[{"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.","file":[{"file_id":"9090","creator":"dernst","file_name":"2021_CurrentBiology_MarquesBueno.pdf","checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","file_size":3458646,"date_created":"2021-02-04T11:37:50Z","date_updated":"2021-02-04T11:37:50Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"month":"01","_id":"8824","citation":{"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>.","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>","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.","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>","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).","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).","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>."},"date_updated":"2024-10-21T06:02:09Z","date_published":"2021-01-11T00:00:00Z","has_accepted_license":"1","type":"journal_article","isi":1,"title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","author":[{"full_name":"Marquès-Bueno, MM","last_name":"Marquès-Bueno","first_name":"MM"},{"last_name":"Armengot","first_name":"L","full_name":"Armengot, L"},{"full_name":"Noack, LC","first_name":"LC","last_name":"Noack"},{"last_name":"Bareille","first_name":"J","full_name":"Bareille, J"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Platre","first_name":"MP","full_name":"Platre, MP"},{"full_name":"Bayle, V","first_name":"V","last_name":"Bayle"},{"full_name":"Liu, M","last_name":"Liu","first_name":"M"},{"first_name":"D","last_name":"Opdenacker","full_name":"Opdenacker, D"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"full_name":"Möller, BK","last_name":"Möller","first_name":"BK"},{"full_name":"Nimchuk, ZL","first_name":"ZL","last_name":"Nimchuk"},{"full_name":"Beeckman, T","first_name":"T","last_name":"Beeckman"},{"full_name":"Caño-Delgado, AI","last_name":"Caño-Delgado","first_name":"AI"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Y","last_name":"Jaillais","full_name":"Jaillais, Y"}],"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"quality_controlled":"1","publication":"Current Biology","ddc":["570"],"oa":1,"file_date_updated":"2021-02-04T11:37:50Z","issue":"1","doi":"10.1016/j.cub.2020.10.011","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"day":"11","publication_status":"published","status":"public","volume":31,"date_created":"2020-12-01T13:39:46Z","article_type":"original","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"        31","scopus_import":"1","external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2004.08133","open_access":"1"}],"status":"public","publication_status":"published","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"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF","grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425"},{"grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells"}],"day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GeKa"}],"doi":"10.1038/s41578-020-00262-z","oa_version":"Preprint","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"}],"article_type":"original","date_created":"2020-12-02T10:52:51Z","volume":6,"external_id":{"isi":["000600826100003"],"arxiv":["2004.08133"]},"scopus_import":"1","intvolume":"         6","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","_id":"8911","date_updated":"2024-10-22T09:41:03Z","page":"926–943 ","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>.","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>","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.","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>","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.","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."},"month":"10","language":[{"iso":"eng"}],"publisher":"Springer Nature","author":[{"full_name":"Scappucci, Giordano","first_name":"Giordano","last_name":"Scappucci"},{"last_name":"Kloeffel","first_name":"Christoph","full_name":"Kloeffel, Christoph"},{"first_name":"Floris A.","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris A."},{"full_name":"Loss, Daniel","first_name":"Daniel","last_name":"Loss"},{"first_name":"Maksym","last_name":"Myronov","full_name":"Myronov, Maksym"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"last_name":"Franceschi","first_name":"Silvano De","full_name":"Franceschi, Silvano De"},{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"},{"full_name":"Veldhorst, Menno","first_name":"Menno","last_name":"Veldhorst"}],"title":"The germanium quantum information route","arxiv":1,"ec_funded":1,"isi":1,"type":"journal_article","date_published":"2021-10-01T00:00:00Z","publication":"Nature Reviews Materials","quality_controlled":"1","publication_identifier":{"eissn":["2058-8437"]},"article_processing_charge":"No"},{"has_accepted_license":"1","type":"journal_article","date_published":"2021-07-01T00:00:00Z","title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"isi":1,"ec_funded":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","ddc":["516"],"publication":"Discrete & Computational Geometry","year":"2021","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).","file":[{"date_created":"2021-08-06T09:52:29Z","file_size":983307,"checksum":"c848986091e56699dc12de85adb1e39c","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","creator":"kschuh","file_id":"9795","relation":"main_file","content_type":"application/pdf","success":1,"date_updated":"2021-08-06T09:52:29Z","access_level":"open_access"}],"month":"07","page":"386-434","_id":"8940","date_updated":"2025-04-14T07:43:50Z","citation":{"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>.","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.","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>","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.","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>.","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>"},"corr_author":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"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"}],"date_created":"2020-12-12T11:07:02Z","volume":66,"article_type":"original","oa_version":"Published Version","intvolume":"        66","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000597770300001"]},"scopus_import":"1","file_date_updated":"2021-08-06T09:52:29Z","oa":1,"keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"issue":"1","day":"01","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1007/s00454-020-00250-8","department":[{"_id":"HeEd"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_status":"published"},{"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).","year":"2021","language":[{"iso":"eng"}],"publisher":"Elsevier","citation":{"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.","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>","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>.","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.","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>","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165."},"_id":"8992","page":"151-165","date_updated":"2025-07-10T12:01:28Z","month":"01","file":[{"file_name":"2020_MolecularPlant_Tan.pdf","date_created":"2021-01-07T14:03:53Z","file_size":871088,"checksum":"917e60e57092f22e16beac70b1775ea6","file_id":"8995","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-01-07T14:03:53Z","success":1}],"ec_funded":1,"isi":1,"author":[{"last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","date_published":"2021-01-04T00:00:00Z","type":"journal_article","has_accepted_license":"1","publication":"Molecular Plant","ddc":["580"],"article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1752-9867"],"issn":["1674-2052"]},"issue":"1","oa":1,"file_date_updated":"2021-01-07T14:03:53Z","publication_status":"published","status":"public","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molp.2020.11.004","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"day":"04","oa_version":"Published Version","pmid":1,"article_type":"original","volume":14,"date_created":"2021-01-03T23:01:23Z","abstract":[{"lang":"eng","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."}],"scopus_import":"1","external_id":{"isi":["000605359400014"],"pmid":["33186755"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        14"},{"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.). ","year":"2021","language":[{"iso":"eng"}],"publisher":"Public Library of Science","_id":"8997","citation":{"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.","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>","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.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","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>","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>."},"date_updated":"2025-06-12T06:33:18Z","month":"01","file":[{"relation":"main_file","content_type":"application/pdf","success":1,"date_updated":"2021-02-04T12:30:48Z","access_level":"open_access","date_created":"2021-02-04T12:30:48Z","file_size":3690053,"checksum":"e29f2b42651bef8e034781de8781ffac","file_name":"2021_PlosComBio_Kavcic.pdf","creator":"dernst","file_id":"9092"}],"isi":1,"author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X"}],"title":"Minimal biophysical model of combined antibiotic action","date_published":"2021-01-07T00:00:00Z","has_accepted_license":"1","type":"journal_article","publication":"PLOS Computational Biology","ddc":["570"],"article_processing_charge":"Yes","quality_controlled":"1","publication_identifier":{"issn":["1553-7358"]},"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"oa":1,"file_date_updated":"2021-02-04T12:30:48Z","publication_status":"published","status":"public","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1371/journal.pcbi.1008529","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"day":"07","oa_version":"Published Version","pmid":1,"article_type":"original","volume":17,"date_created":"2021-01-08T07:16:18Z","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."}],"article_number":"e1008529","related_material":{"record":[{"relation":"research_data","id":"8930","status":"public"},{"status":"public","relation":"earlier_version","id":"7673"}]},"scopus_import":"1","external_id":{"pmid":["33411759"],"isi":["000608045000010"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        17"},{"month":"01","date_updated":"2023-08-07T13:31:07Z","_id":"8999","citation":{"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>.","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>","short":"K. Avila, B. Hof, Entropy 23 (2021).","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58.","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>","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>.","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."},"publisher":"MDPI","language":[{"iso":"eng"}],"file":[{"date_updated":"2021-01-11T07:50:32Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"9003","creator":"dernst","file_name":"2021_Entropy_Avila.pdf","file_size":9456389,"checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","date_created":"2021-01-11T07:50:32Z"}],"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","ddc":["530"],"publication":"Entropy","publication_identifier":{"eissn":["1099-4300"]},"quality_controlled":"1","article_processing_charge":"No","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","author":[{"full_name":"Avila, Kerstin","first_name":"Kerstin","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757","last_name":"Avila"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"isi":1,"has_accepted_license":"1","type":"journal_article","date_published":"2021-01-01T00:00:00Z","status":"public","publication_status":"published","day":"01","doi":"10.3390/e23010058","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BjHo"}],"issue":"1","file_date_updated":"2021-01-11T07:50:32Z","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["33396499"],"isi":["000610135400001"]},"scopus_import":"1","intvolume":"        23","pmid":1,"oa_version":"Published Version","article_number":"58","abstract":[{"lang":"eng","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. "}],"date_created":"2021-01-10T23:01:17Z","volume":23,"article_type":"original"},{"status":"public","publication_status":"published","day":"01","department":[{"_id":"MaMo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1109/TIT.2020.3038806","issue":"9","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1711.01339","open_access":"1"}],"oa":1,"external_id":{"isi":["000690440100007"],"arxiv":["1711.01339"]},"scopus_import":"1","intvolume":"        67","oa_version":"Preprint","OA_type":"green","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"}],"related_material":{"record":[{"relation":"earlier_version","id":"6665","status":"public"}]},"article_type":"original","date_created":"2021-01-10T23:01:18Z","volume":67,"_id":"9002","date_updated":"2025-09-10T09:59:12Z","citation":{"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>.","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.","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>","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>.","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.","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","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>"},"page":"5693-5710","month":"09","language":[{"iso":"eng"}],"publisher":"IEEE","OA_place":"repository","year":"2021","publication":"IEEE Transactions on Information Theory","quality_controlled":"1","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"article_processing_charge":"No","author":[{"full_name":"Fazeli, Arman","last_name":"Fazeli","first_name":"Arman"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"}],"title":"Binary linear codes with optimal scaling: Polar codes with large kernels","arxiv":1,"isi":1,"type":"journal_article","date_published":"2021-09-01T00:00:00Z"},{"volume":26,"date_created":"2021-01-17T23:01:11Z","article_type":"original","abstract":[{"lang":"eng","text":"Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane."}],"pmid":1,"oa_version":"Submitted Version","intvolume":"        26","scopus_import":"1","external_id":{"isi":["000606722600001"],"pmid":["33426618"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/","open_access":"1"}],"oa":1,"issue":"2","doi":"10.1007/s10495-020-01654-w","department":[{"_id":"SaSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","publication_status":"published","status":"public","date_published":"2021-02-01T00:00:00Z","type":"journal_article","isi":1,"title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","author":[{"full_name":"Grosser, Joshua A.","last_name":"Grosser","first_name":"Joshua A."},{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"article_processing_charge":"No","publication_identifier":{"issn":["1360-8185"],"eissn":["1573-675X"]},"quality_controlled":"1","publication":"Apoptosis","year":"2021","acknowledgement":"This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"02","date_updated":"2023-08-07T13:32:40Z","_id":"9009","citation":{"chicago":"Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>.","ieee":"J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” <i>Apoptosis</i>, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.","mla":"Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>.","ama":"Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. 2021;26(2):132-145. doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.","apa":"Grosser, J. A., Maes, M. E., &#38; Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>","short":"J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145."},"page":"132-145"},{"doi":"10.3390/e23010125","department":[{"_id":"MaSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"day":"19","publication_status":"published","status":"public","oa":1,"file_date_updated":"2021-01-19T11:11:14Z","issue":"1","intvolume":"        23","scopus_import":"1","external_id":{"isi":["000610122000001"],"arxiv":["2012.01390"],"pmid":["33477903"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2021-01-19T11:12:06Z","volume":23,"article_type":"original","article_number":"e23010125","abstract":[{"text":"We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. ","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-01-19T11:11:14Z","file_name":"Final published paper.pdf","checksum":"6cd0e706156827c45c740534bd32c179","file_size":981285,"date_created":"2021-01-19T11:11:14Z","file_id":"9021","creator":"tgulden"}],"publisher":"MDPI","language":[{"iso":"eng"}],"month":"01","_id":"9020","date_updated":"2025-06-12T06:33:38Z","citation":{"chicago":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>.","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","apa":"Gulden, T., &#38; Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","mla":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>, vol. 23, no. 1, e23010125, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>.","ama":"Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>"},"year":"2021","acknowledgement":"A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing.","article_processing_charge":"Yes","publication_identifier":{"eissn":["1099-4300"]},"quality_controlled":"1","publication":"Entropy","ddc":["530"],"date_published":"2021-01-19T00:00:00Z","type":"journal_article","has_accepted_license":"1","isi":1,"arxiv":1,"ec_funded":1,"title":"Dynamics of ion channels via non-hermitian quantum mechanics","author":[{"orcid":"0000-0001-6814-7541","first_name":"Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","full_name":"Gulden, Tobias"},{"first_name":"Alex","last_name":"Kamenev","full_name":"Kamenev, Alex"}]},{"acknowledgement":"D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","year":"2021","language":[{"iso":"eng"}],"publisher":"Elsevier","_id":"9036","date_updated":"2025-04-14T07:50:40Z","citation":{"ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021.","mla":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>, vol. 380, no. 3, 107595, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>.","ama":"Virosztek D. The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. 2021;380(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>","ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","short":"D. Virosztek, Advances in Mathematics 380 (2021).","apa":"Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>","chicago":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>."},"month":"03","arxiv":1,"ec_funded":1,"isi":1,"author":[{"full_name":"Virosztek, Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Virosztek","orcid":"0000-0003-1109-5511"}],"title":"The metric property of the quantum Jensen-Shannon divergence","date_published":"2021-03-26T00:00:00Z","type":"journal_article","publication":"Advances in Mathematics","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0001-8708"]},"issue":"3","keyword":["General Mathematics"],"main_file_link":[{"url":"https://arxiv.org/abs/1910.10447","open_access":"1"}],"oa":1,"publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LaEr"}],"doi":"10.1016/j.aim.2021.107595","project":[{"name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020","grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"day":"26","oa_version":"Preprint","article_type":"original","volume":380,"date_created":"2021-01-22T17:55:17Z","abstract":[{"lang":"eng","text":"In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space."}],"article_number":"107595","scopus_import":"1","external_id":{"isi":["000619676100035"],"arxiv":["1910.10447"]},"intvolume":"       380"},{"issue":"2","oa":1,"file_date_updated":"2021-08-06T09:59:45Z","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"doi":"10.1112/blms.12449","day":"01","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","article_type":"original","date_created":"2021-01-24T23:01:08Z","volume":53,"abstract":[{"text":"We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak  𝜀 ‐net theorem in Banach spaces of type  𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.","lang":"eng"}],"scopus_import":"1","external_id":{"isi":["000607265100001"],"arxiv":["1912.08561"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"intvolume":"        53","acknowledgement":"I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926.","year":"2021","language":[{"iso":"eng"}],"publisher":"London Mathematical Society","_id":"9037","date_updated":"2025-07-10T12:01:31Z","citation":{"mla":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>.","ama":"Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):631-641. doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>","ieee":"G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021.","short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","apa":"Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>","ista":"Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.","chicago":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2021. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>."},"page":"631-641","month":"04","file":[{"success":1,"access_level":"open_access","date_updated":"2021-08-06T09:59:45Z","relation":"main_file","content_type":"application/pdf","creator":"kschuh","file_id":"9796","date_created":"2021-08-06T09:59:45Z","file_size":194550,"checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1","file_name":"2021_BLMS_Ivanov.pdf"}],"arxiv":1,"isi":1,"author":[{"last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"}],"title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","date_published":"2021-04-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","publication":"Bulletin of the London Mathematical Society","ddc":["510"],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]}},{"day":"14","doi":"10.1371/journal.ppat.1009172","department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","oa":1,"file_date_updated":"2021-02-03T12:13:03Z","issue":"1","intvolume":"        17","external_id":{"pmid":["33444399"],"isi":["000610190400007"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","article_number":"e1009172","volume":17,"date_created":"2021-01-31T23:01:21Z","article_type":"original","pmid":1,"oa_version":"Published Version","file":[{"file_id":"9070","creator":"dernst","file_name":"2021_PlosPathogens_Roemhild.pdf","date_created":"2021-02-03T12:13:03Z","file_size":570066,"checksum":"d745d7f8fcbb9b95fea16a36f94dee31","access_level":"open_access","date_updated":"2021-02-03T12:13:03Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"month":"01","date_updated":"2025-07-10T12:01:33Z","_id":"9046","citation":{"chicago":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>.","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).","apa":"Römhild, R., &#38; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>","ieee":"R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” <i>PLoS Pathogens</i>, vol. 17, no. 1. Public Library of Science, 2021.","mla":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>.","ama":"Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. 2021;17(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>"},"publisher":"Public Library of Science","language":[{"iso":"eng"}],"year":"2021","acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":"PLoS Pathogens","has_accepted_license":"1","type":"journal_article","date_published":"2021-01-14T00:00:00Z","title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","author":[{"full_name":"Römhild, Roderich","last_name":"Römhild","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","first_name":"Roderich","orcid":"0000-0001-9480-5261"},{"first_name":"Dan I.","last_name":"Andersson","full_name":"Andersson, Dan I."}],"isi":1},{"scopus_import":"1","external_id":{"isi":["000607808800002"],"arxiv":["1909.04892"]},"intvolume":"        20","oa_version":"Preprint","date_created":"2021-01-31T23:01:21Z","volume":20,"article_type":"original","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8536"}]},"abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.","lang":"eng"}],"publication_status":"published","status":"public","doi":"10.1109/TWC.2020.3022922","department":[{"_id":"MaMo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"1","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"oa":1,"publication":"IEEE Transactions on Wireless Communications","article_processing_charge":"No","publication_identifier":{"eissn":["1558-2248"],"issn":["1536-1276"]},"quality_controlled":"1","isi":1,"arxiv":1,"title":"Sublinear latency for simplified successive cancellation decoding of polar codes","author":[{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco"},{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"full_name":"Cioffi, John M.","first_name":"John M.","last_name":"Cioffi"},{"full_name":"Goldsmith, Andrea","first_name":"Andrea","last_name":"Goldsmith"}],"date_published":"2021-01-01T00:00:00Z","type":"journal_article","publisher":"IEEE","corr_author":"1","language":[{"iso":"eng"}],"month":"01","_id":"9047","date_updated":"2025-09-10T10:27:04Z","page":"18-27","citation":{"ista":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J. M., &#38; Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27.","ieee":"M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1. IEEE, pp. 18–27, 2021.","mla":"Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>.","ama":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2021;20(1):18-27. doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>."},"acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript.","year":"2021"},{"file":[{"access_level":"open_access","date_updated":"2021-02-03T12:47:04Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"9074","creator":"dernst","file_name":"2021_PhysicalRevLett_DeNicola.pdf","date_created":"2021-02-03T12:47:04Z","file_size":398075,"checksum":"d9acbc502390ed7a97e631d23ae19ecd"}],"publisher":"American Physical Society","language":[{"iso":"eng"}],"month":"01","date_updated":"2025-04-14T07:43:50Z","_id":"9048","citation":{"chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>.","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602."},"year":"2021","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","article_processing_charge":"Yes","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"quality_controlled":"1","publication":"Physical Review Letters","ddc":["530"],"date_published":"2021-01-29T00:00:00Z","has_accepted_license":"1","type":"journal_article","isi":1,"arxiv":1,"ec_funded":1,"title":"Entanglement view of dynamical quantum phase transitions","author":[{"orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"doi":"10.1103/physrevlett.126.040602","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaSe"}],"day":"29","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"publication_status":"published","status":"public","keyword":["General Physics and Astronomy"],"oa":1,"file_date_updated":"2021-02-03T12:47:04Z","issue":"4","intvolume":"       126","scopus_import":"1","external_id":{"arxiv":["2008.04894"],"isi":["000613148200001"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2021-02-01T09:20:00Z","volume":126,"article_type":"original","article_number":"040602","abstract":[{"text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.","lang":"eng"}],"oa_version":"Published Version"},{"publication":"bioRxiv","article_processing_charge":"No","title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","oa_version":"Preprint","author":[{"full_name":"Anderson, Donovan J.","first_name":"Donovan J.","last_name":"Anderson"},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"first_name":"Aaron","last_name":"McKenna","full_name":"McKenna, Aaron"},{"full_name":"Shendure, Jay","first_name":"Jay","last_name":"Shendure"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"ec_funded":1,"type":"preprint","abstract":[{"text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.","lang":"eng"}],"date_published":"2021-01-01T00:00:00Z","date_created":"2021-02-04T07:23:23Z","month":"01","_id":"9082","date_updated":"2025-04-14T07:43:04Z","citation":{"chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>","short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.).","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>","mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"status":"public","publisher":"Cold Spring Harbor Laboratory","publication_status":"submitted","language":[{"iso":"eng"}],"day":"01","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1101/2020.12.31.425016","department":[{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","main_file_link":[{"url":"https://doi.org/10.1101/2020.12.31.425016","open_access":"1"}],"oa":1,"year":"2021"},{"publication_identifier":{"issn":["2542-4653"]},"quality_controlled":"1","article_processing_charge":"No","ddc":["530"],"publication":"SciPost Physics","type":"journal_article","has_accepted_license":"1","date_published":"2021-02-03T00:00:00Z","title":"Shape of a sound wave in a weakly-perturbed Bose gas","author":[{"first_name":"Oleksandr","last_name":"Marchukov","full_name":"Marchukov, Oleksandr"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev"}],"isi":1,"arxiv":1,"ec_funded":1,"file":[{"file_name":"2021_SciPostPhysics_Marchukov.pdf","date_created":"2021-02-09T07:06:22Z","checksum":"9fd614b7ab49999e7267874df2582f7e","file_size":666512,"file_id":"9105","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-02-09T07:06:22Z","success":1}],"month":"02","citation":{"chicago":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>.","ieee":"O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed Bose gas,” <i>SciPost Physics</i>, vol. 10, no. 2. SciPost Foundation, 2021.","ama":"Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. 2021;10(2). doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>","mla":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>, vol. 10, no. 2, 025, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>.","ista":"Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025.","short":"O. Marchukov, A. Volosniev, SciPost Physics 10 (2021).","apa":"Marchukov, O., &#38; Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>"},"_id":"9093","date_updated":"2025-04-14T07:43:51Z","publisher":"SciPost Foundation","language":[{"iso":"eng"}],"year":"2021","acknowledgement":"We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221, and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17) and from the German Aeronautics and Space Administration\r\n(DLR) through Grant No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248 [VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)","intvolume":"        10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000646783100027"],"arxiv":["2004.08075"]},"scopus_import":"1","article_number":"025","abstract":[{"lang":"eng","text":"We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation."}],"volume":10,"date_created":"2021-02-04T12:39:24Z","article_type":"original","oa_version":"Published Version","day":"03","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"doi":"10.21468/scipostphys.10.2.025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"status":"public","publication_status":"published","file_date_updated":"2021-02-09T07:06:22Z","oa":1,"issue":"2"},{"status":"public","publication_status":"published","day":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"}],"doi":"10.1083/jcb.202006081","issue":"4","file_date_updated":"2022-05-12T14:16:21Z","oa":1,"external_id":{"isi":["000626365700001"],"pmid":["33533935"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"scopus_import":"1","intvolume":"       220","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","pmid":1,"abstract":[{"text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.","lang":"eng"}],"article_number":"e202006081","article_type":"original","date_created":"2021-02-05T10:08:04Z","volume":220,"date_updated":"2024-10-09T21:00:23Z","_id":"9094","citation":{"ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081.","short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>","ieee":"A. F. Leithner <i>et al.</i>, “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>","mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>.","chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>."},"month":"04","language":[{"iso":"eng"}],"corr_author":"1","publisher":"Rockefeller University Press","file":[{"date_updated":"2022-05-12T14:16:21Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11367","creator":"dernst","file_name":"2021_JournCellBiology_Leithner.pdf","file_size":5102328,"checksum":"843ebc153847c8626e13c9c5ce71d533","date_created":"2022-05-12T14:16:21Z"}],"year":"2021","ddc":["570"],"publication":"Journal of Cell Biology","quality_controlled":"1","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","last_name":"Leithner"},{"last_name":"Altenburger","first_name":"LM","full_name":"Altenburger, LM"},{"first_name":"R","last_name":"Hauschild","full_name":"Hauschild, R"},{"orcid":"0000-0003-3470-6119","last_name":"Assen","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P"},{"full_name":"Rottner, K","first_name":"K","last_name":"Rottner"},{"full_name":"TEB, Stradal","last_name":"TEB","first_name":"Stradal"},{"last_name":"Diz-Muñoz","first_name":"A","full_name":"Diz-Muñoz, A"},{"last_name":"Stein","first_name":"JV","full_name":"Stein, JV"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","isi":1,"type":"journal_article","has_accepted_license":"1","date_published":"2021-04-05T00:00:00Z"},{"publisher":"Elsevier","language":[{"iso":"eng"}],"month":"05","date_updated":"2025-07-10T12:01:36Z","_id":"9098","citation":{"ista":"Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete Mathematics. 344(5), 112312.","apa":"Ivanov, G. (2021). On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>","short":"G. Ivanov, Discrete Mathematics 344 (2021).","ieee":"G. Ivanov, “On the volume of projections of the cross-polytope,” <i>Discrete Mathematics</i>, vol. 344, no. 5. Elsevier, 2021.","ama":"Ivanov G. On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. 2021;344(5). doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>","mla":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>, vol. 344, no. 5, 112312, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>.","chicago":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>."},"acknowledgement":"Research was supported by the Russian Foundation for Basic Research, project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926 (Theorems 1.2 and 7.3).","year":"2021","publication":"Discrete Mathematics","article_processing_charge":"No","publication_identifier":{"issn":["0012-365X"]},"quality_controlled":"1","isi":1,"arxiv":1,"title":"On the volume of projections of the cross-polytope","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov"}],"date_published":"2021-05-01T00:00:00Z","type":"journal_article","publication_status":"published","status":"public","doi":"10.1016/j.disc.2021.112312","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"5","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.09165"}],"scopus_import":"1","external_id":{"arxiv":["1808.09165"],"isi":["000633365200001"]},"intvolume":"       344","oa_version":"Preprint","volume":344,"date_created":"2021-02-07T23:01:12Z","article_type":"original","article_number":"112312","abstract":[{"text":"We study properties of the volume of projections of the n-dimensional\r\ncross-polytope $\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.","lang":"eng"}]},{"date_published":"2021-05-01T00:00:00Z","type":"journal_article","ec_funded":1,"arxiv":1,"isi":1,"author":[{"full_name":"Srivastava, Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","first_name":"Tanya K","last_name":"Srivastava"}],"title":"Lifting automorphisms on Abelian varieties as derived autoequivalences","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1420-8938"],"issn":["0003-889X"]},"publication":"Archiv der Mathematik","year":"2021","acknowledgement":"I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas Hausel for hosting me in his research group at IST Austria, and the referees for their valuable suggestions. This research has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Grant Agreement No. 754411.","language":[{"iso":"eng"}],"publisher":"Springer Nature","_id":"9099","page":"515-527","date_updated":"2025-07-10T12:01:36Z","citation":{"chicago":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>.","apa":"Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv Der Mathematik</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>","short":"T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.","ista":"Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 116(5), 515–527.","ama":"Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv der Mathematik</i>. 2021;116(5):515-527. doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>","mla":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>, vol. 116, no. 5, Springer Nature, 2021, pp. 515–27, doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>.","ieee":"T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,” <i>Archiv der Mathematik</i>, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021."},"month":"05","article_type":"original","date_created":"2021-02-07T23:01:13Z","volume":116,"abstract":[{"text":"We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations.","lang":"eng"}],"oa_version":"Preprint","intvolume":"       116","scopus_import":"1","external_id":{"isi":["000612580200001"],"arxiv":["2001.07762"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.07762"}],"issue":"5","department":[{"_id":"TaHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00013-020-01564-y","day":"01","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"publication_status":"published","status":"public"},{"issue":"1","file_date_updated":"2021-02-09T09:04:02Z","oa":1,"status":"public","publication_status":"published","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"doi":"10.1111/jeb.13756","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity."}],"article_type":"original","date_created":"2021-02-07T23:01:13Z","volume":34,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000608367500001"]},"scopus_import":"1","intvolume":"        34","acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","year":"2021","page":"4-15","_id":"9100","citation":{"apa":"Faria, R., Johannesson, K., &#38; Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>.","ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. 2021;34(1):4-15. doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>."},"date_updated":"2025-07-10T12:01:37Z","month":"01","language":[{"iso":"eng"}],"publisher":"Wiley","file":[{"access_level":"open_access","date_updated":"2021-02-09T09:04:02Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"9108","creator":"dernst","file_name":"2021_JourEvolBiology_Faria.pdf","file_size":561340,"checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","date_created":"2021-02-09T09:04:02Z"}],"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"title":"Speciation in marine environments: Diving under the surface","isi":1,"has_accepted_license":"1","type":"journal_article","date_published":"2021-01-18T00:00:00Z","ddc":["570"],"publication":"Journal of Evolutionary Biology","quality_controlled":"1","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"article_processing_charge":"No"}]