[{"publication_status":"published","quality_controlled":"1","file_date_updated":"2021-02-04T10:34:22Z","oa":1,"has_accepted_license":"1","ddc":["570"],"author":[{"last_name":"Bozelos","full_name":"Bozelos, Panagiotis","id":"52e9c652-2982-11eb-81d4-b43d94c63700","first_name":"Panagiotis"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P"}],"_id":"8757","publisher":"Springer Nature","date_updated":"2025-07-10T12:01:24Z","page":"1-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","external_id":{"isi":["000588256300001"],"pmid":["33173190"]},"status":"public","abstract":[{"lang":"eng","text":"Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test."}],"volume":22,"isi":1,"month":"01","article_processing_charge":"No","department":[{"_id":"TiVo"}],"date_created":"2020-11-15T23:01:18Z","article_type":"letter_note","file":[{"file_id":"9088","creator":"dernst","date_created":"2021-02-04T10:34:22Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NatureNeuroScience_Bozelos.pdf","file_size":683634,"date_updated":"2021-02-04T10:34:22Z","checksum":"7985d7dff94c086e35b94a911d78d9ad","success":1}],"oa_version":"Published Version","citation":{"ista":"Bozelos P, Vogels TP. 2021. Talking science, online. Nature Reviews Neuroscience. 22(1), 1–2.","ieee":"P. Bozelos and T. P. Vogels, “Talking science, online,” <i>Nature Reviews Neuroscience</i>, vol. 22, no. 1. Springer Nature, pp. 1–2, 2021.","mla":"Bozelos, Panagiotis, and Tim P. Vogels. “Talking Science, Online.” <i>Nature Reviews Neuroscience</i>, vol. 22, no. 1, Springer Nature, 2021, pp. 1–2, doi:<a href=\"https://doi.org/10.1038/s41583-020-00408-6\">10.1038/s41583-020-00408-6</a>.","apa":"Bozelos, P., &#38; Vogels, T. P. (2021). Talking science, online. <i>Nature Reviews Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41583-020-00408-6\">https://doi.org/10.1038/s41583-020-00408-6</a>","chicago":"Bozelos, Panagiotis, and Tim P Vogels. “Talking Science, Online.” <i>Nature Reviews Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41583-020-00408-6\">https://doi.org/10.1038/s41583-020-00408-6</a>.","ama":"Bozelos P, Vogels TP. Talking science, online. <i>Nature Reviews Neuroscience</i>. 2021;22(1):1-2. doi:<a href=\"https://doi.org/10.1038/s41583-020-00408-6\">10.1038/s41583-020-00408-6</a>","short":"P. Bozelos, T.P. Vogels, Nature Reviews Neuroscience 22 (2021) 1–2."},"doi":"10.1038/s41583-020-00408-6","language":[{"iso":"eng"}],"publication":"Nature Reviews Neuroscience","date_published":"2021-01-01T00:00:00Z","scopus_import":"1","type":"journal_article","issue":"1","intvolume":"        22","year":"2021","title":"Talking science, online","pmid":1,"publication_identifier":{"issn":["1471-003X"],"eissn":["1471-0048"]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","external_id":{"arxiv":["1910.08286"],"isi":["000600416300004"]},"keyword":["Applied Mathematics","General Mathematics"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"date_updated":"2025-04-14T07:43:50Z","page":"37-52","main_file_link":[{"url":"https://arxiv.org/abs/1910.08286","open_access":"1"}],"oa":1,"author":[{"full_name":"Brown, Adam","last_name":"Brown","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"first_name":"Anna","full_name":"Romanov, Anna","last_name":"Romanov"}],"_id":"8773","publisher":"American Mathematical Society","publication_status":"published","quality_controlled":"1","acknowledgement":"We would like to thank Peter Trapa for useful discussions, and Dragan Milicic and Arun Ram for valuable feedback on the structure of the paper. The first author acknowledges the support of the European Unions Horizon 2020 research and innovation programme under the Marie Skodowska-Curie Grant Agreement No. 754411. The second author is\r\nsupported by the National Science Foundation Award No. 1803059.","issue":"1","intvolume":"       149","year":"2021","title":"Contravariant forms on Whittaker modules","arxiv":1,"publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"doi":"10.1090/proc/15205","date_published":"2021-01-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","language":[{"iso":"eng"}],"scopus_import":"1","type":"journal_article","article_type":"original","ec_funded":1,"date_created":"2020-11-19T10:17:40Z","oa_version":"Preprint","citation":{"ama":"Brown A, Romanov A. Contravariant forms on Whittaker modules. <i>Proceedings of the American Mathematical Society</i>. 2021;149(1):37-52. doi:<a href=\"https://doi.org/10.1090/proc/15205\">10.1090/proc/15205</a>","short":"A. Brown, A. Romanov, Proceedings of the American Mathematical Society 149 (2021) 37–52.","ieee":"A. Brown and A. Romanov, “Contravariant forms on Whittaker modules,” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 1. American Mathematical Society, pp. 37–52, 2021.","ista":"Brown A, Romanov A. 2021. Contravariant forms on Whittaker modules. Proceedings of the American Mathematical Society. 149(1), 37–52.","mla":"Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 1, American Mathematical Society, 2021, pp. 37–52, doi:<a href=\"https://doi.org/10.1090/proc/15205\">10.1090/proc/15205</a>.","apa":"Brown, A., &#38; Romanov, A. (2021). Contravariant forms on Whittaker modules. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/15205\">https://doi.org/10.1090/proc/15205</a>","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/proc/15205\">https://doi.org/10.1090/proc/15205</a>."},"status":"public","isi":1,"month":"01","volume":149,"abstract":[{"text":"Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell.","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"HeEd"}]},{"intvolume":"       274","year":"2021","issue":"2","acknowledgement":"G. Schimperna has been partially supported by GNAMPA (Gruppo Nazionale per l'Analisi Matematica, la Probabilità e le loro Applicazioni) of INdAM (Istituto Nazionale di Alta Matematica).","publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"arxiv":1,"title":"On a non-isothermal Cahn-Hilliard model based on a microforce balance","doi":"10.1016/j.jde.2020.10.030","type":"journal_article","publication":"Journal of Differential Equations","date_published":"2021-02-15T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2020-11-22T23:01:26Z","article_type":"original","citation":{"ama":"Marveggio A, Schimperna G. On a non-isothermal Cahn-Hilliard model based on a microforce balance. <i>Journal of Differential Equations</i>. 2021;274(2):924-970. doi:<a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">10.1016/j.jde.2020.10.030</a>","short":"A. Marveggio, G. Schimperna, Journal of Differential Equations 274 (2021) 924–970.","ista":"Marveggio A, Schimperna G. 2021. On a non-isothermal Cahn-Hilliard model based on a microforce balance. Journal of Differential Equations. 274(2), 924–970.","ieee":"A. Marveggio and G. Schimperna, “On a non-isothermal Cahn-Hilliard model based on a microforce balance,” <i>Journal of Differential Equations</i>, vol. 274, no. 2. Elsevier, pp. 924–970, 2021.","apa":"Marveggio, A., &#38; Schimperna, G. (2021). On a non-isothermal Cahn-Hilliard model based on a microforce balance. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">https://doi.org/10.1016/j.jde.2020.10.030</a>","mla":"Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” <i>Journal of Differential Equations</i>, vol. 274, no. 2, Elsevier, 2021, pp. 924–70, doi:<a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">10.1016/j.jde.2020.10.030</a>.","chicago":"Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” <i>Journal of Differential Equations</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">https://doi.org/10.1016/j.jde.2020.10.030</a>."},"oa_version":"Preprint","status":"public","department":[{"_id":"JuFi"}],"month":"02","abstract":[{"text":"This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system.","lang":"eng"}],"isi":1,"volume":274,"article_processing_charge":"No","day":"15","external_id":{"arxiv":["2004.02618"],"isi":["000600845300023"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"924-970","date_updated":"2025-07-10T12:01:25Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.02618"}],"oa":1,"publisher":"Elsevier","_id":"8792","author":[{"full_name":"Marveggio, Alice","last_name":"Marveggio","id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice"},{"first_name":"Giulio","full_name":"Schimperna, Giulio","last_name":"Schimperna"}],"publication_status":"published","quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication":"Discrete Applied Mathematics","date_published":"2021-01-31T00:00:00Z","scopus_import":"1","type":"journal_article","doi":"10.1016/j.dam.2020.10.022","title":"Optimal strategies for selecting coordinators","publication_identifier":{"issn":["0166-218X"],"eissn":["1872-6771"]},"issue":"1","acknowledgement":"We are grateful to Matthias Függer and Thomas Nowak for having raised our interest in the problem studied in this paper.\r\nThis work has been supported the Austrian Science Fund (FWF) projects S11405, S11407 (RiSE), and P28182 (ADynNet).","intvolume":"       289","year":"2021","isi":1,"volume":289,"abstract":[{"text":"We study optimal election sequences for repeatedly selecting a (very) small group of leaders among a set of participants (players) with publicly known unique ids. In every time slot, every player has to select exactly one player that it considers to be the current leader, oblivious to the selection of the other players, but with the overarching goal of maximizing a given parameterized global (“social”) payoff function in the limit. We consider a quite generic model, where the local payoff achieved by a given player depends, weighted by some arbitrary but fixed real parameter, on the number of different leaders chosen in a round, the number of players that choose the given player as the leader, and whether the chosen leader has changed w.r.t. the previous round or not. The social payoff can be the maximum, average or minimum local payoff of the players. Possible applications include quite diverse examples such as rotating coordinator-based distributed algorithms and long-haul formation flying of social birds. Depending on the weights and the particular social payoff, optimal sequences can be very different, from simple round-robin where all players chose the same leader alternatingly every time slot to very exotic patterns, where a small group of leaders (at most 2) is elected in every time slot. Moreover, we study the question if and when a single player would not benefit w.r.t. its local payoff when deviating from the given optimal sequence, i.e., when our optimal sequences are Nash equilibria in the restricted strategy space of oblivious strategies. As this is the case for many parameterizations of our model, our results reveal that no punishment is needed to make it rational for the players to optimize the social payoff.","lang":"eng"}],"month":"01","article_processing_charge":"No","department":[{"_id":"KrCh"}],"status":"public","file":[{"access_level":"open_access","file_id":"9089","relation":"main_file","date_created":"2021-02-04T11:28:42Z","creator":"dernst","checksum":"f1039ff5a2d6ca116720efdb84ee9d5e","success":1,"file_size":652739,"date_updated":"2021-02-04T11:28:42Z","file_name":"2021_DiscreteApplMath_Zeiner.pdf","content_type":"application/pdf"}],"oa_version":"Published Version","citation":{"ama":"Zeiner M, Schmid U, Chatterjee K. Optimal strategies for selecting coordinators. <i>Discrete Applied Mathematics</i>. 2021;289(1):392-415. doi:<a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">10.1016/j.dam.2020.10.022</a>","short":"M. Zeiner, U. Schmid, K. Chatterjee, Discrete Applied Mathematics 289 (2021) 392–415.","apa":"Zeiner, M., Schmid, U., &#38; Chatterjee, K. (2021). Optimal strategies for selecting coordinators. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">https://doi.org/10.1016/j.dam.2020.10.022</a>","mla":"Zeiner, Martin, et al. “Optimal Strategies for Selecting Coordinators.” <i>Discrete Applied Mathematics</i>, vol. 289, no. 1, Elsevier, 2021, pp. 392–415, doi:<a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">10.1016/j.dam.2020.10.022</a>.","chicago":"Zeiner, Martin, Ulrich Schmid, and Krishnendu Chatterjee. “Optimal Strategies for Selecting Coordinators.” <i>Discrete Applied Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">https://doi.org/10.1016/j.dam.2020.10.022</a>.","ieee":"M. Zeiner, U. Schmid, and K. Chatterjee, “Optimal strategies for selecting coordinators,” <i>Discrete Applied Mathematics</i>, vol. 289, no. 1. Elsevier, pp. 392–415, 2021.","ista":"Zeiner M, Schmid U, Chatterjee K. 2021. Optimal strategies for selecting coordinators. Discrete Applied Mathematics. 289(1), 392–415."},"article_type":"original","date_created":"2020-11-22T23:01:26Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2026-04-16T09:15:13Z","page":"392-415","project":[{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"31","external_id":{"isi":["000596823800035"]},"quality_controlled":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","ddc":["510"],"_id":"8793","author":[{"full_name":"Zeiner, Martin","last_name":"Zeiner","first_name":"Martin"},{"first_name":"Ulrich","full_name":"Schmid, Ulrich","last_name":"Schmid"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"publisher":"Elsevier","oa":1,"file_date_updated":"2021-02-04T11:28:42Z"},{"department":[{"_id":"MiLe"}],"article_processing_charge":"Yes (via OA deal)","isi":1,"volume":381,"month":"01","abstract":[{"lang":"eng","text":"Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail."}],"status":"public","citation":{"ama":"Runkel I, Szegedy L. Area-dependent quantum field theory. <i>Communications in Mathematical Physics</i>. 2021;381(1):83–117. doi:<a href=\"https://doi.org/10.1007/s00220-020-03902-1\">10.1007/s00220-020-03902-1</a>","short":"I. Runkel, L. Szegedy, Communications in Mathematical Physics 381 (2021) 83–117.","ista":"Runkel I, Szegedy L. 2021. Area-dependent quantum field theory. Communications in Mathematical Physics. 381(1), 83–117.","ieee":"I. Runkel and L. Szegedy, “Area-dependent quantum field theory,” <i>Communications in Mathematical Physics</i>, vol. 381, no. 1. Springer Nature, pp. 83–117, 2021.","apa":"Runkel, I., &#38; Szegedy, L. (2021). Area-dependent quantum field theory. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-020-03902-1\">https://doi.org/10.1007/s00220-020-03902-1</a>","mla":"Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” <i>Communications in Mathematical Physics</i>, vol. 381, no. 1, Springer Nature, 2021, pp. 83–117, doi:<a href=\"https://doi.org/10.1007/s00220-020-03902-1\">10.1007/s00220-020-03902-1</a>.","chicago":"Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-020-03902-1\">https://doi.org/10.1007/s00220-020-03902-1</a>."},"oa_version":"Published Version","file":[{"relation":"main_file","date_created":"2021-02-03T15:00:30Z","creator":"dernst","file_id":"9081","access_level":"open_access","file_size":790526,"date_updated":"2021-02-03T15:00:30Z","file_name":"2021_CommMathPhys_Runkel.pdf","content_type":"application/pdf","success":1,"checksum":"6f451f9c2b74bedbc30cf884a3e02670"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_created":"2020-11-29T23:01:17Z","type":"journal_article","scopus_import":"1","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"date_published":"2021-01-01T00:00:00Z","doi":"10.1007/s00220-020-03902-1","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"title":"Area-dependent quantum field theory","year":"2021","intvolume":"       381","acknowledgement":"The authors thank Yuki Arano, Nils Carqueville, Alexei Davydov, Reiner Lauterbach, Pau Enrique Moliner, Chris Heunen, André Henriques, Ehud Meir, Catherine Meusburger, Gregor Schaumann, Richard Szabo and Stefan Wagner for helpful discussions and comments. We also thank the referees for their detailed comments which significantly improved the exposition of this paper. LS is supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory”. Open access funding provided by Institute of Science and Technology (IST Austria).","issue":"1","quality_controlled":"1","publication_status":"published","publisher":"Springer Nature","_id":"8816","author":[{"first_name":"Ingo","full_name":"Runkel, Ingo","last_name":"Runkel"},{"full_name":"Szegedy, Lorant","last_name":"Szegedy","orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","first_name":"Lorant"}],"ddc":["510"],"has_accepted_license":"1","file_date_updated":"2021-02-03T15:00:30Z","oa":1,"page":"83–117","date_updated":"2025-07-10T12:01:25Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"external_id":{"isi":["000591139000001"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ec_funded":1,"date_created":"2020-11-29T23:01:18Z","article_type":"original","oa_version":"None","citation":{"chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>.","mla":"Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>.","apa":"Shehu, Y., Iyiola, O. S., Thong, D. V., &#38; Van, N. T. C. (2021). An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>","ista":"Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 93(2), 213–242.","ieee":"Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems,” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2. Springer Nature, pp. 213–242, 2021.","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 213–242.","ama":"Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. 2021;93(2):213-242. doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>"},"status":"public","article_processing_charge":"No","volume":93,"month":"04","abstract":[{"text":"The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model.","lang":"eng"}],"isi":1,"department":[{"_id":"VlKo"}],"acknowledgement":"The authors are grateful to the two referees and the Associate Editor for their comments and suggestions which have improved the earlier version of the paper greatly. The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","issue":"2","year":"2021","intvolume":"        93","title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","publication_identifier":{"issn":["1432-2994"],"eissn":["1432-5217"]},"doi":"10.1007/s00186-020-00730-w","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2021-04-01T00:00:00Z","publication":"Mathematical Methods of Operations Research","type":"journal_article","author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"last_name":"Iyiola","full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S."},{"full_name":"Thong, Duong Viet","last_name":"Thong","first_name":"Duong Viet"},{"last_name":"Van","full_name":"Van, Nguyen Thi Cam","first_name":"Nguyen Thi Cam"}],"_id":"8817","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000590497300001"]},"day":"01","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7"}],"date_updated":"2024-11-04T13:52:33Z","page":"213-242"},{"intvolume":"       589","year":"2021","issue":"7840","acknowledgement":"We thank O. Eschenko and M. Constantinou for providing feedback on earlier versions of this work, and J. Werner and M. Schnabel for technical support during the development of this study. This research was supported by the Max Planck Society.","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"pmid":1,"title":"Coupling of hippocampal theta and ripples with pontogeniculooccipital waves","doi":"10.1038/s41586-020-2914-4","type":"journal_article","publication":"Nature","date_published":"2021-01-07T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2020-11-29T23:01:19Z","article_type":"original","citation":{"chicago":"Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard, Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>.","mla":"Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>, vol. 589, no. 7840, Springer Nature, 2021, pp. 96–102, doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>.","apa":"Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann, A., &#38; Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>","ieee":"J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann, and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital waves,” <i>Nature</i>, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.","ista":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 589(7840), 96–102.","short":"J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102.","ama":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. 2021;589(7840):96-102. doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>"},"oa_version":"None","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-020-03068-9","relation":"erratum"}]},"department":[{"_id":"JoCs"}],"abstract":[{"lang":"eng","text":"The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis."}],"month":"01","isi":1,"volume":589,"article_processing_charge":"No","day":"07","external_id":{"isi":["000591047800005"],"pmid":["33208951"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"96-102","date_updated":"2025-07-10T12:01:26Z","publisher":"Springer Nature","author":[{"last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F"},{"first_name":"Michel","full_name":"Besserve, Michel","last_name":"Besserve"},{"first_name":"Yusuke","full_name":"Murayama, Yusuke","last_name":"Murayama"},{"first_name":"Henry C.","full_name":"Evrard, Henry C.","last_name":"Evrard"},{"full_name":"Oeltermann, Axel","last_name":"Oeltermann","first_name":"Axel"},{"full_name":"Logothetis, Nikos K.","last_name":"Logothetis","first_name":"Nikos K."}],"_id":"8818","publication_status":"published","quality_controlled":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_created":"2020-12-01T13:39:46Z","citation":{"ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. 2021;31(1). doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>","mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>.","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>.","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1).","ieee":"M. Marquès-Bueno <i>et al.</i>, “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, 2021."},"file":[{"checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","success":1,"content_type":"application/pdf","file_name":"2021_CurrentBiology_MarquesBueno.pdf","date_updated":"2021-02-04T11:37:50Z","file_size":3458646,"access_level":"open_access","file_id":"9090","date_created":"2021-02-04T11:37:50Z","creator":"dernst","relation":"main_file"}],"oa_version":"Published Version","status":"public","department":[{"_id":"JiFr"}],"month":"01","volume":31,"abstract":[{"text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1,  2,  3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1,  2,  3,  4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7,  8,  9,  10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.","lang":"eng"}],"isi":1,"article_processing_charge":"Yes (via OA deal)","intvolume":"        31","year":"2021","acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","issue":"1","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"pmid":1,"title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","doi":"10.1016/j.cub.2020.10.011","type":"journal_article","date_published":"2021-01-11T00:00:00Z","publication":"Current Biology","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-02-04T11:37:50Z","oa":1,"publisher":"Elsevier","ddc":["570"],"has_accepted_license":"1","author":[{"first_name":"MM","full_name":"Marquès-Bueno, MM","last_name":"Marquès-Bueno"},{"first_name":"L","full_name":"Armengot, L","last_name":"Armengot"},{"last_name":"Noack","full_name":"Noack, LC","first_name":"LC"},{"full_name":"Bareille, J","last_name":"Bareille","first_name":"J"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"first_name":"MP","full_name":"Platre, MP","last_name":"Platre"},{"full_name":"Bayle, V","last_name":"Bayle","first_name":"V"},{"full_name":"Liu, M","last_name":"Liu","first_name":"M"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Möller","full_name":"Möller, BK","first_name":"BK"},{"first_name":"ZL","full_name":"Nimchuk, ZL","last_name":"Nimchuk"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"last_name":"Caño-Delgado","full_name":"Caño-Delgado, AI","first_name":"AI"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Jaillais, Y","last_name":"Jaillais","first_name":"Y"}],"_id":"8824","publication_status":"published","quality_controlled":"1","day":"11","external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-10-21T06:02:09Z"},{"date_updated":"2026-04-07T13:27:22Z","main_file_link":[{"url":"https://arxiv.org/abs/2008.02348","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","external_id":{"pmid":["34210881"],"arxiv":["2008.02348"],"isi":["000677843100034"]},"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511","call_identifier":"H2020"}],"publication_status":"published","quality_controlled":"1","oa":1,"_id":"8910","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini"},{"first_name":"Fernando","last_name":"Peñaranda","full_name":"Peñaranda, Fernando"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"full_name":"Brauns, Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krogstrup","full_name":"Krogstrup, Peter","first_name":"Peter"},{"last_name":"San-Jose","full_name":"San-Jose, Pablo","first_name":"Pablo"},{"full_name":"Prada, Elsa","last_name":"Prada","first_name":"Elsa"},{"full_name":"Aguado, Ramón","last_name":"Aguado","first_name":"Ramón"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"publisher":"American Association for the Advancement of Science","doi":"10.1126/science.abf1513","publication":"Science","language":[{"iso":"eng"}],"date_published":"2021-07-02T00:00:00Z","scopus_import":"1","type":"journal_article","acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","issue":"6550","intvolume":"       373","year":"2021","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","pmid":1,"article_number":"82-88","arxiv":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","relation":"press_release"}],"record":[{"id":"9389","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"13286","status":"public"}]},"status":"public","isi":1,"abstract":[{"text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.","lang":"eng"}],"volume":373,"month":"07","article_processing_charge":"No","department":[{"_id":"GeKa"},{"_id":"Bio"}],"ec_funded":1,"date_created":"2020-12-02T10:51:52Z","article_type":"original","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"citation":{"ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>","mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>.","chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>.","ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88.","ieee":"M. Valentini <i>et al.</i>, “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021."}},{"article_processing_charge":"No","month":"10","volume":6,"abstract":[{"text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. ","lang":"eng"}],"isi":1,"department":[{"_id":"GeKa"}],"status":"public","oa_version":"Preprint","citation":{"chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>, vol. 6, Springer Nature, 2021, pp. 926–943, doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>.","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. <i>Nature Reviews Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","ieee":"G. Scappucci <i>et al.</i>, “The germanium quantum information route,” <i>Nature Reviews Materials</i>, vol. 6. Springer Nature, pp. 926–943, 2021.","short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. <i>Nature Reviews Materials</i>. 2021;6:926–943. doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>"},"ec_funded":1,"article_type":"original","date_created":"2020-12-02T10:52:51Z","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2021-10-01T00:00:00Z","publication":"Nature Reviews Materials","type":"journal_article","doi":"10.1038/s41578-020-00262-z","title":"The germanium quantum information route","publication_identifier":{"eissn":["2058-8437"]},"arxiv":1,"acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","year":"2021","intvolume":"         6","quality_controlled":"1","publication_status":"published","_id":"8911","author":[{"last_name":"Scappucci","full_name":"Scappucci, Giordano","first_name":"Giordano"},{"first_name":"Christoph","last_name":"Kloeffel","full_name":"Kloeffel, Christoph"},{"first_name":"Floris A.","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris A."},{"full_name":"Loss, Daniel","last_name":"Loss","first_name":"Daniel"},{"last_name":"Myronov","full_name":"Myronov, Maksym","first_name":"Maksym"},{"last_name":"Zhang","full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun"},{"last_name":"Franceschi","full_name":"Franceschi, Silvano De","first_name":"Silvano De"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"full_name":"Veldhorst, Menno","last_name":"Veldhorst","first_name":"Menno"}],"publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"date_updated":"2024-10-22T09:41:03Z","page":"926–943 ","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7"},{"_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715","call_identifier":"FWF"},{"grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2004.08133"],"isi":["000600826100003"]},"day":"01"},{"isi":1,"month":"04","abstract":[{"lang":"eng","text":"For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance."}],"volume":167,"article_processing_charge":"No","department":[{"_id":"ToHe"}],"status":"public","file":[{"checksum":"600c2f81bc898a725bcfa7cf26ff4fed","content_type":"application/pdf","date_updated":"2020-12-02T13:33:51Z","file_name":"synchroPaperRevised.pdf","file_size":634967,"access_level":"open_access","file_id":"8913","date_created":"2020-12-02T13:33:51Z","creator":"esarac","relation":"main_file"}],"oa_version":"Submitted Version","citation":{"chicago":"Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>.","apa":"Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., &#38; Yenigün, H. (2021). Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>","mla":"Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>, vol. 167, no. 4, 114203, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>.","ista":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203.","ieee":"N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” <i>Expert Systems with Applications</i>, vol. 167, no. 4. Elsevier, 2021.","short":"N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021).","ama":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. 2021;167(4). doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>"},"date_created":"2020-12-02T13:34:25Z","article_type":"original","publication":"Expert Systems with Applications","date_published":"2021-04-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","type":"journal_article","doi":"10.1016/j.eswa.2020.114203","title":"Boosting expensive synchronizing heuristics","article_number":"114203","publication_identifier":{"eissn":["1873-6793"],"issn":["0957-4174"]},"acknowledgement":"This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11.","issue":"4","intvolume":"       167","year":"2021","quality_controlled":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","ddc":["000"],"_id":"8912","author":[{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"},{"full_name":"Altun, Ömer Faruk","last_name":"Altun","first_name":"Ömer Faruk"},{"full_name":"Atam, Kamil Tolga","last_name":"Atam","first_name":"Kamil Tolga"},{"first_name":"Sertac","full_name":"Karahoda, Sertac","last_name":"Karahoda"},{"last_name":"Kaya","full_name":"Kaya, Kamer","first_name":"Kamer"},{"first_name":"Hüsnü","full_name":"Yenigün, Hüsnü","last_name":"Yenigün"}],"publisher":"Elsevier","oa":1,"file_date_updated":"2020-12-02T13:33:51Z","date_updated":"2026-04-16T09:15:47Z","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000640531100038"]},"day":"01"},{"doi":"10.1111/liv.14730","type":"journal_article","language":[{"iso":"eng"}],"publication":"Liver International","date_published":"2021-01-01T00:00:00Z","scopus_import":"1","intvolume":"        41","year":"2021","acknowledgement":"This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com.","issue":"1","publication_identifier":{"eissn":["1478-3231"],"issn":["1478-3223"]},"pmid":1,"title":"Pathophysiological mechanisms of liver injury in COVID-19","status":"public","department":[{"_id":"CampIT"}],"abstract":[{"lang":"eng","text":"The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19."}],"isi":1,"volume":41,"month":"01","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-12-06T23:01:16Z","article_type":"original","citation":{"short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","ama":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. 2021;41(1):20-32. doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>","ieee":"A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax, and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” <i>Liver International</i>, vol. 41, no. 1. Wiley, pp. 20–32, 2021.","ista":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. 2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 41(1), 20–32.","chicago":"Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>.","apa":"Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S. F., &#38; Trauner, M. (2021). Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. Wiley. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>","mla":"Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>, vol. 41, no. 1, Wiley, 2021, pp. 20–32, doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>."},"file":[{"access_level":"open_access","file_id":"9091","relation":"main_file","date_created":"2021-02-04T12:01:45Z","creator":"dernst","checksum":"6e4f21b77ef22c854e016240974fc473","success":1,"date_updated":"2021-02-04T12:01:45Z","file_name":"2021_Liver_Nardo.pdf","file_size":930414,"content_type":"application/pdf"}],"oa_version":"Published Version","page":"20-32","date_updated":"2025-06-12T06:33:00Z","external_id":{"pmid":["33190346"],"isi":["000594239200001"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","quality_controlled":"1","oa":1,"file_date_updated":"2021-02-04T12:01:45Z","publisher":"Wiley","ddc":["570"],"has_accepted_license":"1","author":[{"last_name":"Nardo","full_name":"Nardo, Alexander D.","first_name":"Alexander D."},{"first_name":"Mathias","full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner"},{"full_name":"Bakail, May M","last_name":"Bakail","orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"full_name":"Dixon, Emmanuel D.","last_name":"Dixon","first_name":"Emmanuel D."},{"full_name":"Lax, Sigurd F.","last_name":"Lax","first_name":"Sigurd F."},{"last_name":"Trauner","full_name":"Trauner, Michael","first_name":"Michael"}],"_id":"8927"},{"related_material":{"record":[{"relation":"research_data","id":"13065","status":"public"}]},"status":"public","abstract":[{"text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.","lang":"eng"}],"month":"02","volume":34,"isi":1,"article_processing_charge":"No","department":[{"_id":"NiBa"}],"article_type":"original","date_created":"2020-12-06T23:01:16Z","oa_version":"Published Version","citation":{"ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283."},"doi":"10.1111/jeb.13723","date_published":"2021-02-01T00:00:00Z","publication":"Journal of Evolutionary Biology","language":[{"iso":"eng"}],"scopus_import":"1","type":"journal_article","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","issue":"2","intvolume":"        34","year":"2021","title":"Genomic inference of complex domestication histories in three Solanaceae species","pmid":1,"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"published","quality_controlled":"1","oa":1,"ddc":["570"],"author":[{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sauvage","full_name":"Sauvage, Christopher","first_name":"Christopher"}],"_id":"8928","publisher":"Wiley","date_updated":"2026-06-18T19:37:17Z","page":"270-283","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"project":[{"call_identifier":"FWF","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers"}]},{"date_updated":"2025-04-14T07:43:50Z","page":"386-434","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","external_id":{"isi":["000597770300001"]},"quality_controlled":"1","corr_author":"1","publication_status":"published","_id":"8940","author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken"}],"has_accepted_license":"1","ddc":["516"],"publisher":"Springer Nature","oa":1,"file_date_updated":"2021-08-06T09:52:29Z","scopus_import":"1","date_published":"2021-07-01T00:00:00Z","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1007/s00454-020-00250-8","title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","issue":"1","year":"2021","intvolume":"        66","article_processing_charge":"Yes (via OA deal)","month":"07","abstract":[{"text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric.","lang":"eng"}],"isi":1,"volume":66,"department":[{"_id":"HeEd"}],"status":"public","oa_version":"Published Version","file":[{"access_level":"open_access","file_id":"9795","relation":"main_file","date_created":"2021-08-06T09:52:29Z","creator":"kschuh","checksum":"c848986091e56699dc12de85adb1e39c","success":1,"date_updated":"2021-08-06T09:52:29Z","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","file_size":983307,"content_type":"application/pdf"}],"citation":{"ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. 2021;66(1):386-434. doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete &#38; Computational Geometry. 66(1), 386–434.","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>.","apa":"Boissonnat, J.-D., Kachanovich, S., &#38; Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>."},"date_created":"2020-12-12T11:07:02Z","ec_funded":1,"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"quality_controlled":"1","corr_author":"1","publication_status":"published","ddc":["570"],"_id":"8988","author":[{"first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg"},{"id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","last_name":"Auer"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola"},{"id":"3760F32C-F248-11E8-B48F-1D18A9856A87","first_name":"Katrin","full_name":"Loibl, Katrin","last_name":"Loibl","orcid":"0000-0002-2429-7668"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publisher":"National Academy of Sciences","oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"date_updated":"2026-06-18T19:37:53Z","project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"month":"01","volume":118,"isi":1,"abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"article_processing_charge":"No","department":[{"_id":"MaLo"},{"_id":"MiSi"}],"status":"public","oa_version":"Published Version","citation":{"short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_type":"original","date_created":"2021-01-03T23:01:23Z","language":[{"iso":"eng"}],"date_published":"2021-01-05T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","scopus_import":"1","type":"journal_article","doi":"10.1073/pnas.2010054118","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","article_number":"e2010054118","pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"1","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","intvolume":"       118","year":"2021"},{"oa":1,"file_date_updated":"2021-01-07T14:03:53Z","publisher":"Elsevier","author":[{"orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"_id":"8992","has_accepted_license":"1","ddc":["580"],"publication_status":"published","quality_controlled":"1","day":"04","external_id":{"pmid":["33186755"],"isi":["000605359400014"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","grant_number":"723-2015"}],"page":"151-165","date_updated":"2025-07-10T12:01:28Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-01-03T23:01:23Z","article_type":"original","ec_funded":1,"citation":{"mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>.","apa":"Tan, S., Luschnig, C., &#38; Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>","chicago":"Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>.","ieee":"S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” <i>Molecular Plant</i>, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.","ista":"Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.","ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. 2021;14(1):151-165. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165."},"oa_version":"Published Version","file":[{"file_id":"8995","relation":"main_file","date_created":"2021-01-07T14:03:53Z","creator":"dernst","access_level":"open_access","file_size":871088,"date_updated":"2021-01-07T14:03:53Z","file_name":"2020_MolecularPlant_Tan.pdf","content_type":"application/pdf","checksum":"917e60e57092f22e16beac70b1775ea6","success":1}],"status":"public","department":[{"_id":"JiFr"}],"article_processing_charge":"No","isi":1,"abstract":[{"text":"The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.","lang":"eng"}],"volume":14,"month":"01","year":"2021","intvolume":"        14","issue":"1","acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","publication_identifier":{"issn":["1674-2052"],"eissn":["1752-9867"]},"pmid":1,"title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","doi":"10.1016/j.molp.2020.11.004","type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Molecular Plant","date_published":"2021-01-04T00:00:00Z"},{"quality_controlled":"1","publication_status":"published","ddc":["580"],"_id":"8993","author":[{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"full_name":"Stadlmann, Johannes","last_name":"Stadlmann","first_name":"Johannes"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"orcid":"0000-0003-1581-881X","last_name":"Lukic","full_name":"Lukic, Kristina","first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"},{"first_name":"Lukas","last_name":"Mach","full_name":"Mach, Lukas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z."}],"publisher":"National Academy of Sciences","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2020857118"}],"date_updated":"2026-06-18T19:38:20Z","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"day":"05","month":"01","isi":1,"volume":118,"abstract":[{"lang":"eng","text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism."}],"article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]},"status":"public","oa_version":"Published Version","citation":{"ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>.","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2020857118.","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021."},"article_type":"original","ec_funded":1,"date_created":"2021-01-03T23:01:23Z","date_published":"2021-01-05T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","scopus_import":"1","type":"journal_article","doi":"10.1073/pnas.2020857118","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","article_number":"e2020857118","pmid":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","issue":"1","intvolume":"       118","year":"2021"},{"quality_controlled":"1","publication_status":"published","publisher":"Public Library of Science","author":[{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","full_name":"Kavcic, Bor","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"_id":"8997","has_accepted_license":"1","ddc":["570"],"oa":1,"file_date_updated":"2021-02-04T12:30:48Z","date_updated":"2025-06-12T06:33:18Z","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"day":"07","external_id":{"isi":["000608045000010"],"pmid":["33411759"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"article_processing_charge":"Yes","volume":17,"isi":1,"month":"01","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"status":"public","related_material":{"record":[{"status":"public","id":"8930","relation":"research_data"},{"relation":"earlier_version","status":"public","id":"7673"}]},"citation":{"chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>"},"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3690053,"date_updated":"2021-02-04T12:30:48Z","file_name":"2021_PlosComBio_Kavcic.pdf","success":1,"checksum":"e29f2b42651bef8e034781de8781ffac","date_created":"2021-02-04T12:30:48Z","creator":"dernst","relation":"main_file","file_id":"9092","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-01-08T07:16:18Z","article_type":"original","type":"journal_article","scopus_import":"1","publication":"PLOS Computational Biology","language":[{"iso":"eng"}],"date_published":"2021-01-07T00:00:00Z","doi":"10.1371/journal.pcbi.1008529","article_number":"e1008529","pmid":1,"publication_identifier":{"issn":["1553-7358"]},"title":"Minimal biophysical model of combined antibiotic action","year":"2021","intvolume":"        17","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). "},{"status":"public","article_processing_charge":"No","isi":1,"abstract":[{"text":"In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not\r\narise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. ","lang":"eng"}],"volume":23,"month":"01","department":[{"_id":"BjHo"}],"article_type":"original","date_created":"2021-01-10T23:01:17Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":9456389,"date_updated":"2021-01-11T07:50:32Z","file_name":"2021_Entropy_Avila.pdf","success":1,"checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","date_created":"2021-01-11T07:50:32Z","creator":"dernst","relation":"main_file","file_id":"9003","access_level":"open_access"}],"citation":{"ieee":"K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58.","apa":"Avila, K., &#38; Hof, B. (2021). Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>","mla":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>, vol. 23, no. 1, 58, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>.","chicago":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>.","ama":"Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>","short":"K. Avila, B. Hof, Entropy 23 (2021)."},"doi":"10.3390/e23010058","scopus_import":"1","publication":"Entropy","language":[{"iso":"eng"}],"date_published":"2021-01-01T00:00:00Z","type":"journal_article","issue":"1","acknowledgement":"This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n","year":"2021","intvolume":"        23","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","publication_identifier":{"eissn":["1099-4300"]},"pmid":1,"article_number":"58","publication_status":"published","quality_controlled":"1","oa":1,"file_date_updated":"2021-01-11T07:50:32Z","_id":"8999","author":[{"last_name":"Avila","full_name":"Avila, Kerstin","first_name":"Kerstin","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"}],"has_accepted_license":"1","ddc":["530"],"publisher":"MDPI","date_updated":"2023-08-07T13:31:07Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000610135400001"],"pmid":["33396499"]},"day":"01"},{"related_material":{"record":[{"relation":"earlier_version","id":"6665","status":"public"}]},"status":"public","abstract":[{"text":" We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn).","lang":"eng"}],"month":"09","isi":1,"volume":67,"article_processing_charge":"No","department":[{"_id":"MaMo"}],"article_type":"original","date_created":"2021-01-10T23:01:18Z","oa_version":"Preprint","citation":{"ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 67(9), 5693–5710.","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>.","mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9, IEEE, 2021, pp. 5693–710, doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>.","apa":"Fazeli, A., Hassani, H., Mondelli, M., &#38; Vardy, A. (2021). Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. 2021;67(9):5693-5710. doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>"},"OA_place":"repository","doi":"10.1109/TIT.2020.3038806","date_published":"2021-09-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","scopus_import":"1","type":"journal_article","issue":"9","intvolume":"        67","year":"2021","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"arxiv":1,"publication_status":"published","quality_controlled":"1","oa":1,"author":[{"full_name":"Fazeli, Arman","last_name":"Fazeli","first_name":"Arman"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"full_name":"Vardy, Alexander","last_name":"Vardy","first_name":"Alexander"}],"_id":"9002","publisher":"IEEE","date_updated":"2025-09-10T09:59:12Z","page":"5693-5710","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1711.01339","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000690440100007"],"arxiv":["1711.01339"]},"day":"01","OA_type":"green"}]