[{"publisher":"Springer Nature","oa":1,"intvolume":"        19","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"ec_funded":1,"publication":"Nature Physics","oa_version":"Published Version","page":"1630-1635","doi":"10.1038/s41567-023-02161-w","type":"journal_article","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"keyword":["General Physics and Astronomy"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","month":"11","author":[{"full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham"},{"full_name":"Senior, Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295","first_name":"Jorden L"},{"first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime"},{"last_name":"Puglia","full_name":"Puglia, Denise","first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"file":[{"checksum":"1fc86d71bfbf836e221c1e925343adc5","creator":"dernst","date_created":"2024-01-29T11:25:38Z","relation":"main_file","date_updated":"2024-01-29T11:25:38Z","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","success":1,"file_id":"14899","content_type":"application/pdf","access_level":"open_access","file_size":1977706}],"abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"ddc":["530"],"date_published":"2023-11-01T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","date_created":"2023-08-11T07:41:17Z","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"citation":{"ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>"},"date_updated":"2024-01-29T11:27:49Z","_id":"14032","project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"name":"Protected states of quantum matter","_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344"}],"file_date_updated":"2024-01-29T11:25:38Z","year":"2023","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","volume":19,"external_id":{"isi":["001054563800006"]},"title":"Superconductivity from a melted insulator in Josephson junction arrays","day":"01"},{"oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"status":"public","relation":"research_data","id":"12933"},{"id":"6831","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"14077","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","degree_awarded":"PhD","page":"230","doi":"10.15479/at:ista:14058","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"has_accepted_license":"1","article_processing_charge":"No","month":"08","author":[{"last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"4e44e169f2724ee8c9324cd60bcc2b71","creator":"gpuixeus","date_created":"2023-08-16T18:15:17Z","relation":"source_file","file_name":"Thesis_latex_forpdfa.zip","date_updated":"2023-08-17T06:55:24Z","file_id":"14075","content_type":"application/zip","access_level":"closed","file_size":10891454},{"access_level":"open_access","file_size":19856686,"file_id":"14079","content_type":"application/pdf","success":1,"file_name":"PhDThesis_PuixeuG.pdf","date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-18T10:47:55Z","relation":"main_file","creator":"gpuixeus","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8"}],"ddc":["576"],"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"date_published":"2023-08-15T00:00:00Z","status":"public","date_created":"2023-08-15T10:20:40Z","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"citation":{"ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>"},"date_updated":"2023-12-13T12:15:36Z","_id":"14058","file_date_updated":"2023-08-18T10:47:55Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"year":"2023","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","day":"15"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Oxford University Press","oa":1,"isi":1,"intvolume":"        13","doi":"10.1093/g3journal/jkad121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2160-1836"]},"type":"journal_article","related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"status":"public","id":"14058","relation":"dissertation_contains"}]},"oa_version":"Published Version","publication":"G3: Genes, Genomes, Genetics","language":[{"iso":"eng"}],"ec_funded":1,"scopus_import":"1","article_processing_charge":"Yes","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"month":"08","has_accepted_license":"1","article_type":"original","status":"public","quality_controlled":"1","file":[{"file_id":"14498","content_type":"application/pdf","access_level":"open_access","file_size":845642,"date_updated":"2023-11-07T09:00:19Z","file_name":"2023_G3_Puixeu.pdf","success":1,"date_created":"2023-11-07T09:00:19Z","relation":"main_file","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","creator":"dernst"}],"date_published":"2023-08-01T00:00:00Z","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"ddc":["570"],"publication_status":"published","date_created":"2023-08-18T06:52:14Z","_id":"14077","date_updated":"2023-12-13T12:15:37Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"file_date_updated":"2023-11-07T09:00:19Z","citation":{"ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>."},"department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"issue":"8","year":"2023","external_id":{"isi":["001002997200001"]},"day":"01","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","volume":13,"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385)."},{"day":"01","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","external_id":{"isi":["001035766100001"],"arxiv":["2303.07063"]},"volume":39,"acknowledgement":"J. Rø and L. A. acknowledge support from the Research Council of Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab). A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142 and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.","year":"2023","file_date_updated":"2024-01-30T12:48:24Z","_id":"14087","date_updated":"2024-01-30T12:49:24Z","citation":{"ieee":"J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” <i>Soft Matter</i>, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.","chicago":"Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>.","ama":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. 2023;39:7513-7527. doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>","mla":"Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>.","short":"J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527.","ista":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 39, 7513–7527.","apa":"Rønning, J., Renaud, J. B., Doostmohammadi, A., &#38; Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>"},"department":[{"_id":"GradSch"}],"publication_status":"published","date_created":"2023-08-20T22:01:15Z","quality_controlled":"1","article_type":"original","status":"public","date_published":"2023-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter."}],"ddc":["540"],"file":[{"checksum":"b936747170d0b708172b518078c4081a","creator":"dernst","date_created":"2024-01-30T12:48:24Z","relation":"main_file","file_name":"2023_SoftMatter_Ronning.pdf","date_updated":"2024-01-30T12:48:24Z","success":1,"file_id":"14908","content_type":"application/pdf","access_level":"open_access","file_size":7660662}],"author":[{"full_name":"Rønning, Jonas","last_name":"Rønning","first_name":"Jonas"},{"first_name":"Julian B","id":"7af6767d-14eb-11ed-b536-a32449ae867c","last_name":"Renaud","full_name":"Renaud, Julian B"},{"first_name":"Amin","last_name":"Doostmohammadi","full_name":"Doostmohammadi, Amin"},{"last_name":"Angheluta","full_name":"Angheluta, Luiza","first_name":"Luiza"}],"month":"09","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","has_accepted_license":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","page":"7513-7527","doi":"10.1039/d3sm00316g","oa_version":"Published Version","publication":"Soft Matter","arxiv":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"intvolume":"        39","oa":1,"publisher":"Royal Society of Chemistry"},{"has_accepted_license":"1","article_processing_charge":"No","month":"08","author":[{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson"}],"file":[{"checksum":"453caf851d75c3478c10ed09bd242a91","creator":"cchlebak","relation":"source_file","date_created":"2023-08-24T13:02:49Z","file_name":"documents-export-2023-08-24.zip","date_updated":"2024-02-26T23:30:03Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"14227","file_size":15501411,"access_level":"closed"},{"relation":"main_file","date_created":"2023-08-24T13:03:42Z","embargo":"2024-02-25","checksum":"7349d29963d6695e555e171748648d9a","creator":"cchlebak","content_type":"application/pdf","file_id":"14228","file_size":6854783,"access_level":"open_access","date_updated":"2024-02-26T23:30:03Z","file_name":"thesis_pdf_a.pdf"}],"abstract":[{"lang":"eng","text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes."}],"ddc":["500"],"date_published":"2023-08-24T00:00:00Z","status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"43","degree_awarded":"MS","doi":"10.15479/at:ista:14226","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2791-4585"]},"year":"2023","supervisor":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"title":"Generalizing medial axes with homology switches","day":"24","date_created":"2023-08-24T13:01:18Z","alternative_title":["ISTA Master's Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"citation":{"ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","apa":"Stephenson, E. R. (2023). <i>Generalizing medial axes with homology switches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","mla":"Stephenson, Elizabeth R. <i>Generalizing Medial Axes with Homology Switches</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023."},"date_updated":"2024-02-26T23:30:04Z","_id":"14226","file_date_updated":"2024-02-26T23:30:03Z"},{"status":"public","quality_controlled":"1","file":[{"success":1,"date_updated":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","file_size":421408,"access_level":"open_access","content_type":"application/pdf","file_id":"14275","creator":"dernst","checksum":"c346016393123a0a2338ad4d976f61bc","relation":"main_file","date_created":"2023-09-06T08:16:25Z"}],"ddc":["000"],"abstract":[{"lang":"eng","text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness."}],"date_published":"2023-07-17T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","month":"07","author":[{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"first_name":"Maria","last_name":"Sokolova","full_name":"Sokolova, Maria"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"has_accepted_license":"1","page":"156-169","doi":"10.1007/978-3-031-37706-8_8","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"related_material":{"record":[{"relation":"research_data","id":"14995","status":"public"}]},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"35th International Conference on Computer Aided Verification ","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Springer Nature","oa":1,"intvolume":"     13964","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","day":"17","volume":13964,"year":"2023","date_updated":"2024-02-27T07:46:52Z","_id":"14260","file_date_updated":"2023-09-06T08:16:25Z","conference":{"start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification","end_date":"2023-07-22"},"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"citation":{"chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169."},"alternative_title":["LNCS"],"publication_status":"published","date_created":"2023-09-03T22:01:16Z"},{"oa_version":"Published Version","publication":"Journal of Physical Chemistry Letters","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1948-7185"]},"type":"journal_article","page":"7395-7403","doi":"10.1021/acs.jpclett.3c01707","isi":1,"intvolume":"        14","oa":1,"publisher":"American Chemical Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2023-08-11T00:00:00Z","abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"ddc":["530","540"],"file":[{"creator":"dernst","checksum":"637454e2b3a357498d8d622d241c4bf6","relation":"main_file","date_created":"2023-09-06T07:32:39Z","success":1,"date_updated":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","file_size":4986859,"access_level":"open_access","content_type":"application/pdf","file_id":"14272"}],"quality_controlled":"1","article_type":"original","status":"public","has_accepted_license":"1","author":[{"first_name":"Jakob","full_name":"Gamper, Jakob","last_name":"Gamper"},{"first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian"},{"first_name":"Alexander K.H.","full_name":"Weiss, Alexander K.H.","last_name":"Weiss"},{"last_name":"Hofer","full_name":"Hofer, Thomas S.","first_name":"Thomas S."}],"month":"08","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>","ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>"},"department":[{"_id":"GradSch"}],"file_date_updated":"2023-09-06T07:32:39Z","_id":"14261","date_updated":"2023-09-06T11:04:31Z","pmid":1,"date_created":"2023-09-03T22:01:16Z","publication_status":"published","volume":14,"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","day":"11","title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"issue":"33","year":"2023"},{"article_processing_charge":"No","month":"09","author":[{"first_name":"Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp"}],"has_accepted_license":"1","status":"public","file":[{"date_created":"2023-10-04T10:11:53Z","relation":"source_file","creator":"pradler","checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed","file_size":114932847,"file_id":"14390","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_updated":"2023-10-04T10:28:35Z"},{"file_id":"14391","content_type":"application/pdf","access_level":"closed","file_size":37838778,"embargo_to":"open_access","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_updated":"2023-10-04T10:28:35Z","date_created":"2023-10-04T10:11:21Z","relation":"main_file","embargo":"2024-10-04","checksum":"3253e099b7126469d941fd9419d68b4f","creator":"pradler"}],"ddc":["572"],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"date_published":"2023-09-25T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14280","page":"156","degree_awarded":"PhD","type":"dissertation","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"id":"11373","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7387"},{"status":"public","id":"10934","relation":"research_data"}]},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","year":"2023","supervisor":[{"full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","day":"25","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-09-06T10:58:25Z","date_updated":"2024-02-21T12:35:18Z","_id":"14280","file_date_updated":"2023-10-04T10:28:35Z","project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"},{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"citation":{"short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023."}},{"has_accepted_license":"1","author":[{"first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna"}],"month":"09","article_processing_charge":"No","date_published":"2023-09-13T00:00:00Z","ddc":["570"],"abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"file":[{"access_level":"closed","file_size":10147911,"file_id":"14324","content_type":"application/pdf","embargo_to":"open_access","date_updated":"2023-09-13T10:08:25Z","file_name":"PhDThesis_KK_final_pdfA.pdf","embargo":"2025-03-13","date_created":"2023-09-13T09:52:52Z","relation":"main_file","creator":"kkuzmicz","checksum":"bd83596869c814b24aeff7077d031c0e"},{"creator":"kkuzmicz","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","relation":"source_file","date_created":"2023-09-13T09:53:29Z","date_updated":"2023-09-13T09:53:29Z","file_name":"thesis_KK_final_corrections_092023.docx","file_size":103980668,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14325"}],"status":"public","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","doi":"10.15479/at:ista:14323","page":"151","degree_awarded":"PhD","supervisor":[{"first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna"}],"year":"2023","day":"13","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2023-09-13T10:07:18Z","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"file_date_updated":"2023-09-13T10:08:25Z","_id":"14323","date_updated":"2024-03-07T15:02:59Z"},{"article_number":"e74","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","month":"08","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László"},{"orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","last_name":"Henheik"},{"last_name":"Kolupaiev","full_name":"Kolupaiev, Oleksii","first_name":"Oleksii","id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61"}],"file":[{"checksum":"eb747420e6a88a7796fa934151957676","creator":"dernst","date_created":"2023-09-20T11:09:35Z","relation":"main_file","file_name":"2023_ForumMathematics_Cipolloni.pdf","date_updated":"2023-09-20T11:09:35Z","success":1,"file_id":"14352","content_type":"application/pdf","access_level":"open_access","file_size":852652}],"abstract":[{"lang":"eng","text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation."}],"ddc":["510"],"date_published":"2023-08-23T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","oa":1,"publisher":"Cambridge University Press","intvolume":"        11","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"oa_version":"Published Version","publication":"Forum of Mathematics, Sigma","doi":"10.1017/fms.2023.70","type":"journal_article","publication_identifier":{"eissn":["2050-5094"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","volume":11,"external_id":{"arxiv":["2301.05181"],"isi":["001051980200001"]},"title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","day":"23","date_created":"2023-09-17T22:01:09Z","publication_status":"published","department":[{"_id":"LaEr"},{"_id":"GradSch"}],"citation":{"ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” <i>Forum of Mathematics, Sigma</i>, vol. 11. Cambridge University Press, 2023.","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. 2023;11. doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>","mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>, vol. 11, e74, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>.","chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>.","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., &#38; Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>","ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74.","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023)."},"date_updated":"2023-12-13T12:24:23Z","_id":"14343","file_date_updated":"2023-09-20T11:09:35Z","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}]},{"title":"Boundary superconductivity in BCS theory","day":"30","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"year":"2023","file_date_updated":"2023-10-06T11:38:01Z","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"date_updated":"2023-10-27T10:37:30Z","_id":"14374","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>","mla":"Roos, Barbara. <i>Boundary Superconductivity in BCS Theory</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","apa":"Roos, B. (2023). <i>Boundary superconductivity in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>"},"publication_status":"published","alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_created":"2023-09-28T14:23:04Z","status":"public","abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap  in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}],"ddc":["515","539"],"date_published":"2023-09-30T00:00:00Z","file":[{"date_created":"2023-10-06T11:35:56Z","relation":"main_file","checksum":"ef039ffc3de2cb8dee5b14110938e9b6","creator":"broos","file_id":"14398","content_type":"application/pdf","access_level":"open_access","file_size":2365702,"file_name":"phd-thesis-draft_pdfa_acrobat.pdf","date_updated":"2023-10-06T11:35:56Z"},{"date_updated":"2023-10-06T11:38:01Z","file_name":"Version5.zip","content_type":"application/x-zip-compressed","file_id":"14399","file_size":4691734,"access_level":"closed","checksum":"81dcac33daeefaf0111db52f41bb1fd0","creator":"broos","relation":"source_file","date_created":"2023-10-06T11:38:01Z"}],"month":"09","author":[{"full_name":"Roos, Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara"}],"article_processing_charge":"No","has_accepted_license":"1","type":"dissertation","publication_identifier":{"issn":["2663 - 337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","page":"206","doi":"10.15479/at:ista:14374","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13207"},{"relation":"part_of_dissertation","id":"10850","status":"public"}]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Institute of Science and Technology Austria","oa":1},{"volume":56,"acknowledgement":"J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331.","day":"11","title":"Creation rate of Dirac particles at a point source","external_id":{"arxiv":["2211.16606"],"isi":["001080908000001"]},"issue":"44","year":"2023","citation":{"short":"S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).","apa":"Henheik, S. J., &#38; Tumulka, R. (2023). Creation rate of Dirac particles at a point source. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1751-8121/acfe62\">https://doi.org/10.1088/1751-8121/acfe62</a>","ista":"Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.","chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing, 2023. <a href=\"https://doi.org/10.1088/1751-8121/acfe62\">https://doi.org/10.1088/1751-8121/acfe62</a>.","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:<a href=\"https://doi.org/10.1088/1751-8121/acfe62\">10.1088/1751-8121/acfe62</a>.","ama":"Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2023;56(44). doi:<a href=\"https://doi.org/10.1088/1751-8121/acfe62\">10.1088/1751-8121/acfe62</a>","ieee":"S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 56, no. 44. IOP Publishing, 2023."},"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"file_date_updated":"2023-10-16T07:07:24Z","_id":"14421","date_updated":"2023-12-13T13:01:25Z","date_created":"2023-10-12T12:42:53Z","publication_status":"published","date_published":"2023-10-11T00:00:00Z","ddc":["510"],"abstract":[{"lang":"eng","text":"Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\\in\\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission)."}],"file":[{"file_id":"14429","content_type":"application/pdf","access_level":"open_access","file_size":721399,"date_updated":"2023-10-16T07:07:24Z","file_name":"2023_JourPhysics_Henheik.pdf","success":1,"date_created":"2023-10-16T07:07:24Z","relation":"main_file","checksum":"5b68de147dd4c608b71a6e0e844d2ce9","creator":"dernst"}],"quality_controlled":"1","article_type":"original","status":"public","has_accepted_license":"1","article_number":"445201","author":[{"first_name":"Sven Joscha","orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","last_name":"Henheik","full_name":"Henheik, Sven Joscha"},{"full_name":"Tumulka, Roderich","last_name":"Tumulka","first_name":"Roderich"}],"month":"10","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","publication":"Journal of Physics A: Mathematical and Theoretical","arxiv":1,"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1751-8121"],"issn":["1751-8113"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1088/1751-8121/acfe62","isi":1,"intvolume":"        56","publisher":"IOP Publishing","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"_id":"14422","date_updated":"2023-10-18T09:20:56Z","file_date_updated":"2023-10-18T07:56:08Z","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"citation":{"ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>"},"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-10-12T14:13:25Z","day":"12","title":"Synapseek: Meta-learning synaptic plasticity rules","year":"2023","supervisor":[{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P","last_name":"Vogels"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:14422","page":"148","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","related_material":{"record":[{"id":"9633","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Institute of Science and Technology Austria","status":"public","file":[{"embargo":"2024-10-12","date_created":"2023-10-12T14:53:50Z","relation":"main_file","creator":"cchlebak","checksum":"7f636555eae7803323df287672fd13ed","access_level":"closed","file_size":30599717,"file_id":"14424","content_type":"application/pdf","embargo_to":"open_access","date_updated":"2023-10-12T14:54:52Z","file_name":"Confavreux_Thesis_2A.pdf"},{"access_level":"closed","file_size":68406739,"file_id":"14440","content_type":"application/x-zip-compressed","file_name":"Confavreux Thesis.zip","date_updated":"2023-10-18T07:56:08Z","date_created":"2023-10-18T07:38:34Z","relation":"source_file","creator":"cchlebak","checksum":"725e85946db92290a4583a0de9779e1b"}],"date_published":"2023-10-12T00:00:00Z","ddc":["610"],"abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"article_processing_charge":"No","author":[{"last_name":"Confavreux","full_name":"Confavreux, Basile J","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E"}],"month":"10","has_accepted_license":"1"},{"intvolume":"        14","isi":1,"oa":1,"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","arxiv":1,"publication":"Nature Communications","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/TiO2-water"}]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-41865-8","has_accepted_license":"1","article_number":"6131","month":"10","author":[{"full_name":"Zeng, Zezhu","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu"},{"first_name":"Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","orcid":"0009-0000-1457-795X","last_name":"Wodaczek","full_name":"Wodaczek, Felix"},{"last_name":"Liu","full_name":"Liu, Keyang","first_name":"Keyang"},{"first_name":"Frederick","last_name":"Stein","full_name":"Stein, Frederick"},{"first_name":"Jürg","last_name":"Hutter","full_name":"Hutter, Jürg"},{"first_name":"Ji","full_name":"Chen, Ji","last_name":"Chen"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng"}],"scopus_import":"1","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces."}],"ddc":["540","000"],"date_published":"2023-10-02T00:00:00Z","file":[{"date_created":"2023-10-16T07:34:49Z","relation":"main_file","creator":"dernst","checksum":"7d1dffd36b672ec679f08f70ce79da87","access_level":"open_access","file_size":3194116,"file_id":"14432","content_type":"application/pdf","success":1,"date_updated":"2023-10-16T07:34:49Z","file_name":"2023_NatureComm_Zeng.pdf"}],"quality_controlled":"1","status":"public","article_type":"original","pmid":1,"date_created":"2023-10-15T22:01:10Z","publication_status":"published","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"citation":{"apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., &#38; Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>","ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131.","short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023).","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>, vol. 14, 6131, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>.","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>.","ieee":"Z. Zeng <i>et al.</i>, “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"file_date_updated":"2023-10-16T07:34:49Z","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"date_updated":"2023-12-13T13:02:07Z","_id":"14425","year":"2023","acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","volume":14,"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","day":"02","external_id":{"pmid":["37783698"],"arxiv":["2303.07433"],"isi":["001084354900008"]}},{"month":"11","author":[{"orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","full_name":"Marensi, Elena","last_name":"Marensi"},{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan","full_name":"Yalniz, Gökhan","last_name":"Yalniz"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_number":"A21","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"text":"The first long-lived turbulent structures observable in planar shear flows take the form of localized stripes, inclined with respect to the mean flow direction. The dynamics of these stripes is central to transition, and recent studies proposed an analogy to directed percolation where the stripes’ proliferation is ultimately responsible for the turbulence becoming sustained. In the present study we focus on the internal stripe dynamics as well as on the eventual stripe expansion, and we compare the underlying mechanisms in pressure- and shear-driven planar flows, respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities of the overall laminar–turbulence patterns, the stripe proliferation processes in the two cases are fundamentally different. Starting from the growth and sustenance of individual stripes, we find that in plane-Couette flow new streaks are created stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation is deterministic and occurs locally at the downstream tip. Because of the up/downstream symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and two strong laminar turbulent interfaces. These differences in symmetry as well as in internal growth give rise to two fundamentally different stripe splitting mechanisms. In plane-Poiseuille flow splitting is connected to the elongational growth of the original stripe, and it results from a break-off/shedding of the stripe's tail. In plane-Couette flow splitting follows from a broadening of the original stripe and a division along the stripe into two slimmer stripes.","lang":"eng"}],"ddc":["530"],"date_published":"2023-11-10T00:00:00Z","file":[{"checksum":"17c64c1fb0d5f73252364bf98b0b9e1a","creator":"dernst","relation":"main_file","date_created":"2024-02-15T09:05:21Z","file_name":"2023_JourFluidMechanics_Marensi.pdf","date_updated":"2024-02-15T09:05:21Z","success":1,"content_type":"application/pdf","file_id":"14996","file_size":2804641,"access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"       974","isi":1,"oa":1,"publisher":"Cambridge University Press","type":"journal_article","keyword":["turbulence","transition to turbulence","patterns"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"doi":"10.1017/jfm.2023.780","language":[{"iso":"eng"}],"arxiv":1,"publication":"Journal of Fluid Mechanics","oa_version":"Published Version","year":"2023","title":"Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows","day":"10","external_id":{"isi":["001088363700001"],"arxiv":["2212.12406"]},"acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH).","volume":974,"publication_status":"published","date_created":"2023-10-30T09:32:28Z","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"}],"file_date_updated":"2024-02-15T09:05:21Z","date_updated":"2024-02-15T09:06:23Z","_id":"14466","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"citation":{"ieee":"E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows,” <i>Journal of Fluid Mechanics</i>, vol. 974. Cambridge University Press, 2023.","chicago":"Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/jfm.2023.780\">https://doi.org/10.1017/jfm.2023.780</a>.","mla":"Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” <i>Journal of Fluid Mechanics</i>, vol. 974, A21, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/jfm.2023.780\">10.1017/jfm.2023.780</a>.","ama":"Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. <i>Journal of Fluid Mechanics</i>. 2023;974. doi:<a href=\"https://doi.org/10.1017/jfm.2023.780\">10.1017/jfm.2023.780</a>","short":"E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023).","apa":"Marensi, E., Yalniz, G., &#38; Hof, B. (2023). Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2023.780\">https://doi.org/10.1017/jfm.2023.780</a>","ista":"Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. 974, A21."}},{"file_date_updated":"2023-11-06T11:45:21Z","conference":{"name":"DISC: Symposium on Distributed Computing","end_date":"2023-10-13","start_date":"2023-10-09","location":"L'Aquila, Italy"},"date_updated":"2023-11-07T07:48:01Z","_id":"14485","department":[{"_id":"GradSch"}],"citation":{"ieee":"V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement: BatchBoost: Universal batching for concurrent data structures,” in <i>37th International Symposium on Distributed Computing</i>, L’Aquila, Italy, 2023, vol. 281.","ista":"Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost: Universal batching for concurrent data structures. 37th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 281, 35.","apa":"Aksenov, V., Anoprenko, M., Fedorov, A., &#38; Spear, M. (2023). Brief announcement: BatchBoost: Universal batching for concurrent data structures. In <i>37th International Symposium on Distributed Computing</i> (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2023.35\">https://doi.org/10.4230/LIPIcs.DISC.2023.35</a>","short":"V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost: Universal batching for concurrent data structures. In: <i>37th International Symposium on Distributed Computing</i>. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2023.35\">10.4230/LIPIcs.DISC.2023.35</a>","mla":"Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” <i>37th International Symposium on Distributed Computing</i>, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2023.35\">10.4230/LIPIcs.DISC.2023.35</a>.","chicago":"Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” In <i>37th International Symposium on Distributed Computing</i>, Vol. 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2023.35\">https://doi.org/10.4230/LIPIcs.DISC.2023.35</a>."},"publication_status":"published","alternative_title":["LIPIcs"],"date_created":"2023-11-05T23:00:53Z","title":"Brief announcement: BatchBoost: Universal batching for concurrent data structures","day":"01","volume":281,"year":"2023","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773010"]},"doi":"10.4230/LIPIcs.DISC.2023.35","language":[{"iso":"eng"}],"publication":"37th International Symposium on Distributed Computing","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"       281","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"quality_controlled":"1","status":"public","ddc":["000"],"abstract":[{"text":"Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching.\r\nIn this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct \"data\" and \"index\" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is \"close\" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.","lang":"eng"}],"date_published":"2023-10-01T00:00:00Z","file":[{"file_size":646665,"access_level":"open_access","content_type":"application/pdf","file_id":"14492","success":1,"date_updated":"2023-11-06T11:45:21Z","file_name":"2023_LIPIcs_Aksenov.pdf","relation":"main_file","date_created":"2023-11-06T11:45:21Z","creator":"dernst","checksum":"d9f8d2915cccdf2df5905b7cd1b4a560"}],"month":"10","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"first_name":"Michael","full_name":"Anoprenko, Michael","last_name":"Anoprenko"},{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"first_name":"Michael","full_name":"Spear, Michael","last_name":"Spear"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","article_number":"35"},{"date_created":"2023-11-10T08:10:43Z","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"citation":{"ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>","mla":"Yeo, Michelle X. <i>Advances in Efficiency and Privacy in Payment Channel Network Analysis</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>.","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>.","apa":"Yeo, M. X. (2023). <i>Advances in efficiency and privacy in payment channel network analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023."},"date_updated":"2025-07-14T09:09:52Z","_id":"14506","file_date_updated":"2023-11-23T10:30:08Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"year":"2023","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"title":"Advances in efficiency and privacy in payment channel network analysis","day":"10","publisher":"Institute of Science and Technology Austria","oa":1,"related_material":{"record":[{"id":"9969","relation":"part_of_dissertation","status":"public"},{"id":"14490","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13238"}]},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","page":"162","degree_awarded":"PhD","doi":"10.15479/14506","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"]},"has_accepted_license":"1","article_processing_charge":"No","month":"11","author":[{"last_name":"Yeo","full_name":"Yeo, Michelle X","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0001-3676-4809"}],"file":[{"date_created":"2023-11-23T10:29:55Z","relation":"source_file","checksum":"521c72818d720a52b377207b2ee87b6a","creator":"cchlebak","file_id":"14598","content_type":"application/x-zip-compressed","access_level":"closed","file_size":3037720,"file_name":"thesis_yeo.zip","date_updated":"2023-11-23T10:29:55Z"},{"content_type":"application/pdf","file_id":"14599","file_size":2717256,"access_level":"open_access","date_updated":"2023-11-23T10:30:08Z","file_name":"thesis_yeo.pdf","success":1,"relation":"main_file","date_created":"2023-11-23T10:30:08Z","checksum":"0ed5d16899687aecf13d843c9878c9f2","creator":"cchlebak"}],"abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios."}],"ddc":["000"],"date_published":"2023-11-10T00:00:00Z","status":"public"},{"title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","day":"10","year":"2023","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023."},"date_updated":"2024-03-25T23:30:25Z","_id":"14510","file_date_updated":"2023-11-23T13:10:55Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"date_created":"2023-11-10T09:10:06Z","alternative_title":["ISTA Thesis"],"publication_status":"published","file":[{"access_level":"closed","file_size":20824903,"file_id":"14567","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","relation":"source_file","creator":"ngnyliuk","checksum":"3d5e680bfc61f98e308c434f45cc9bd6"},{"relation":"main_file","date_created":"2023-11-20T09:23:11Z","embargo":"2024-11-23","checksum":"bfc96d47fc4e7e857dd71656097214a4","creator":"ngnyliuk","content_type":"application/pdf","file_id":"14568","file_size":24871844,"access_level":"closed","date_updated":"2023-11-23T13:10:55Z","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access"}],"ddc":["570"],"date_published":"2023-11-10T00:00:00Z","status":"public","has_accepted_license":"1","article_processing_charge":"No","month":"11","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia"}],"related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9887"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.15479/at:ista:14510","degree_awarded":"PhD","page":"180","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"year":"2023","day":"16","title":"Synchronization in collectively moving active matter","publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-11-15T09:59:03Z","file_date_updated":"2023-11-15T09:52:54Z","_id":"14530","date_updated":"2023-11-30T10:55:13Z","citation":{"ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>"},"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"author":[{"last_name":"Riedl","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"}],"month":"11","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2023-11-16T00:00:00Z","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  "}],"ddc":["530","570"],"file":[{"file_size":36743942,"access_level":"open_access","content_type":"application/pdf","file_id":"14536","success":1,"date_updated":"2023-11-15T09:52:54Z","file_name":"Thesis_Riedl_2023_corr.pdf","relation":"main_file","date_created":"2023-11-15T09:52:54Z","creator":"mriedl","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a"}],"oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"]},"keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"type":"dissertation","page":"260","doi":"10.15479/14530","degree_awarded":"PhD","oa_version":"Updated Version","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"10703","relation":"part_of_dissertation","status":"public"},{"id":"10791","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7932","status":"public"},{"status":"public","id":"461","relation":"part_of_dissertation"},{"id":"12726","relation":"old_edition","status":"public"}]}},{"citation":{"ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>."},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"file_date_updated":"2023-11-15T13:44:24Z","_id":"14539","date_updated":"2025-07-14T09:10:10Z","date_created":"2023-11-15T13:39:10Z","publication_status":"published","alternative_title":["ISTA Thesis"],"day":"15","title":"Automated verification and control of infinite state stochastic systems","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"year":"2023","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1194","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12000","status":"public"},{"relation":"part_of_dissertation","id":"12511","status":"public"},{"status":"public","id":"14600","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14601","status":"public"},{"relation":"part_of_dissertation","id":"9644","status":"public"},{"status":"public","id":"10414","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"type":"dissertation","degree_awarded":"PhD","doi":"10.15479/14539","page":"256","oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"date_published":"2023-11-15T00:00:00Z","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"ddc":["000"],"file":[{"file_name":"main.pdf","date_updated":"2023-11-15T13:43:28Z","success":1,"file_id":"14540","content_type":"application/pdf","access_level":"open_access","file_size":2116426,"checksum":"f23e002b0059ca78e1fbb864da52dd7e","creator":"cchlebak","date_created":"2023-11-15T13:43:28Z","relation":"main_file"},{"date_updated":"2023-11-15T13:44:24Z","file_name":"thesis_source.zip","access_level":"closed","file_size":35884057,"file_id":"14541","content_type":"application/x-zip-compressed","creator":"cchlebak","checksum":"80ca37618a3c7b59866875f8be9b15ed","date_created":"2023-11-15T13:44:24Z","relation":"source_file"}],"status":"public","author":[{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"month":"11","article_processing_charge":"No"}]