[{"publication_status":"published","date_published":"2015-02-02T00:00:00Z","status":"public","month":"02","year":"2015","author":[{"full_name":"Dell, Emma J.","last_name":"Dell","first_name":"Emma J."},{"last_name":"Capozzi","first_name":"Brian","full_name":"Capozzi, Brian"},{"first_name":"Jianlong","last_name":"Xia","full_name":"Xia, Jianlong"},{"first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"full_name":"Campos, Luis M.","first_name":"Luis M.","last_name":"Campos"}],"intvolume":"         7","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"date_created":"2024-09-09T10:55:42Z","external_id":{"pmid":["25698329"]},"oa_version":"None","doi":"10.1038/nchem.2160","title":"Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","pmid":1,"publication":"Nature Chemistry","page":"209-214","OA_type":"closed access","_id":"17976","article_type":"original","extern":"1","publisher":"Springer Nature","day":"02","citation":{"ama":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. 2015;7(3):209-214. doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>","short":"E.J. Dell, B. Capozzi, J. Xia, L. Venkataraman, L.M. Campos, Nature Chemistry 7 (2015) 209–214.","mla":"Dell, Emma J., et al. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 209–14, doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>.","ista":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. 2015. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. Nature Chemistry. 7(3), 209–214.","chicago":"Dell, Emma J., Brian Capozzi, Jianlong Xia, Latha Venkataraman, and Luis M. Campos. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>.","ieee":"E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, “Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 209–214, 2015.","apa":"Dell, E. J., Capozzi, B., Xia, J., Venkataraman, L., &#38; Campos, L. M. (2015). Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>"},"issue":"3","type":"journal_article","volume":7,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials."}],"language":[{"iso":"eng"}],"date_updated":"2025-01-02T13:35:46Z"},{"date_published":"2015-07-01T00:00:00Z","page":"1008 - 1016","publication_status":"published","date_created":"2018-12-11T11:54:05Z","publisher":"Nature Publishing Group","day":"01","author":[{"full_name":"Sandra Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"},{"full_name":"Seo, Jinsoo","last_name":"Seo","first_name":"Jinsoo"},{"last_name":"Kwon","first_name":"Ester","full_name":"Kwon, Ester J"},{"full_name":"Rudenko, Andrii","first_name":"Andrii","last_name":"Rudenko"},{"full_name":"Cho, Sukhee","last_name":"Cho","first_name":"Sukhee"},{"first_name":"Wenyuan","last_name":"Wang","full_name":"Wang, Wenyuan"},{"last_name":"Flood","first_name":"Zachary","full_name":"Flood, Zachary C"},{"full_name":"Martorell, Anthony J","last_name":"Martorell","first_name":"Anthony"},{"last_name":"Ericsson","first_name":"Maria","full_name":"Ericsson, Maria"},{"last_name":"Mungenast","first_name":"Alison","full_name":"Mungenast, Alison E"},{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"}],"extern":1,"publist_id":"5308","intvolume":"        18","year":"2015","status":"public","_id":"1802","month":"07","title":"The schizophrenia risk gene product miR-137 alters presynaptic plasticity","quality_controlled":0,"citation":{"mla":"Siegert, Sandra, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” <i>Nature Neuroscience</i>, vol. 18, Nature Publishing Group, 2015, pp. 1008–16, doi:<a href=\"https://doi.org/10.1038/nn.4023\">10.1038/nn.4023</a>.","ama":"Siegert S, Seo J, Kwon E, et al. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. <i>Nature Neuroscience</i>. 2015;18:1008-1016. doi:<a href=\"https://doi.org/10.1038/nn.4023\">10.1038/nn.4023</a>","short":"S. Siegert, J. Seo, E. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, A. Martorell, M. Ericsson, A. Mungenast, L. Tsai, Nature Neuroscience 18 (2015) 1008–1016.","ieee":"S. Siegert <i>et al.</i>, “The schizophrenia risk gene product miR-137 alters presynaptic plasticity,” <i>Nature Neuroscience</i>, vol. 18. Nature Publishing Group, pp. 1008–1016, 2015.","chicago":"Siegert, Sandra, Jinsoo Seo, Ester Kwon, Andrii Rudenko, Sukhee Cho, Wenyuan Wang, Zachary Flood, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nn.4023\">https://doi.org/10.1038/nn.4023</a>.","apa":"Siegert, S., Seo, J., Kwon, E., Rudenko, A., Cho, S., Wang, W., … Tsai, L. (2015). The schizophrenia risk gene product miR-137 alters presynaptic plasticity. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.4023\">https://doi.org/10.1038/nn.4023</a>","ista":"Siegert S, Seo J, Kwon E, Rudenko A, Cho S, Wang W, Flood Z, Martorell A, Ericsson M, Mungenast A, Tsai L. 2015. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 18, 1008–1016."},"doi":"10.1038/nn.4023","date_updated":"2021-01-12T06:53:18Z","acknowledgement":"S.S. was supported by a Human Frontier Science Program (HFSP) long-term postdoctoral fellowship and a Swiss National Science Foundation fellowship for prospective researchers. E.J.K. was supported by a Simons Foundation Postdoctoral Fellowship. A.R. was supported by a NARSAD Young Investigator Award. This work was supported by a Seed Grant from the Simons Center for the Social Brain and US National Institutes of Health grant RO1 MH 091115 to L.-H.T.","abstract":[{"text":"Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.","lang":"eng"}],"publication":"Nature Neuroscience","type":"journal_article","volume":18},{"quality_controlled":0,"title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","issue":"23","citation":{"short":"D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert, S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296.","ama":"Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. 2015;112(23):7291-7296. doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>","mla":"Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>, vol. 112, no. 23, National Academy of Sciences, 2015, pp. 7291–96, doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>.","ista":"Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 112(23), 7291–7296.","apa":"Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015). Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>","chicago":"Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>.","ieee":"D. Rei <i>et al.</i>, “Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway,” <i>PNAS</i>, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296, 2015."},"doi":"10.1073/pnas.1415845112","publication":"PNAS","abstract":[{"text":"Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.","lang":"eng"}],"acknowledgement":"AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nNS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nSNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung","date_updated":"2021-01-12T06:53:18Z","type":"journal_article","volume":112,"date_published":"2015-06-09T00:00:00Z","page":"7291 - 7296","publication_status":"published","publist_id":"5307","intvolume":"       112","author":[{"full_name":"Rei, Damien","first_name":"Damien","last_name":"Rei"},{"first_name":"Xenos","last_name":"Mason","full_name":"Mason, Xenos"},{"full_name":"Seo, Jinsoo","first_name":"Jinsoo","last_name":"Seo"},{"last_name":"Gräff","first_name":"Johannes","full_name":"Gräff, Johannes"},{"full_name":"Rudenko, Andrii","first_name":"Andrii","last_name":"Rudenko"},{"full_name":"Wang, Jùn","last_name":"Wang","first_name":"Jùn"},{"first_name":"Richard","last_name":"Rueda","full_name":"Rueda, Richard"},{"first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Sandra Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cho","first_name":"Sukhee","full_name":"Cho, Sukhee"},{"first_name":"Rebecca","last_name":"Canter","full_name":"Canter, Rebecca G"},{"full_name":"Mungenast, Alison E","first_name":"Alison","last_name":"Mungenast"},{"full_name":"Deisseroth, Karl A","first_name":"Karl","last_name":"Deisseroth"},{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"}],"extern":1,"publisher":"National Academy of Sciences","day":"09","date_created":"2018-12-11T11:54:06Z","month":"06","_id":"1803","status":"public","year":"2015"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","article_number":"10781","citation":{"ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>.","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>"},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"date_updated":"2025-09-29T10:58:13Z","type":"journal_article","volume":5,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"day":"12","publisher":"Nature Publishing Group","_id":"1804","quality_controlled":"1","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","scopus_import":"1","ddc":["530"],"doi":"10.1038/srep10781","external_id":{"isi":["000356150200001"]},"file_date_updated":"2020-07-14T12:45:16Z","oa_version":"Published Version","file":[{"relation":"main_file","access_level":"open_access","file_name":"IST-2016-450-v1+1_srep10781.pdf","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-12T10:17:26Z","file_id":"5280","content_type":"application/pdf","creator":"system","checksum":"7716f582f8c9d82d8f2bf80bf896b440","file_size":2449723}],"publication":"Scientific Reports","article_processing_charge":"No","date_published":"2015-06-12T00:00:00Z","corr_author":"1","department":[{"_id":"BjHo"}],"pubrep_id":"450","publication_status":"published","intvolume":"         5","publist_id":"5306","author":[{"orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer"},{"last_name":"Do","first_name":"Younghae","full_name":"Do, Younghae"},{"first_name":"Ying","last_name":"Lai","full_name":"Lai, Ying"}],"date_created":"2018-12-11T11:54:06Z","isi":1,"month":"06","status":"public","year":"2015"},{"doi":"10.1016/j.comgeo.2014.08.010","oa_version":"Published Version","external_id":{"isi":["000357353200006"]},"OA_place":"publisher","quality_controlled":"1","title":"Homological reconstruction and simplification in R3","scopus_import":"1","article_processing_charge":"No","publication":"Computational Geometry: Theory and Applications","department":[{"_id":"HeEd"}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.comgeo.2014.08.010","open_access":"1"}],"date_published":"2015-06-03T00:00:00Z","ec_funded":1,"corr_author":"1","month":"06","status":"public","year":"2015","intvolume":"        48","publist_id":"5305","author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","last_name":"Bauer"},{"last_name":"Devillers","first_name":"Olivier","full_name":"Devillers, Olivier"},{"last_name":"Glisse","first_name":"Marc","full_name":"Glisse, Marc"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"}],"date_created":"2018-12-11T11:54:06Z","isi":1,"citation":{"ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2015). Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. 2015;48(8):606-621. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>."},"issue":"8","volume":48,"type":"journal_article","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"date_updated":"2025-09-23T09:18:30Z","page":"606 - 621","OA_type":"free access","article_type":"original","_id":"1805","related_material":{"record":[{"relation":"earlier_version","id":"2812","status":"public"}]},"publisher":"Elsevier","day":"03"},{"page":"603 - 624","_id":"1807","day":"01","publisher":"EDP Sciences","citation":{"ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624.","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>."},"issue":"3","type":"journal_article","volume":21,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-23T10:45:09Z","department":[{"_id":"RoSe"}],"publication_status":"published","date_published":"2015-05-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"corr_author":"1","status":"public","month":"05","year":"2015","author":[{"full_name":"Goldman, Michael","first_name":"Michael","last_name":"Goldman"},{"full_name":"Royo-Letelier, Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena","last_name":"Royo-Letelier"}],"publist_id":"5303","intvolume":"        21","date_created":"2018-12-11T11:54:07Z","isi":1,"arxiv":1,"oa_version":"Preprint","doi":"10.1051/cocv/2014040","external_id":{"isi":["000356012000001"],"arxiv":["1401.1727"]},"title":"Sharp interface limit for two components Bose-Einstein condensates","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"ESAIM - Control, Optimisation and Calculus of Variations"},{"department":[{"_id":"ToHe"}],"publication_status":"published","date_published":"2015-05-01T00:00:00Z","status":"public","_id":"1808","month":"05","year":"2015","author":[{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"publist_id":"5302","intvolume":"        25","date_created":"2018-12-11T11:54:07Z","isi":1,"day":"01","publisher":"ACM","oa_version":"None","doi":"10.1145/2745799","external_id":{"isi":["000354789200001"]},"citation":{"ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>"},"title":"Guest editors' introduction to special issue on computational methods in systems biology","quality_controlled":"1","scopus_import":"1","issue":"2","article_number":"7","article_processing_charge":"No","type":"journal_article","volume":25,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"date_updated":"2025-09-23T09:11:51Z"},{"date_published":"2015-05-18T00:00:00Z","corr_author":"1","pubrep_id":"453","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"intvolume":"        10","publist_id":"5299","date_created":"2018-12-11T11:54:07Z","isi":1,"status":"public","month":"05","year":"2015","title":"Indirect genetic effects and the dynamics of social interactions","quality_controlled":"1","scopus_import":"1","external_id":{"isi":["000354917300064"]},"file_date_updated":"2020-07-14T12:45:17Z","oa_version":"Published Version","doi":"10.1371/journal.pone.0126907","ddc":["570","576"],"file":[{"relation":"main_file","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_size":2748982,"content_type":"application/pdf","creator":"system","file_id":"4730","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:09:07Z","access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"publication":"PLoS One","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"9715","relation":"research_data"},{"relation":"research_data","status":"public","id":"9772"}]},"day":"18","publisher":"Public Library of Science","_id":"1809","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"5","citation":{"short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015."},"abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-23T09:21:54Z","type":"journal_article","volume":10,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"page":"1 - 9","_id":"1810","publisher":"Elsevier","day":"01","citation":{"ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":27,"date_updated":"2025-09-23T07:55:38Z","language":[{"iso":"eng"}],"abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"publication_status":"published","department":[{"_id":"ToBo"}],"pubrep_id":"493","corr_author":"1","date_published":"2015-06-01T00:00:00Z","ec_funded":1,"year":"2015","month":"06","status":"public","isi":1,"date_created":"2018-12-11T11:54:08Z","publist_id":"5298","intvolume":"        27","author":[{"first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"file":[{"content_type":"application/pdf","creator":"system","file_id":"5277","file_size":1047255,"checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:17:23Z","relation":"main_file"}],"ddc":["570"],"doi":"10.1016/j.mib.2015.05.008","file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000365065400003"]},"oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","article_processing_charge":"No","publication":"Current Opinion in Microbiology"},{"scopus_import":"1","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","doi":"10.1063/1.4921227","oa_version":"Preprint","external_id":{"arxiv":["1409.0110"],"isi":["000355920800016"]},"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","publication":"Journal of Mathematical Physics","article_processing_charge":"No","corr_author":"1","ec_funded":1,"date_published":"2015-05-20T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"publication_status":"published","department":[{"_id":"MiLe"}],"date_created":"2018-12-11T11:54:08Z","isi":1,"arxiv":1,"author":[{"first_name":"Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Jänkälä, Kari","first_name":"Kari","last_name":"Jänkälä"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"}],"publist_id":"5295","intvolume":"        56","year":"2015","status":"public","month":"05","issue":"5","article_number":"052105","citation":{"ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>"},"date_updated":"2025-09-23T07:53:00Z","abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"type":"journal_article","volume":56,"day":"20","publisher":"American Institute of Physics","_id":"1811"},{"_id":"1812","publisher":"IOP Publishing","day":"01","type":"journal_article","volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"date_updated":"2025-09-23T08:45:19Z","citation":{"mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>, vol. 17, no. 4, 045005, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. 2015;17(4). doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>","apa":"Lahrz, M., Lemeshko, M., &#38; Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>.","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” <i>New Journal of Physics</i>, vol. 17, no. 4. IOP Publishing, 2015.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"045005","issue":"4","month":"04","status":"public","year":"2015","publist_id":"5294","intvolume":"        17","author":[{"full_name":"Lahrz, Martin","first_name":"Martin","last_name":"Lahrz"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"last_name":"Mathey","first_name":"Ludwig","full_name":"Mathey, Ludwig"}],"isi":1,"date_created":"2018-12-11T11:54:09Z","department":[{"_id":"MiLe"}],"pubrep_id":"446","publication_status":"published","date_published":"2015-04-01T00:00:00Z","article_processing_charge":"No","publication":"New Journal of Physics","ddc":["530"],"doi":"10.1088/1367-2630/17/4/045005","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000354022400001"]},"file":[{"relation":"main_file","file_id":"5184","content_type":"application/pdf","creator":"system","file_size":1900925,"checksum":"551f751a75b39b89a1db2f7f498f9a49","file_name":"IST-2016-446-v1+1_document.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:59Z","date_updated":"2020-07-14T12:45:17Z"}],"quality_controlled":"1","title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","scopus_import":"1"},{"_id":"1813","publisher":"American Physical Society","day":"18","citation":{"short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>."},"article_number":"203001","issue":"20","type":"journal_article","volume":114,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}],"date_updated":"2025-09-23T10:40:28Z","department":[{"_id":"MiLe"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.03447"}],"date_published":"2015-05-18T00:00:00Z","corr_author":"1","month":"05","status":"public","year":"2015","intvolume":"       114","publist_id":"5293","author":[{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"arxiv":1,"date_created":"2018-12-11T11:54:09Z","isi":1,"doi":"10.1103/PhysRevLett.114.203001","oa_version":"Preprint","external_id":{"isi":["000354969900003"],"arxiv":["1502.03447"]},"quality_controlled":"1","title":"Rotation of quantum impurities in the presence of a many-body environment","scopus_import":"1","article_processing_charge":"No","publication":"Physical Review Letters"},{"ec_funded":1,"date_published":"2015-04-01T00:00:00Z","corr_author":"1","pubrep_id":"575","department":[{"_id":"ChWo"}],"publication_status":"published","author":[{"full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"publist_id":"5292","intvolume":"        34","date_created":"2018-12-11T11:54:09Z","isi":1,"status":"public","month":"04","year":"2015","title":"Water wave animation via wavefront parameter interpolation","quality_controlled":"1","scopus_import":"1","doi":"10.1145/2714572","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000354800700004"]},"ddc":["000"],"file":[{"relation":"main_file","creator":"system","content_type":"application/pdf","file_id":"4933","file_size":23712153,"checksum":"67c9f4fa370def68cdf31299e48bc91f","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:12:15Z"}],"publication":"ACM Transactions on Graphics","article_processing_charge":"No","publisher":"ACM","day":"01","_id":"1814","has_accepted_license":"1","issue":"3","article_number":"27","citation":{"ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015)."},"abstract":[{"lang":"eng","text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:05:55Z","volume":34,"type":"journal_article","oa":1,"project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF"},{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"article_processing_charge":"No","publication":"Nature","pmid":1,"doi":"10.1038/nature14215","oa_version":"Submitted Version","external_id":{"pmid":["25778702"],"isi":["000354377800058"]},"scopus_import":"1","quality_controlled":"1","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","year":"2015","month":"03","status":"public","isi":1,"date_created":"2018-12-11T11:54:10Z","publist_id":"5289","intvolume":"       521","author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"full_name":"Asaoka, Yoichi","first_name":"Yoichi","last_name":"Asaoka"},{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"last_name":"Miyamoto","first_name":"Tatsuo","full_name":"Miyamoto, Tatsuo"},{"last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hata, Shoji","last_name":"Hata","first_name":"Shoji"},{"first_name":"Takashi","last_name":"Sasaki","full_name":"Sasaki, Takashi"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"last_name":"Asaka","first_name":"Satoshi","full_name":"Asaka, Satoshi"},{"full_name":"Momoi, Akihiro","first_name":"Akihiro","last_name":"Momoi"},{"first_name":"Sarah","last_name":"Linton","full_name":"Linton, Sarah"},{"last_name":"Miesfeld","first_name":"Joel","full_name":"Miesfeld, Joel"},{"full_name":"Link, Brian","last_name":"Link","first_name":"Brian"},{"first_name":"Takeshi","last_name":"Senga","full_name":"Senga, Takeshi"},{"first_name":"Atahualpa","last_name":"Castillo Morales","full_name":"Castillo Morales, Atahualpa"},{"full_name":"Urrutia, Araxi","first_name":"Araxi","last_name":"Urrutia"},{"full_name":"Shimizu, Nobuyoshi","last_name":"Shimizu","first_name":"Nobuyoshi"},{"full_name":"Nagase, Hideaki","last_name":"Nagase","first_name":"Hideaki"},{"last_name":"Matsuura","first_name":"Shinya","full_name":"Matsuura, Shinya"},{"first_name":"Stefan","last_name":"Bagby","full_name":"Bagby, Stefan"},{"last_name":"Kondoh","first_name":"Hisato","full_name":"Kondoh, Hisato"},{"last_name":"Nishina","first_name":"Hiroshi","full_name":"Nishina, Hiroshi"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Furutani Seiki","first_name":"Makoto","full_name":"Furutani Seiki, Makoto"}],"publication_status":"published","department":[{"_id":"CaHe"}],"corr_author":"1","date_published":"2015-03-16T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":521,"date_updated":"2025-09-29T11:07:11Z","language":[{"iso":"eng"}],"abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"citation":{"ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>."},"issue":"7551","_id":"1817","publisher":"Nature Publishing Group","day":"16","page":"217 - 221"},{"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"type":"journal_article","volume":112,"date_updated":"2025-09-23T09:27:16Z","abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>"},"issue":"20","_id":"1818","day":"19","publisher":"National Academy of Sciences","page":"6401 - 6406","article_processing_charge":"No","publication":"PNAS","pmid":1,"oa_version":"Submitted Version","doi":"10.1073/pnas.1421515112","external_id":{"pmid":["25941385"],"isi":["000354729500058"]},"scopus_import":"1","title":"Limits to adaptation along environmental gradients","quality_controlled":"1","year":"2015","status":"public","month":"05","date_created":"2018-12-11T11:54:11Z","isi":1,"author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"publist_id":"5288","intvolume":"       112","publication_status":"published","department":[{"_id":"NiBa"}],"corr_author":"1","ec_funded":1,"date_published":"2015-05-19T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}]},{"doi":"10.1016/j.molp.2015.03.007","oa_version":"None","external_id":{"isi":["000359136100006"]},"quality_controlled":"1","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","scopus_import":"1","article_processing_charge":"No","publication":"Molecular Plant","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","department":[{"_id":"JiFr"}],"publication_status":"published","date_published":"2015-08-03T00:00:00Z","ec_funded":1,"corr_author":"1","month":"08","status":"public","year":"2015","publist_id":"5287","intvolume":"         8","author":[{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Friml, Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiřĺ"}],"isi":1,"date_created":"2018-12-11T11:54:11Z","citation":{"apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>"},"issue":"8","volume":8,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"date_updated":"2025-09-23T09:47:17Z","page":"1175 - 1187","_id":"1819","day":"03","publisher":"Elsevier"},{"external_id":{"isi":["000372683700002"],"arxiv":["1411.3880"]},"oa_version":"Preprint","title":"Optimal cost almost-sure reachability in POMDPs","quality_controlled":"1","scopus_import":"1","alternative_title":["Artifical Intelligence"],"article_processing_charge":"No","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"date_published":"2015-06-01T00:00:00Z","corr_author":"1","status":"public","month":"06","year":"2015","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"full_name":"Kanodia, Ayush","first_name":"Ayush","last_name":"Kanodia"}],"publist_id":"5286","intvolume":"         5","date_created":"2018-12-11T11:54:11Z","isi":1,"arxiv":1,"citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502."},"conference":{"location":"Austin, TX, USA","name":"IAAI: Innovative Applications of Artificial Intelligence","end_date":"2015-01-30","start_date":"2015-01-25"},"volume":5,"type":"conference","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-18T11:05:08Z","page":"3496-3502","_id":"1820","related_material":{"record":[{"id":"1529","status":"public","relation":"later_version"}]},"publisher":"AAAI Press","day":"01"},{"publication_status":"published","pubrep_id":"395","department":[{"_id":"ToBo"}],"corr_author":"1","ec_funded":1,"date_published":"2015-04-01T00:00:00Z","year":"2015","status":"public","month":"04","isi":1,"date_created":"2018-12-11T11:54:12Z","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau","first_name":"Guillaume"},{"last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"publist_id":"5283","intvolume":"        11","file":[{"file_name":"IST-2015-395-v1+1_807.full.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:14:34Z","creator":"system","file_id":"5087","content_type":"application/pdf","file_size":1273573,"checksum":"4289b518fbe2166682fb1a1ef9b405f3","relation":"main_file"}],"oa_version":"Published Version","doi":"10.15252/msb.20156098","file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000354022300005"]},"ddc":["570"],"scopus_import":"1","title":"Systematic discovery of drug interaction mechanisms","quality_controlled":"1","article_processing_charge":"No","publication":"Molecular Systems Biology","_id":"1823","day":"01","publisher":"Nature Publishing Group","citation":{"mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. 2015;11(4). doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>","apa":"Chevereau, G., &#38; Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>.","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” <i>Molecular Systems Biology</i>, vol. 11, no. 4. Nature Publishing Group, 2015.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807."},"issue":"4","article_number":"807","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","oa":1,"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":11,"date_updated":"2025-09-23T13:38:00Z","abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}],"language":[{"iso":"eng"}]},{"date_published":"2015-04-24T00:00:00Z","publication_status":"published","pubrep_id":"451","department":[{"_id":"LaEr"}],"date_created":"2018-12-11T11:54:13Z","isi":1,"author":[{"last_name":"Knebel","first_name":"Johannes","full_name":"Knebel, Johannes"},{"first_name":"Markus","last_name":"Weber","full_name":"Weber, Markus"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger"},{"full_name":"Frey, Erwin","last_name":"Frey","first_name":"Erwin"}],"intvolume":"         6","publist_id":"5282","year":"2015","status":"public","month":"04","scopus_import":"1","title":"Evolutionary games of condensates in coupled birth-death processes","quality_controlled":"1","file":[{"file_name":"IST-2016-451-v1+1_ncomms7977.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:16:54Z","creator":"system","file_id":"5245","content_type":"application/pdf","file_size":1151501,"checksum":"c4cffb5c8b245e658a34eac71a03e7cc","relation":"main_file"}],"doi":"10.1038/ncomms7977","oa_version":"Published Version","external_id":{"isi":["000353705000003"]},"file_date_updated":"2020-07-14T12:45:17Z","ddc":["530"],"publication":"Nature Communications","article_processing_charge":"No","publisher":"Nature Publishing Group","day":"24","_id":"1824","article_number":"6977","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","citation":{"ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","apa":"Knebel, J., Weber, M., Krüger, T. H., &#38; Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>, vol. 6, 6977, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>."},"date_updated":"2025-09-23T08:44:01Z","abstract":[{"lang":"eng","text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":6},{"year":"2015","month":"03","status":"public","date_created":"2018-12-11T11:54:14Z","isi":1,"publist_id":"5278","intvolume":"        11","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","first_name":"Tamar","last_name":"Friedlander"},{"last_name":"Mayo","first_name":"Avraham","full_name":"Mayo, Avraham"},{"last_name":"Tlusty","first_name":"Tsvi","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"publication_status":"published","department":[{"_id":"GaTk"}],"pubrep_id":"452","date_published":"2015-03-23T00:00:00Z","ec_funded":1,"article_processing_charge":"No","publication":"PLoS Computational Biology","file":[{"date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:39Z","access_level":"open_access","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_size":1811647,"file_id":"5161","creator":"system","content_type":"application/pdf","relation":"main_file"}],"ddc":["576"],"oa_version":"Published Version","external_id":{"isi":["000352195700006"]},"file_date_updated":"2020-07-14T12:45:17Z","doi":"10.1371/journal.pcbi.1004055","scopus_import":"1","quality_controlled":"1","title":"Evolution of bow-tie architectures in biology","_id":"1827","publisher":"Public Library of Science","day":"23","related_material":{"record":[{"status":"public","id":"9718","relation":"research_data"},{"id":"9773","status":"public","relation":"research_data"}]},"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":11,"date_updated":"2025-09-23T08:43:16Z","language":[{"iso":"eng"}],"abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"citation":{"short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. 2015;11(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>, vol. 11, no. 3, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>.","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","apa":"Friedlander, T., Mayo, A., Tlusty, T., &#38; Alon, U. (2015). Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” <i>PLoS Computational Biology</i>, vol. 11, no. 3. Public Library of Science, 2015.","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>."},"issue":"3","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}}]