[{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"day":"01","quality_controlled":"1","publication":"Journal of Evolutionary Biology","intvolume":"        34","abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"publication_status":"published","title":"Genomic inference of complex domestication histories in three Solanaceae species","volume":34,"month":"02","scopus_import":"1","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"oa":1,"acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","author":[{"full_name":"Arnoux, Stéphanie","last_name":"Arnoux","first_name":"Stéphanie"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"project":[{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463"}],"language":[{"iso":"eng"}],"page":"270-283","article_processing_charge":"No","isi":1,"citation":{"ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>"},"department":[{"_id":"NiBa"}],"external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"related_material":{"record":[{"relation":"research_data","id":"13065","status":"public"}]},"date_updated":"2026-06-18T19:37:17Z","doi":"10.1111/jeb.13723","oa_version":"Published Version","_id":"8928","ddc":["570"],"pmid":1,"issue":"2","year":"2021","type":"journal_article","article_type":"original","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-12-06T23:01:16Z","status":"public","date_published":"2021-02-01T00:00:00Z"},{"author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Kachanovich","first_name":"Siargey","full_name":"Kachanovich, Siargey"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"language":[{"iso":"eng"}],"page":"386-434","article_processing_charge":"Yes (via OA deal)","citation":{"short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","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.","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>.","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>","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>","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>.","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."},"isi":1,"oa":1,"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).","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"volume":66,"scopus_import":"1","month":"07","publication":"Discrete & Computational Geometry","intvolume":"        66","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"}],"has_accepted_license":"1","publication_status":"published","corr_author":"1","title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","ec_funded":1,"day":"01","quality_controlled":"1","status":"public","date_published":"2021-07-01T00:00:00Z","date_created":"2020-12-12T11:07:02Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"article_type":"original","type":"journal_article","publisher":"Springer Nature","ddc":["516"],"issue":"1","year":"2021","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2021-08-06T09:52:29Z","oa_version":"Published Version","file":[{"creator":"kschuh","file_id":"9795","file_size":983307,"file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","checksum":"c848986091e56699dc12de85adb1e39c","date_updated":"2021-08-06T09:52:29Z","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2021-08-06T09:52:29Z","relation":"main_file"}],"_id":"8940","doi":"10.1007/s00454-020-00250-8","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"]},"date_updated":"2025-04-14T07:43:50Z","department":[{"_id":"HeEd"}]},{"quality_controlled":"1","day":"05","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"publication_status":"published","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","corr_author":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":118,"month":"01","scopus_import":"1","article_processing_charge":"No","isi":1,"citation":{"ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118.","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021."},"author":[{"orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","last_name":"Düllberg","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert","last_name":"Auer","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906"},{"orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","last_name":"Canigova","id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola"},{"full_name":"Loibl, Katrin","orcid":"0000-0002-2429-7668","first_name":"Katrin","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","last_name":"Loibl"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"}],"project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","oa":1,"date_updated":"2026-06-18T19:37:53Z","external_id":{"pmid":["33443153"],"isi":["000607270100018"]},"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"article_number":"e2010054118","_id":"8988","oa_version":"Published Version","doi":"10.1073/pnas.2010054118","article_type":"original","type":"journal_article","publisher":"National Academy of Sciences","year":"2021","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"pmid":1,"issue":"1","status":"public","date_published":"2021-01-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-03T23:01:23Z"},{"oa_version":"Published Version","file_date_updated":"2021-01-07T14:03:53Z","_id":"8992","file":[{"file_size":871088,"file_name":"2020_MolecularPlant_Tan.pdf","file_id":"8995","creator":"dernst","access_level":"open_access","date_updated":"2021-01-07T14:03:53Z","checksum":"917e60e57092f22e16beac70b1775ea6","date_created":"2021-01-07T14:03:53Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"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)"},"doi":"10.1016/j.molp.2020.11.004","external_id":{"pmid":["33186755"],"isi":["000605359400014"]},"date_updated":"2025-07-10T12:01:28Z","department":[{"_id":"JiFr"}],"date_published":"2021-01-04T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-03T23:01:23Z","publisher":"Elsevier","type":"journal_article","article_type":"original","issue":"1","pmid":1,"ddc":["580"],"year":"2021","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."}],"intvolume":"        14","publication":"Molecular Plant","publication_status":"published","title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","has_accepted_license":"1","ec_funded":1,"day":"04","quality_controlled":"1","language":[{"iso":"eng"}],"project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"723-2015","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"isi":1,"citation":{"mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>.","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.","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>.","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>","ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. 2021;14(1):151-165. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165."},"article_processing_charge":"No","page":"151-165","oa":1,"acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","publication_identifier":{"issn":["1674-2052"],"eissn":["1752-9867"]},"scopus_import":"1","month":"01","volume":14},{"day":"05","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","publication_status":"published","ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"volume":118,"month":"01","scopus_import":"1","author":[{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"full_name":"Kolb, Martina","last_name":"Kolb","first_name":"Martina"},{"full_name":"Stadlmann, Johannes","last_name":"Stadlmann","first_name":"Johannes"},{"full_name":"Janacek, Dorina P.","first_name":"Dorina P.","last_name":"Janacek"},{"full_name":"Lukic, Kristina","orcid":"0000-0003-1581-881X","first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","last_name":"Lukic"},{"full_name":"Schwechheimer, Claus","last_name":"Schwechheimer","first_name":"Claus"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"full_name":"Mach, Lukas","last_name":"Mach","first_name":"Lukas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hammes","first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z."}],"language":[{"iso":"eng"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"isi":1,"article_processing_charge":"No","citation":{"mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>.","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2020857118."},"oa":1,"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","external_id":{"pmid":["33443187"],"isi":["000607270100073"]},"date_updated":"2026-06-18T19:38:20Z","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2102232118","relation":"erratum"}]},"department":[{"_id":"JiFr"},{"_id":"LeSa"}],"oa_version":"Published Version","_id":"8993","article_number":"e2020857118","doi":"10.1073/pnas.2020857118","article_type":"original","type":"journal_article","publisher":"National Academy of Sciences","ddc":["580"],"pmid":1,"issue":"1","year":"2021","status":"public","date_published":"2021-01-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-03T23:01:23Z"},{"ddc":["530"],"pmid":1,"issue":"1","year":"2021","type":"journal_article","article_type":"original","publisher":"MDPI","date_created":"2021-01-10T23:01:17Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2021-01-01T00:00:00Z","department":[{"_id":"BjHo"}],"external_id":{"isi":["000610135400001"],"pmid":["33396499"]},"date_updated":"2023-08-07T13:31:07Z","doi":"10.3390/e23010058","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)"},"file_date_updated":"2021-01-11T07:50:32Z","oa_version":"Published Version","file":[{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2021-01-11T07:50:32Z","checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","date_updated":"2021-01-11T07:50:32Z","access_level":"open_access","creator":"dernst","file_id":"9003","file_name":"2021_Entropy_Avila.pdf","file_size":9456389}],"_id":"8999","article_number":"58","volume":23,"month":"01","scopus_import":"1","publication_identifier":{"eissn":["1099-4300"]},"oa":1,"acknowledgement":"This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n","author":[{"full_name":"Avila, Kerstin","last_name":"Avila","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757","first_name":"Kerstin"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"language":[{"iso":"eng"}],"isi":1,"citation":{"ieee":"K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","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>.","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.","chicago":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>.","ama":"Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>","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>"},"article_processing_charge":"No","day":"01","quality_controlled":"1","publication":"Entropy","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. "}],"intvolume":"        23","has_accepted_license":"1","publication_status":"published","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment"},{"language":[{"iso":"eng"}],"author":[{"full_name":"Fazeli, Arman","last_name":"Fazeli","first_name":"Arman"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"last_name":"Vardy","first_name":"Alexander","full_name":"Vardy, Alexander"}],"citation":{"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>.","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.","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>","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>","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>.","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."},"article_processing_charge":"No","isi":1,"page":"5693-5710","oa":1,"arxiv":1,"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"month":"09","scopus_import":"1","volume":67,"abstract":[{"lang":"eng","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)."}],"intvolume":"        67","OA_place":"repository","publication":"IEEE Transactions on Information Theory","publication_status":"published","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","OA_type":"green","day":"01","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1711.01339"}],"date_published":"2021-09-01T00:00:00Z","status":"public","date_created":"2021-01-10T23:01:18Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"IEEE","type":"journal_article","article_type":"original","issue":"9","year":"2021","oa_version":"Preprint","_id":"9002","doi":"10.1109/TIT.2020.3038806","external_id":{"arxiv":["1711.01339"],"isi":["000690440100007"]},"date_updated":"2025-09-10T09:59:12Z","related_material":{"record":[{"id":"6665","relation":"earlier_version","status":"public"}]},"department":[{"_id":"MaMo"}]},{"oa":1,"acknowledgement":"We are grateful to A. Ghazaryan for valuable discussions and also thank the anonymous referees for comments. D.L. acknowledges financial support from the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully acknowledges financial support\r\nby the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 801770).","arxiv":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"author":[{"last_name":"Brooks","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lundholm, D.","first_name":"D.","last_name":"Lundholm"},{"last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"}],"isi":1,"citation":{"ista":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. 126(1), 015301.","chicago":"Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>.","ama":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. 2021;126(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>","apa":"Brooks, M., Lemeshko, M., Lundholm, D., &#38; Yakaboylu, E. (2021). Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>","short":"M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters 126 (2021).","mla":"Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>, vol. 126, no. 1, 015301, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>.","ieee":"M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities as a realization of anyons on the two-sphere,” <i>Physical Review Letters</i>, vol. 126, no. 1. American Physical Society, 2021."},"article_processing_charge":"No","scopus_import":"1","month":"01","volume":126,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"ec_funded":1,"abstract":[{"text":"Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field.","lang":"eng"}],"intvolume":"       126","publication":"Physical Review Letters","title":"Molecular impurities as a realization of anyons on the two-sphere","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.05948"}],"day":"08","quality_controlled":"1","date_created":"2021-01-17T23:01:10Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-01-08T00:00:00Z","status":"public","pmid":1,"issue":"1","year":"2021","publisher":"American Physical Society","type":"journal_article","article_type":"original","doi":"10.1103/PhysRevLett.126.015301","oa_version":"Preprint","_id":"9005","article_number":"015301","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"external_id":{"pmid":["33480760"],"arxiv":["2009.05948"],"isi":["000606325000003"]},"date_updated":"2026-04-16T08:20:53Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"12390","status":"public"}]}},{"status":"public","date_published":"2021-02-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-01-17T23:01:11Z","type":"journal_article","article_type":"original","publisher":"Springer Nature","year":"2021","pmid":1,"issue":"2","_id":"9009","oa_version":"Submitted Version","doi":"10.1007/s10495-020-01654-w","date_updated":"2023-08-07T13:32:40Z","external_id":{"pmid":["33426618"],"isi":["000606722600001"]},"department":[{"_id":"SaSi"}],"page":"132-145","isi":1,"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>.","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.","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>","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.","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>."},"article_processing_charge":"No","author":[{"full_name":"Grosser, Joshua A.","last_name":"Grosser","first_name":"Joshua A."},{"last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"language":[{"iso":"eng"}],"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.","oa":1,"publication_identifier":{"issn":["1360-8185"],"eissn":["1573-675X"]},"volume":26,"scopus_import":"1","month":"02","publication_status":"published","title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","publication":"Apoptosis","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."}],"intvolume":"        26","quality_controlled":"1","day":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/"}]},{"date_updated":"2025-06-12T06:33:38Z","external_id":{"pmid":["33477903"],"arxiv":["2012.01390"],"isi":["000610122000001"]},"department":[{"_id":"MaSe"}],"file":[{"date_created":"2021-01-19T11:11:14Z","content_type":"application/pdf","relation":"main_file","file_name":"Final published paper.pdf","file_size":981285,"file_id":"9021","creator":"tgulden","access_level":"open_access","date_updated":"2021-01-19T11:11:14Z","checksum":"6cd0e706156827c45c740534bd32c179"}],"_id":"9020","article_number":"e23010125","oa_version":"Published Version","file_date_updated":"2021-01-19T11:11:14Z","doi":"10.3390/e23010125","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)"},"publisher":"MDPI","article_type":"original","type":"journal_article","year":"2021","pmid":1,"issue":"1","ddc":["530"],"date_published":"2021-01-19T00:00:00Z","status":"public","date_created":"2021-01-19T11:12:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","day":"19","publication_status":"published","title":"Dynamics of ion channels via non-hermitian quantum mechanics","has_accepted_license":"1","intvolume":"        23","abstract":[{"lang":"eng","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. "}],"publication":"Entropy","ec_funded":1,"publication_identifier":{"eissn":["1099-4300"]},"scopus_import":"1","month":"01","volume":23,"citation":{"short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","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>.","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>","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>","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>.","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021."},"isi":1,"article_processing_charge":"Yes","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"author":[{"id":"1083E038-9F73-11E9-A4B5-532AE6697425","first_name":"Tobias","last_name":"Gulden","full_name":"Gulden, Tobias","orcid":"0000-0001-6814-7541"},{"last_name":"Kamenev","first_name":"Alex","full_name":"Kamenev, Alex"}],"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.","arxiv":1,"oa":1},{"publication_identifier":{"issn":["2663-337X"]},"month":"01","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"}],"citation":{"ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","mla":"Cipolloni, Giorgio. <i>Fluctuations in the Spectrum of Random Matrices</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>","apa":"Cipolloni, G. (2021). <i>Fluctuations in the spectrum of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>"},"article_processing_charge":"No","page":"380","oa":1,"acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","day":"25","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"OA_place":"publisher","publication_status":"published","corr_author":"1","title":"Fluctuations in the spectrum of random matrices","has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","type":"dissertation","ddc":["510"],"year":"2021","date_published":"2021-01-25T00:00:00Z","status":"public","date_created":"2021-01-21T18:16:54Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T06:59:33Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"oa_version":"Published Version","file_date_updated":"2021-01-25T14:19:10Z","file":[{"file_id":"9043","file_size":4127796,"file_name":"thesis.pdf","creator":"gcipollo","date_updated":"2021-01-25T14:19:03Z","access_level":"open_access","checksum":"5a93658a5f19478372523ee232887e2b","content_type":"application/pdf","success":1,"date_created":"2021-01-25T14:19:03Z","relation":"main_file"},{"file_id":"9044","file_name":"Thesis_files.zip","file_size":12775206,"creator":"gcipollo","date_updated":"2021-01-25T14:19:10Z","access_level":"closed","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","content_type":"application/zip","date_created":"2021-01-25T14:19:10Z","relation":"source_file"}],"_id":"9022","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"}],"doi":"10.15479/AT:ISTA:9022"},{"publication_identifier":{"issn":["0001-8708"]},"volume":380,"month":"03","scopus_import":"1","author":[{"last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","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>.","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>","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>","short":"D. Virosztek, Advances in Mathematics 380 (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>.","ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021."},"article_processing_charge":"No","isi":1,"oa":1,"arxiv":1,"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.","day":"26","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1910.10447","open_access":"1"}],"publication":"Advances in Mathematics","abstract":[{"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.","lang":"eng"}],"intvolume":"       380","title":"The metric property of the quantum Jensen-Shannon divergence","publication_status":"published","ec_funded":1,"type":"journal_article","article_type":"original","publisher":"Elsevier","issue":"3","year":"2021","status":"public","date_published":"2021-03-26T00:00:00Z","date_created":"2021-01-22T17:55:17Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["General Mathematics"],"external_id":{"isi":["000619676100035"],"arxiv":["1910.10447"]},"date_updated":"2025-04-14T07:50:40Z","department":[{"_id":"LaEr"}],"oa_version":"Preprint","article_number":"107595","_id":"9036","doi":"10.1016/j.aim.2021.107595"},{"arxiv":1,"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.","oa":1,"page":"631-641","isi":1,"article_processing_charge":"Yes (via OA deal)","citation":{"short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","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>.","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>","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>","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.","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>."},"author":[{"last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory"}],"language":[{"iso":"eng"}],"volume":53,"scopus_import":"1","month":"04","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"has_accepted_license":"1","title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","publication_status":"published","publication":"Bulletin of the London Mathematical Society","intvolume":"        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"}],"quality_controlled":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-24T23:01:08Z","status":"public","date_published":"2021-04-01T00:00:00Z","year":"2021","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["510"],"issue":"2","article_type":"original","type":"journal_article","publisher":"London Mathematical Society","doi":"10.1112/blms.12449","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)"},"_id":"9037","file":[{"creator":"kschuh","file_size":194550,"file_name":"2021_BLMS_Ivanov.pdf","file_id":"9796","checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1","access_level":"open_access","date_updated":"2021-08-06T09:59:45Z","date_created":"2021-08-06T09:59:45Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"file_date_updated":"2021-08-06T09:59:45Z","oa_version":"Published Version","department":[{"_id":"UlWa"}],"date_updated":"2025-07-10T12:01:31Z","external_id":{"isi":["000607265100001"],"arxiv":["1912.08561"]}},{"publication_identifier":{"eissn":["2079-4991"]},"volume":11,"month":"01","scopus_import":"1","author":[{"first_name":"Patricia","last_name":"Aguilar-Merino","full_name":"Aguilar-Merino, Patricia"},{"full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez","first_name":"Gonzalo"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"last_name":"Álvarez-Prado","first_name":"Luis Manuel","full_name":"Álvarez-Prado, Luis Manuel"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"language":[{"iso":"eng"}],"citation":{"mla":"Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>, vol. 11, no. 1, 120, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>.","ieee":"P. Aguilar-Merino <i>et al.</i>, “Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal,” <i>Nanomaterials</i>, vol. 11, no. 1. MDPI, 2021.","chicago":"Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez, Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin, Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>.","ista":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120.","ama":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>","apa":"Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. MDPI. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>","short":"P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González, Nanomaterials 11 (2021)."},"article_processing_charge":"No","isi":1,"oa":1,"acknowledgement":"P.A.-M. acknowledges financial support through JAE Intro program from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge financial support through the Severo Ochoa Program from the Government of the Principality of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00).","day":"07","quality_controlled":"1","publication":"Nanomaterials","intvolume":"        11","abstract":[{"lang":"eng","text":"Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. "}],"has_accepted_license":"1","publication_status":"published","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","article_type":"original","type":"journal_article","publisher":"MDPI","ddc":["620"],"issue":"1","pmid":1,"year":"2021","status":"public","date_published":"2021-01-07T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2021-01-24T23:01:09Z","external_id":{"isi":["000610636600001"],"pmid":["33430225"]},"date_updated":"2026-04-02T13:57:24Z","department":[{"_id":"NanoFab"}],"file_date_updated":"2021-01-25T08:02:32Z","oa_version":"Published Version","_id":"9038","file":[{"content_type":"application/pdf","success":1,"date_created":"2021-01-25T08:02:32Z","relation":"main_file","creator":"dernst","file_id":"9042","file_size":2730267,"file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","checksum":"1edc13eeda83df5cd9fff9504727b1f5","date_updated":"2021-01-25T08:02:32Z","access_level":"open_access"}],"article_number":"120","doi":"10.3390/nano11010120","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)"}},{"year":"2021","ddc":["570"],"pmid":1,"issue":"1","article_type":"original","type":"journal_article","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-31T23:01:21Z","status":"public","date_published":"2021-01-14T00:00:00Z","department":[{"_id":"CaGu"}],"date_updated":"2025-07-10T12:01:33Z","external_id":{"isi":["000610190400007"],"pmid":["33444399"]},"doi":"10.1371/journal.ppat.1009172","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)"},"article_number":"e1009172","_id":"9046","file":[{"file_id":"9070","file_name":"2021_PlosPathogens_Roemhild.pdf","file_size":570066,"creator":"dernst","date_updated":"2021-02-03T12:13:03Z","access_level":"open_access","checksum":"d745d7f8fcbb9b95fea16a36f94dee31","success":1,"content_type":"application/pdf","date_created":"2021-02-03T12:13:03Z","relation":"main_file"}],"file_date_updated":"2021-02-03T12:13:03Z","oa_version":"Published Version","volume":17,"scopus_import":"1","month":"01","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","oa":1,"article_processing_charge":"No","citation":{"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>.","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.","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>.","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>","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>","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021)."},"isi":1,"author":[{"orcid":"0000-0001-9480-5261","full_name":"Römhild, Roderich","last_name":"Römhild","first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E"},{"full_name":"Andersson, Dan I.","last_name":"Andersson","first_name":"Dan I."}],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"14","has_accepted_license":"1","publication_status":"published","title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","publication":"PLoS Pathogens","intvolume":"        17"},{"publication_identifier":{"eissn":["1558-2248"],"issn":["1536-1276"]},"scopus_import":"1","month":"01","volume":20,"isi":1,"article_processing_charge":"No","citation":{"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>.","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27.","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.","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>.","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>","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>"},"page":"18-27","language":[{"iso":"eng"}],"author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"last_name":"Cioffi","first_name":"John M.","full_name":"Cioffi, John M."},{"full_name":"Goldsmith, Andrea","last_name":"Goldsmith","first_name":"Andrea"}],"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.","arxiv":1,"oa":1,"quality_controlled":"1","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"corr_author":"1","publication_status":"published","title":"Sublinear latency for simplified successive cancellation decoding of polar codes","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"}],"intvolume":"        20","publication":"IEEE Transactions on Wireless Communications","publisher":"IEEE","article_type":"original","type":"journal_article","year":"2021","issue":"1","date_published":"2021-01-01T00:00:00Z","status":"public","date_created":"2021-01-31T23:01:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","id":"8536","status":"public"}]},"date_updated":"2025-09-10T10:27:04Z","external_id":{"arxiv":["1909.04892"],"isi":["000607808800002"]},"department":[{"_id":"MaMo"}],"_id":"9047","oa_version":"Preprint","doi":"10.1109/TWC.2020.3022922"},{"date_published":"2021-01-29T00:00:00Z","status":"public","keyword":["General Physics and Astronomy"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2021-02-01T09:20:00Z","publisher":"American Physical Society","type":"journal_article","article_type":"original","year":"2021","issue":"4","ddc":["530"],"_id":"9048","file":[{"creator":"dernst","file_name":"2021_PhysicalRevLett_DeNicola.pdf","file_size":398075,"file_id":"9074","checksum":"d9acbc502390ed7a97e631d23ae19ecd","access_level":"open_access","date_updated":"2021-02-03T12:47:04Z","date_created":"2021-02-03T12:47:04Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"article_number":"040602","oa_version":"Published Version","file_date_updated":"2021-02-03T12:47:04Z","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)"},"doi":"10.1103/physrevlett.126.040602","date_updated":"2025-04-14T07:43:50Z","external_id":{"arxiv":["2008.04894"],"isi":["000613148200001"]},"department":[{"_id":"MaSe"}],"isi":1,"citation":{"short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","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>.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","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>","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.","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>."},"article_processing_charge":"Yes","language":[{"iso":"eng"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"De Nicola","full_name":"De Nicola, Stefano","orcid":"0000-0002-4842-6671"},{"last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"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).","arxiv":1,"oa":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"01","scopus_import":"1","volume":126,"title":"Entanglement view of dynamical quantum phase transitions","publication_status":"published","has_accepted_license":"1","intvolume":"       126","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"}],"publication":"Physical Review Letters","ec_funded":1,"quality_controlled":"1","day":"29"},{"supervisor":[{"last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"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)"},"doi":"10.15479/AT:ISTA:9056","oa_version":"Published Version","place":"Klosterneuburg","file_date_updated":"2021-02-03T10:37:28Z","_id":"9056","file":[{"relation":"source_file","content_type":"application/zip","date_created":"2021-02-02T14:09:25Z","checksum":"bcf27986147cab0533b6abadd74e7629","date_updated":"2021-02-03T10:37:28Z","access_level":"closed","creator":"patrickd","file_id":"9063","file_name":"thesis_source.zip","file_size":13446994},{"creator":"patrickd","file_name":"thesis_pdfA2b.pdf","file_size":5210329,"file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","access_level":"open_access","date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"187"},{"status":"public","relation":"part_of_dissertation","id":"8703"}]},"date_updated":"2026-04-08T07:01:30Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2021-02-02T14:11:06Z","date_published":"2021-02-01T00:00:00Z","status":"public","ddc":["006","514","516"],"year":"2021","publisher":"Institute of Science and Technology Austria","type":"dissertation","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"OA_place":"publisher","title":"Multi-cover persistence and Delaunay mosaics","publication_status":"published","corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","day":"01","oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F"}],"citation":{"ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","mla":"Osang, Georg F. <i>Multi-Cover Persistence and Delaunay Mosaics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","apa":"Osang, G. F. (2021). <i>Multi-cover persistence and Delaunay mosaics</i>. Institute of Science and Technology Austria, Klosterneuburg. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","page":"134","month":"02","publication_identifier":{"issn":["2663-337X"]}},{"ec_funded":1,"title":"The logic of developing neocortical circuits in health and disease","publication_status":"published","has_accepted_license":"1","intvolume":"        41","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}],"publication":"The Journal of Neuroscience","quality_controlled":"1","day":"03","acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","oa":1,"article_processing_charge":"No","isi":1,"citation":{"ieee":"I. L. Hanganu-Opatz <i>et al.</i>, “The logic of developing neocortical circuits in health and disease,” <i>The Journal of Neuroscience</i>, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>.","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2021. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>.","ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822.","ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. 2021;41(5):813-822. doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., &#38; Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>","short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822."},"page":"813-822","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Ileana L.","last_name":"Hanganu-Opatz","full_name":"Hanganu-Opatz, Ileana L."},{"full_name":"Butt, Simon J. B.","first_name":"Simon J. B.","last_name":"Butt"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"full_name":"De Marco García, Natalia V.","first_name":"Natalia V.","last_name":"De Marco García"},{"full_name":"Cardin, Jessica A.","last_name":"Cardin","first_name":"Jessica A."},{"last_name":"Voytek","first_name":"Bradley","full_name":"Voytek, Bradley"},{"first_name":"Alysson R.","last_name":"Muotri","full_name":"Muotri, Alysson R."}],"scopus_import":"1","month":"02","volume":41,"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"doi":"10.1523/jneurosci.1655-20.2020","file":[{"file_id":"11414","file_name":"2021_JourNeuroscience_Hanganu.pdf","file_size":1031150,"creator":"dernst","date_updated":"2022-05-27T06:59:55Z","access_level":"open_access","checksum":"578fd7ed1a0aef74bce61bea2d987b33","content_type":"application/pdf","success":1,"date_created":"2022-05-27T06:59:55Z","relation":"main_file"}],"_id":"9073","oa_version":"Published Version","file_date_updated":"2022-05-27T06:59:55Z","department":[{"_id":"SiHi"}],"date_updated":"2025-04-15T08:23:06Z","external_id":{"pmid":["33431633"],"isi":["000616763400002"]},"keyword":["General Neuroscience"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2021-02-03T12:23:51Z","date_published":"2021-02-03T00:00:00Z","status":"public","year":"2021","pmid":1,"issue":"5","ddc":["570"],"publisher":"Society for Neuroscience","type":"journal_article","article_type":"original"},{"oa":1,"arxiv":1,"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.)","author":[{"full_name":"Marchukov, Oleksandr","last_name":"Marchukov","first_name":"Oleksandr"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev"}],"language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"citation":{"short":"O. Marchukov, A. Volosniev, SciPost Physics 10 (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>","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>","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>.","ista":"Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025.","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>.","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."},"article_processing_charge":"No","isi":1,"volume":10,"scopus_import":"1","month":"02","publication_identifier":{"issn":["2542-4653"]},"ec_funded":1,"publication":"SciPost Physics","abstract":[{"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.","lang":"eng"}],"intvolume":"        10","has_accepted_license":"1","publication_status":"published","title":"Shape of a sound wave in a weakly-perturbed Bose gas","day":"03","quality_controlled":"1","date_created":"2021-02-04T12:39:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2021-02-03T00:00:00Z","ddc":["530"],"issue":"2","year":"2021","type":"journal_article","article_type":"original","publisher":"SciPost Foundation","doi":"10.21468/scipostphys.10.2.025","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)"},"file_date_updated":"2021-02-09T07:06:22Z","oa_version":"Published Version","article_number":"025","_id":"9093","file":[{"creator":"dernst","file_id":"9105","file_name":"2021_SciPostPhysics_Marchukov.pdf","file_size":666512,"checksum":"9fd614b7ab49999e7267874df2582f7e","date_updated":"2021-02-09T07:06:22Z","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2021-02-09T07:06:22Z","relation":"main_file"}],"department":[{"_id":"MiLe"}],"external_id":{"isi":["000646783100027"],"arxiv":["2004.08075"]},"date_updated":"2025-04-14T07:43:51Z"}]