_version":"Submitted Version","department":[{"_id":"FlSc"}],"_id":"150","scopus_import":"1","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"page":"509–512","article_type":"original","intvolume":"       560","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","isi":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"month":"08","day":"29","publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"pmid":1,"status":"public","doi":"10.1038/s41586-018-0396-4","abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"issue":"7719"},{"status":"public","issue":"10","doi":"10.1016/j.tcb.2018.06.006","abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"publist_id":"7769","isi":1,"month":"07","publication_status":"published","day":"26","publisher":"Elsevier","intvolume":"        28","page":"835 - 867","article_type":"original","language":[{"iso":"eng"}],"_id":"152","external_id":{"isi":["000445118200007"]},"file_date_updated":"2020-07-14T12:45:00Z","scopus_import":"1","type":"journal_article","date_updated":"2023-09-13T08:51:56Z","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_id":"6994","date_created":"2019-11-07T12:55:20Z","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_size":2185385,"checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","creator":"lsazanov"}],"department":[{"_id":"LeSa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>"},"has_accepted_license":"1","author":[{"last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"oa":1,"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2018-07-26T00:00:00Z","title":"Mammalian mitochondrial complex I structure and disease causing mutations","quality_controlled":"1","ddc":["572"],"date_created":"2018-12-11T11:44:54Z","year":"2018","publication":"Trends in Cell Biology","article_processing_charge":"No","volume":28},{"author":[{"last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369"},{"last_name":"Reversat","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","last_name":"Leithner"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"citation":{"mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_updated":"2023-09-13T08:56:35Z","oa_version":"None","type":"book_chapter","scopus_import":"1","external_id":{"isi":["000452412300006"],"pmid":["30165964"]},"_id":"153","article_processing_charge":"No","volume":147,"publication":"Methods in Cell Biology","year":"2018","date_created":"2018-12-11T11:44:54Z","quality_controlled":"1","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","date_published":"2018-07-27T00:00:00Z","day":"27","publication_status":"published","month":"07","isi":1,"abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"publist_id":"7768","doi":"10.1016/bs.mcb.2018.07.004","publication_identifier":{"issn":["0091679X"]},"status":"public","pmid":1,"language":[{"iso":"eng"}],"page":"79 - 91","intvolume":"       147","publisher":"Academic Press"},{"external_id":{"isi":["000439639700001"]},"file_date_updated":"2020-07-14T12:45:01Z","scopus_import":"1","_id":"154","oa_version":"Published Version","date_updated":"2023-09-19T09:31:15Z","department":[{"_id":"RoSe"}],"file":[{"file_name":"2018_MathPhysics_Moser.pdf","file_size":496973,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","date_created":"2018-12-17T16:49:02Z","file_id":"5729","relation":"main_file","checksum":"411c4db5700d7297c9cd8ebc5dd29091","creator":"dernst"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3. Springer, 2018.","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. 2018;21(3). doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3, 19, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>.","apa":"Moser, T., &#38; Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"oa":1,"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"type":"journal_article","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"date_published":"2018-09-01T00:00:00Z","title":"Stability of the 2+2 fermionic system with point interactions","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","publication":"Mathematical Physics Analysis and Geometry","volume":21,"article_processing_charge":"No","ddc":["530"],"date_created":"2018-12-11T11:44:55Z","issue":"3","doi":"10.1007/s11040-018-9275-3","publist_id":"7767","abstract":[{"lang":"eng","text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system."}],"status":"public","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","day":"01","ec_funded":1,"isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"52"}]},"month":"09","publisher":"Springer","language":[{"iso":"eng"}],"article_number":"19","intvolume":"        21","article_type":"original"},{"_id":"155","editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","first_name":"A","last_name":"Ostendorf"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"last_name":"Nunzi","first_name":"J M","full_name":"Nunzi, J M"}],"external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"scopus_import":"1","type":"conference","date_updated":"2023-09-18T08:12:24Z","oa_version":"Preprint","department":[{"_id":"JoFi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>."},"oa":1,"author":[{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"},{"last_name":"Aquilina","first_name":"Matteo","full_name":"Aquilina, Matteo"},{"last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"}],"conference":{"name":"SPIE: The international society for optical engineering","end_date":"2018-04-26","location":"Strasbourg, France","start_date":"2018-04-22"},"title":"Routing thermal noise through quantum networks","date_published":"2018-05-04T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:44:55Z","year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.01000"}],"volume":10672,"article_processing_charge":"No","status":"public","abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"publist_id":"7766","doi":"10.1117/12.2309928","alternative_title":["Proceedings of SPIE"],"isi":1,"month":"05","publication_status":"published","day":"04","publisher":"SPIE","article_number":"106721N","intvolume":"     10672","language":[{"iso":"eng"}],"arxiv":1},{"publisher":"Springer","intvolume":"     10951","page":"147 - 164","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"doi":"10.1007/978-3-319-95582-7_9","publist_id":"7765","alternative_title":["LNCS"],"month":"07","isi":1,"publication_status":"published","day":"12","conference":{"end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-15","name":"FM: International Symposium on Formal Methods"},"title":"The compound interest in relaxing punctuality","date_published":"2018-07-12T00:00:00Z","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","date_created":"2018-12-11T11:44:55Z","ddc":["000"],"year":"2018","article_processing_charge":"No","volume":10951,"_id":"156","external_id":{"isi":["000489765800009"]},"scopus_import":"1","file_date_updated":"2020-10-09T06:22:41Z","type":"conference","file":[{"file_name":"2018_LNCS_Ferrere.pdf","date_updated":"2020-10-09T06:22:41Z","content_type":"application/pdf","file_size":485576,"access_level":"open_access","file_id":"8637","success":1,"date_created":"2020-10-09T06:22:41Z","checksum":"a045c213c42c445f1889326f8db82a0a","relation":"main_file","creator":"dernst"}],"department":[{"_id":"ToHe"}],"date_updated":"2023-09-19T10:05:37Z","oa_version":"Submitted Version","author":[{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"}],"oa":1,"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>."}},{"ddc":["000"],"date_created":"2018-12-11T11:44:56Z","year":"2018","publication":"Nature","volume":559,"article_processing_charge":"No","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Evolution of cooperation in stochastic games","date_published":"2018-07-04T00:00:00Z","quality_controlled":"1","type":"journal_article","date_updated":"2023-09-11T13:43:22Z","oa_version":"Submitted Version","department":[{"_id":"KrCh"}],"file":[{"date_updated":"2020-07-14T12:45:02Z","content_type":"application/pdf","file_size":2834442,"file_name":"2018_Nature_Hilbe.pdf","file_id":"7049","date_created":"2019-11-19T08:09:57Z","access_level":"open_access","creator":"dernst","checksum":"011ab905cf9a410bc2b96f15174d654d","relation":"main_file"}],"citation":{"ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"last_name":"Šimsa","full_name":"Šimsa, Štepán","first_name":"Štepán"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"_id":"157","external_id":{"isi":["000438240900054"]},"file_date_updated":"2020-07-14T12:45:02Z","scopus_import":"1","intvolume":"       559","page":"246 - 249","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","isi":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"month":"07","publication_status":"published","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","day":"04","ec_funded":1,"status":"public","issue":"7713","publist_id":"7764","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"doi":"10.1038/s41586-018-0277-x"},{"_id":"158","external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"scopus_import":"1","type":"journal_article","department":[{"_id":"JiFr"}],"date_updated":"2025-05-07T11:12:31Z","oa_version":"Submitted Version","author":[{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"last_name":"Park","full_name":"Park, Chulmin","first_name":"Chulmin"},{"last_name":"Gutièrrez","full_name":"Gutièrrez, Carla","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","first_name":"Barbara","last_name":"Wójcikowska"},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Chen","first_name":"Junyi","full_name":"Chen, Junyi"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"last_name":"Dresselhaus","first_name":"Thomas","full_name":"Dresselhaus, Thomas"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Laux","full_name":"Laux, Thomas","first_name":"Thomas"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>","ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>."},"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","date_published":"2018-07-16T00:00:00Z","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","date_created":"2018-12-11T11:44:56Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"year":"2018","volume":4,"article_processing_charge":"No","publication":"Nature Plants","status":"public","pmid":1,"issue":"8","publist_id":"7763","doi":"10.1038/s41477-018-0204-z","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","relation":"press_release","description":"News on IST Homepage"}]},"month":"07","isi":1,"acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","publication_status":"published","ec_funded":1,"day":"16","publisher":"Nature Publishing Group","intvolume":"         4","page":"548 - 553","language":[{"iso":"eng"}]},{"status":"public","issue":"8","doi":"10.1038/s41589-018-0090-8","publist_id":"7762","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"isi":1,"month":"07","related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"publication_status":"published","day":"16","publisher":"Nature Publishing Group","intvolume":"        14","page":"764 - 767","article_type":"original","language":[{"iso":"eng"}],"_id":"159","external_id":{"isi":["000438970200010"]},"file_date_updated":"2020-07-14T12:45:03Z","scopus_import":"1","type":"journal_article","date_updated":"2023-09-13T09:36:35Z","oa_version":"Submitted Version","department":[{"_id":"JoDa"}],"file":[{"creator":"dernst","checksum":"d42935094ec845f54a0688bf12986d62","relation":"main_file","date_updated":"2020-07-14T12:45:03Z","content_type":"application/pdf","file_size":6321000,"file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","file_id":"7832","date_created":"2020-05-14T12:14:09Z","access_level":"open_access"}],"citation":{"ieee":"T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767. doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>.","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","oa":1,"author":[{"last_name":"Fehrentz","first_name":"Timm","full_name":"Fehrentz, Timm"},{"last_name":"Huber","first_name":"Florian","full_name":"Huber, Florian"},{"first_name":"Nina","full_name":"Hartrampf, Nina","last_name":"Hartrampf"},{"first_name":"Tobias","full_name":"Bruegmann, Tobias","last_name":"Bruegmann"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"first_name":"Nicholas","full_name":"Fine, Nicholas","last_name":"Fine"},{"last_name":"Malan","first_name":"Daniela","full_name":"Malan, Daniela"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl"},{"first_name":"Denis","full_name":"Tikhonov, Denis","last_name":"Tikhonov"},{"last_name":"Sumser","first_name":"Maritn","full_name":"Sumser, Maritn"},{"first_name":"Philipp","full_name":"Sasse, Philipp","last_name":"Sasse"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"last_name":"Zhorov","full_name":"Zhorov, Boris","first_name":"Boris"},{"last_name":"Klocker","first_name":"Nikolaj","full_name":"Klocker, Nikolaj"},{"last_name":"Trauner","first_name":"Dirk","full_name":"Trauner, Dirk"}],"date_published":"2018-07-16T00:00:00Z","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","quality_controlled":"1","ddc":["570"],"date_created":"2018-12-11T11:44:56Z","year":"2018","publication":"Nature Chemical Biology","article_processing_charge":"No","volume":14},{"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","date_published":"2018-10-16T00:00:00Z","ddc":["532"],"date_created":"2018-12-11T11:44:10Z","publication":"Physical Review Fluids","volume":3,"article_processing_charge":"No","year":"2018","_id":"16","file_date_updated":"2020-07-14T12:45:04Z","scopus_import":"1","external_id":{"isi":["000447469200001"]},"type":"journal_article","pubrep_id":"1062","citation":{"chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","author":[{"last_name":"Varshney","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"},{"last_name":"Steinberg","full_name":"Steinberg, Victor","first_name":"Victor"}],"oa":1,"oa_version":"Submitted Version","date_updated":"2023-09-13T08:57:05Z","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:04Z","file_size":1838431,"file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","file_id":"5043","date_created":"2018-12-12T10:13:56Z","access_level":"open_access","creator":"system","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","relation":"main_file"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","article_type":"original","article_number":"103303","intvolume":"         3","language":[{"iso":"eng"}],"status":"public","doi":"10.1103/PhysRevFluids.3.103303","abstract":[{"lang":"eng","text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives."}],"publist_id":"8039","issue":"10","isi":1,"month":"10","day":"16","ec_funded":1,"acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","publication_status":"published"},{"status":"public","doi":"10.1007/978-3-319-96145-3_5","publist_id":"7761","abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"related_material":{"record":[{"id":"8332","relation":"dissertation_contains","status":"public"}]},"month":"07","isi":1,"alternative_title":["LNCS"],"day":"18","publication_status":"published","publisher":"Springer","page":"79 - 102","intvolume":"     10981","language":[{"iso":"eng"}],"_id":"160","scopus_import":"1","file_date_updated":"2020-07-14T12:45:04Z","external_id":{"isi":["000491481600005"]},"type":"conference","author":[{"last_name":"Kragl","first_name":"Bernhard","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"oa":1,"citation":{"ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","file":[{"creator":"dernst","relation":"main_file","checksum":"c64fff560fe5a7532ec10626ad1c215e","date_created":"2018-12-17T12:52:12Z","file_id":"5705","access_level":"open_access","file_size":1603844,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:04Z","file_name":"2018_LNCS_Kragl.pdf"}],"department":[{"_id":"ToHe"}],"oa_version":"Published Version","date_updated":"2023-09-13T08:45:09Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"location":"Oxford, UK","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"quality_controlled":"1","title":"Layered Concurrent Programs","date_published":"2018-07-18T00:00:00Z","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"date_created":"2018-12-11T11:44:57Z","ddc":["000"],"article_processing_charge":"No","volume":10981,"year":"2018"},{"publist_id":"7760","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"doi":"10.1038/s41467-018-05417-9","issue":"1","status":"public","ec_funded":1,"day":"30","publication_status":"published","related_material":{"record":[{"relation":"popular_science","id":"5587","status":"public"}]},"month":"07","isi":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"         9","article_number":"2988","scopus_import":"1","file_date_updated":"2020-07-14T12:45:06Z","external_id":{"isi":["000440149300021"]},"_id":"161","oa":1,"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"full_name":"Mc, Andersson Anna","first_name":"Andersson Anna","last_name":"Mc"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>."},"file":[{"access_level":"open_access","file_id":"5728","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:06Z","file_size":1043205,"checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","relation":"main_file","creator":"dernst"}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:39Z","type":"journal_article","quality_controlled":"1","title":"Statistical mechanics for metabolic networks during steady state growth","date_published":"2018-07-30T00:00:00Z","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","volume":9,"publication":"Nature Communications","year":"2018","date_created":"2018-12-11T11:44:57Z","ddc":["570"]},{"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7"}]},"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","citation":{"apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>","mla":"Stroeymeyt, Nathalie, et al. <i>Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018."},"oa":1,"author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Crespi, Alessandro","first_name":"Alessandro","last_name":"Crespi"},{"full_name":"Mersch, Danielle","first_name":"Danielle","last_name":"Mersch"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"full_name":"Keller, Laurent","first_name":"Laurent","last_name":"Keller"}],"date_updated":"2023-10-17T11:50:04Z","oa_version":"Published Version","department":[{"_id":"SyCr"}],"status":"public","_id":"13055","abstract":[{"lang":"eng","text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n                                                     - correction of URLs within README.txt file\r\n"}],"doi":"10.5281/ZENODO.1322669","ddc":["570"],"date_created":"2023-05-23T13:24:51Z","article_processing_charge":"No","year":"2018","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"publisher":"Zenodo","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Social network plasticity decreases disease transmission in a eusocial insect","date_published":"2018-10-23T00:00:00Z"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Zenodo","date_published":"2018-12-07T00:00:00Z","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","ddc":["570"],"date_created":"2023-05-23T16:08:20Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"year":"2018","article_processing_charge":"No","status":"public","_id":"13059","doi":"10.5281/ZENODO.2025846","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7181"}]},"month":"12","date_updated":"2023-09-06T14:32:51Z","oa_version":"Published Version","department":[{"_id":"FyKo"}],"citation":{"ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","author":[{"last_name":"Garriga","full_name":"Garriga, Edgar","first_name":"Edgar"},{"full_name":"di Tommaso, Paolo","first_name":"Paolo","last_name":"di Tommaso"},{"full_name":"Magis, Cedrik","first_name":"Cedrik","last_name":"Magis"},{"last_name":"Erb","first_name":"Ionas","full_name":"Erb, Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"last_name":"Laayouni","first_name":"Hafid","full_name":"Laayouni, Hafid"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"oa":1},{"type":"journal_article","oa":1,"author":[{"orcid":"0000-0002-8101-2518","first_name":"Marion A","full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard"},{"last_name":"Cosseau","first_name":"Celine","full_name":"Cosseau, Celine"},{"first_name":"Sabrina","full_name":"Ferré, Sabrina","last_name":"Ferré"},{"full_name":"Quack, Thomas","first_name":"Thomas","last_name":"Quack"},{"last_name":"Grevelding","first_name":"Christoph","full_name":"Grevelding, Christoph"},{"last_name":"Couté","first_name":"Yohann","full_name":"Couté, Yohann"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684."},"file":[{"relation":"main_file","checksum":"d6331d4385b1fffd6b47b45d5949d841","creator":"dernst","file_name":"2018_eLife_Picard.pdf","file_size":3158125,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:43Z","access_level":"open_access","date_created":"2018-12-17T11:55:05Z","file_id":"5695"}],"department":[{"_id":"BeVi"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:12Z","_id":"131","scopus_import":"1","file_date_updated":"2020-07-14T12:44:43Z","external_id":{"isi":["000441388200001"]},"date_created":"2018-12-11T11:44:47Z","ddc":["570"],"article_processing_charge":"No","volume":7,"publication":"eLife","year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","date_published":"2018-08-13T00:00:00Z","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"month":"08","related_material":{"record":[{"id":"5586","relation":"popular_science","status":"public"}]},"isi":1,"day":"13","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","publication_status":"published","status":"public","publist_id":"7792","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"doi":"10.7554/eLife.35684","article_type":"original","intvolume":"         7","article_number":"e35684","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2018-08-06T00:00:00Z","title":"Defining lineage potential and fate behavior of precursors during pancreas development","ddc":["570"],"date_created":"2018-12-11T11:44:48Z","publication":"Developmental Cell","volume":46,"article_processing_charge":"No","year":"2018","_id":"132","file_date_updated":"2020-07-14T12:44:43Z","scopus_import":"1","external_id":{"isi":["000441327300012"]},"type":"journal_article","citation":{"mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. 2018;46(3):360-375. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>","ieee":"M. Sznurkowska <i>et al.</i>, “Defining lineage potential and fate behavior of precursors during pancreas development,” <i>Developmental Cell</i>, vol. 46, no. 3. Cell Press, pp. 360–375, 2018."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Sznurkowska, Magdalena","first_name":"Magdalena","last_name":"Sznurkowska"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Roberta","full_name":"Azzarelli, Roberta","last_name":"Azzarelli"},{"last_name":"Rulands","first_name":"Steffen","full_name":"Rulands, Steffen"},{"last_name":"Nestorowa","first_name":"Sonia","full_name":"Nestorowa, Sonia"},{"full_name":"Hindley, Christopher","first_name":"Christopher","last_name":"Hindley"},{"last_name":"Nichols","first_name":"Jennifer","full_name":"Nichols, Jennifer"},{"last_name":"Göttgens","full_name":"Göttgens, Berthold","first_name":"Berthold"},{"last_name":"Huch","first_name":"Meritxell","full_name":"Huch, Meritxell"},{"full_name":"Philpott, Anna","first_name":"Anna","last_name":"Philpott"},{"last_name":"Simons","first_name":"Benjamin","full_name":"Simons, Benjamin"}],"oa":1,"date_updated":"2023-09-11T12:52:41Z","oa_version":"Published Version","file":[{"date_created":"2018-12-17T10:49:49Z","file_id":"5694","access_level":"open_access","file_size":8948384,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:43Z","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","creator":"dernst","relation":"main_file","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65"}],"department":[{"_id":"EdHa"}],"publisher":"Cell Press","page":"360 - 375","article_type":"original","intvolume":"        46","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"publist_id":"7791","doi":"10.1016/j.devcel.2018.06.028","issue":"3","isi":1,"month":"08","day":"06","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","publication_status":"published"},{"alternative_title":["LIPIcs"],"related_material":{"record":[{"status":"public","id":"6426","relation":"earlier_version"},{"relation":"dissertation_contains","id":"8332","status":"public"}]},"month":"08","publication_status":"published","day":"13","status":"public","publication_identifier":{"issn":["18688969"]},"doi":"10.4230/LIPIcs.CONCUR.2018.21","abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"publist_id":"7790","intvolume":"       118","article_number":"21","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","pubrep_id":"1039","type":"conference","file":[{"creator":"system","relation":"main_file","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_size":745438,"date_updated":"2020-07-14T12:44:44Z","content_type":"application/pdf","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_created":"2018-12-12T10:18:46Z","file_id":"5368","access_level":"open_access"}],"department":[{"_id":"ToHe"}],"oa_version":"Published Version","date_updated":"2023-09-07T13:18:00Z","author":[{"full_name":"Kragl, Bernhard","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>","mla":"Kragl, Bernhard, et al. <i>Synchronizing the Asynchronous</i>. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>."},"_id":"133","scopus_import":1,"file_date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-11T11:44:48Z","ddc":["000"],"year":"2018","volume":118,"conference":{"end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04","name":"CONCUR: International Conference on Concurrency Theory"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Synchronizing the asynchronous","date_published":"2018-08-13T00:00:00Z","project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"quality_controlled":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2018-07-30T00:00:00Z","title":"Water surface wavelets","quality_controlled":"1","ddc":["000"],"date_created":"2018-12-11T11:44:48Z","year":"2018","publication":"ACM Transactions on Graphics","article_processing_charge":"No","volume":37,"_id":"134","external_id":{"isi":["000448185000055"]},"file_date_updated":"2020-07-14T12:44:45Z","scopus_import":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2024-02-28T13:58:51Z","department":[{"_id":"ChWo"}],"file":[{"checksum":"db75ebabe2ec432bf41389e614d6ef62","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"5744","date_created":"2018-12-18T09:59:23Z","file_name":"2018_ACM_Jeschke.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:45Z","file_size":22185016}],"citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4, 94, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., &#38; Wojtan, C. (2018). Water surface wavelets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. <i>ACM Transactions on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4. ACM, 2018."},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"last_name":"Jeschke","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Skrivan, Tomas"},{"full_name":"Mueller Fischer, Matthias","first_name":"Matthias","last_name":"Mueller Fischer"},{"first_name":"Nuttapong","full_name":"Chentanez, Nuttapong","last_name":"Chentanez"},{"full_name":"Macklin, Miles","first_name":"Miles","last_name":"Macklin"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"oa":1,"publisher":"ACM","article_number":"94","intvolume":"        37","language":[{"iso":"eng"}],"status":"public","issue":"4","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.","lang":"eng"}],"doi":"10.1145/3197517.3201336","publist_id":"7789","alternative_title":["SIGGRAPH"],"isi":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","relation":"press_release"}]},"month":"07","publication_status":"published","day":"30","ec_funded":1},{"publication_status":"published","ec_funded":1,"day":"22","alternative_title":["Eurographics"],"month":"05","isi":1,"issue":"2","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"doi":"10.1111/cgf.13351","status":"public","publication_identifier":{"issn":["0167-7055"]},"language":[{"iso":"eng"}],"intvolume":"        37","page":"169 - 177","article_type":"original","publisher":"Wiley","file":[{"creator":"wojtan","checksum":"8edb90da8a72395eb5d970580e0925b6","relation":"main_file","content_type":"application/pdf","date_updated":"2020-10-08T08:38:23Z","file_size":54309947,"file_name":"exnbflip.pdf","file_id":"8627","date_created":"2020-10-08T08:38:23Z","success":1,"access_level":"open_access"}],"department":[{"_id":"ChWo"}],"oa_version":"Submitted Version","date_updated":"2023-09-11T14:00:26Z","author":[{"last_name":"Sato","first_name":"Takahiro","full_name":"Sato, Takahiro"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"},{"last_name":"Igarashi","first_name":"Takeo","full_name":"Igarashi, Takeo"},{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. 2018;37(2):169-177. doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2018). Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177."},"has_accepted_license":"1","type":"journal_article","external_id":{"isi":["000434085600016"]},"scopus_import":"1","file_date_updated":"2020-10-08T08:38:23Z","_id":"135","year":"2018","article_processing_charge":"No","volume":37,"publication":"Computer Graphics Forum","date_created":"2018-12-11T11:44:49Z","ddc":["006"],"date_published":"2018-05-22T00:00:00Z","title":"Extended narrow band FLIP for liquid simulations","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"quality_controlled":"1"},{"language":[{"iso":"eng"}],"arxiv":1,"intvolume":"        98","publisher":"American Physical Society","day":"13","publication_status":"published","month":"08","isi":1,"doi":"10.1103/PhysRevE.98.023105","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"issue":"2","status":"public","article_processing_charge":"No","volume":98,"publication":"Physical Review E","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"date_created":"2018-12-11T11:44:49Z","quality_controlled":"1","date_published":"2018-08-13T00:00:00Z","title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","author":[{"last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","full_name":"Suri, Balachandra"},{"full_name":"Tithof, Jeffrey","first_name":"Jeffrey","last_name":"Tithof"},{"last_name":"Grigoriev","first_name":"Roman","full_name":"Grigoriev, Roman"},{"last_name":"Schatz","first_name":"Michael","full_name":"Schatz, Michael"}],"oa":1,"citation":{"mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 98, no. 2, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>.","apa":"Suri, B., Tithof, J., Grigoriev, R., &#38; Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. 2018;98(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>","ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 98, no. 2. American Physical Society, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"date_updated":"2023-10-10T13:29:10Z","oa_version":"Submitted Version","type":"journal_article","scopus_import":"1","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"_id":"136"}]