[{"day":"20","status":"public","abstract":[{"lang":"eng","text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n"}],"supervisor":[{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2024-09-20T12:13:30Z","date_published":"2024-09-20T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:18104","file":[{"file_size":10778238,"file_id":"18105","access_level":"open_access","file_name":"PhD_DPuglia_Final.pdf","checksum":"7969263451b2356bfa0924725aa9de10","embargo":"2025-05-20","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","date_updated":"2025-05-20T22:30:05Z","date_created":"2024-09-20T12:07:48Z"},{"date_created":"2024-09-20T12:13:09Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","date_updated":"2025-05-20T22:30:05Z","file_name":"PhD_DPuglia_Thesis.zip","checksum":"98dfe7675775e30efffa03f7ff7c091b","creator":"cchlebak","relation":"source_file","file_size":385419748,"file_id":"18106","access_level":"closed"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"has_accepted_license":"1","citation":{"ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","apa":"Puglia, D. (2024). <i>Everyday electromechanics: Capacitive strong coupling to mechanical motion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>","ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>","chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>.","mla":"Puglia, Denise. <i>Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>."},"publication_status":"published","author":[{"full_name":"Puglia, Denise","last_name":"Puglia","first_name":"Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425"}],"file_date_updated":"2025-05-20T22:30:05Z","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Published Version","project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"}],"page":"63","year":"2024","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"18143","relation":"part_of_dissertation"}]},"date_updated":"2026-04-07T13:22:10Z","_id":"18104","OA_place":"publisher","month":"09","oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"ddc":["530"]},{"project":[{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"},{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.15314","open_access":"1"}],"abstract":[{"text":"Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby environmental radiation -- has traditionally required demanding experimental\r\ningredients such as superconducting resonators, high-quality optical cavities,\r\nor large magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric device reaching this regime at radio frequencies, enabled by a\r\nmechanically compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower insertion loss than a comparable commercial quartz crystal, and\r\nachieves a position imprecision rivaling an optical interferometer. With the\r\nhelp of a back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion by a remote cryogenic load. This work provides a\r\ntechnologically accessible route to high-precision sensing, transduction, and\r\nsignal processing.","lang":"eng"}],"arxiv":1,"corr_author":"1","oa_version":"Preprint","status":"public","article_processing_charge":"No","year":"2024","citation":{"ieee":"D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical  motion,” <i>arXiv</i>. .","short":"D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.).","ista":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. arXiv, 2407.15314.","apa":"Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., &#38; Higginbotham, A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical  motion. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2407.15314\">https://doi.org/10.48550/arXiv.2407.15314</a>","ama":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2407.15314\">10.48550/arXiv.2407.15314</a>","chicago":"Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2407.15314\">https://doi.org/10.48550/arXiv.2407.15314</a>.","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” <i>ArXiv</i>, 2407.15314, doi:<a href=\"https://doi.org/10.48550/arXiv.2407.15314\">10.48550/arXiv.2407.15314</a>."},"article_number":"2407.15314","publication_status":"draft","day":"24","publication":"arXiv","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-1144-2763","first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"full_name":"Odessey, Rachel H","last_name":"Odessey","first_name":"Rachel H","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd"},{"full_name":"Burns, Peter S.","last_name":"Burns","first_name":"Peter S."},{"first_name":"Niklas","full_name":"Luhmann, Niklas","last_name":"Luhmann"},{"full_name":"Schmid, Silvan","last_name":"Schmid","first_name":"Silvan"},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"AnHi"}],"external_id":{"arxiv":["2407.15314"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","doi":"10.48550/arXiv.2407.15314","oa":1,"title":"Room temperature, cavity-free capacitive strong coupling to mechanical  motion","_id":"18143","related_material":{"record":[{"relation":"later_version","id":"19026","status":"public"},{"relation":"dissertation_contains","id":"18104","status":"public"}]},"date_updated":"2026-08-30T22:30:55Z","type":"preprint","date_published":"2024-08-24T00:00:00Z","OA_place":"repository","date_created":"2024-09-26T06:58:27Z"},{"acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n","OA_place":"repository","OA_type":"green","related_material":{"record":[{"id":"20865","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"20563","status":"public"}]},"date_updated":"2026-08-30T22:31:09Z","_id":"20571","title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","month":"04","oa":1,"external_id":{"arxiv":["2403.07803"]},"author":[{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","first_name":"Filippo","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo"}],"language":[{"iso":"eng"}],"publication":"arXiv","citation":{"mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, 2403.07803, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>.","ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>","ista":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803.","apa":"Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>","short":"F. Quattrocchi, ArXiv (n.d.).","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>arXiv</i>. ."},"publication_status":"draft","article_number":"2403.07803","year":"2024","article_processing_charge":"No","oa_version":"Preprint","arxiv":1,"corr_author":"1","project":[{"grant_number":"F06504","call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425"}],"date_created":"2025-10-28T13:12:56Z","date_published":"2024-04-09T00:00:00Z","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/arXiv.2403.07803","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"day":"09","keyword":["gradient flows","Jordan–Kinderlehrer–Otto scheme","curves of maximal slope","optimal transport","Dirichlet boundary conditions","Fokker–Planck equation"],"status":"public","abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. "}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2403.07803","open_access":"1"}]},{"author":[{"full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","first_name":"Filippo","orcid":"0009-0000-9773-1931","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308"}],"language":[{"iso":"eng"}],"publication":"arXiv","citation":{"ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>","chicago":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>.","mla":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, 2408.12924, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>.","ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” <i>arXiv</i>. .","short":"F. Quattrocchi, ArXiv (n.d.).","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","apa":"Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>"},"publication_status":"draft","article_number":"2408.12924","year":"2024","article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","corr_author":"1","project":[{"call_identifier":"FWF","grant_number":"F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems"}],"acknowledgement":"The author is thankful to Nicolas Clozeau, Lorenzo Dello Schiavo, Jan Maas, Dejan Slepčev,\r\nand Dario Trevisan for many fruitful discussions and comments. The author gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","OA_type":"green","OA_place":"repository","date_updated":"2026-08-30T22:31:09Z","related_material":{"record":[{"relation":"dissertation_contains","id":"20563","status":"public"}]},"_id":"20570","title":"Asymptotics for optimal empirical quantization of measures","month":"08","oa":1,"external_id":{"arxiv":["2408.12924"]},"keyword":["optimal empirical quantization","vector quantization","Wasserstein distance","semidiscrete optimal transport","Zador’s Theorem","Pierce’s Lemma"],"day":"23","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.12924"}],"abstract":[{"lang":"eng","text":"We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le p<d$, we establish asymptotic upper and\r\nlower bounds as $n \\to \\infty$ on the rescaled minimal error that have the\r\nsame, explicit dependency on $\\mu$.\r\n  In some instances, we prove that the rescaled minimal error has a limit.\r\nThese include general measures in dimension $d = 2$ with $1 \\le p < 2$, and\r\nuniform measures in arbitrary dimension with $1 \\le p < d$. For some uniform\r\nmeasures, we prove the limit existence for $p \\ge d$ as well.\r\n  For a class of compactly supported measures with H\\\"older densities, we\r\ndetermine the convergence speed of the minimal error for every $p \\ge 1$.\r\n  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper\r\nestimate of the minimal error when $1 \\le p < d$.\r\n  In the initial sections, we survey the state of the art and draw connections\r\nwith similar problems, such as classical and random quantization."}],"date_created":"2025-10-28T13:12:22Z","date_published":"2024-08-23T00:00:00Z","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/arXiv.2408.12924","department":[{"_id":"GradSch"},{"_id":"JaMa"}]},{"OA_embargo":"6","date_published":"2024-11-11T00:00:00Z","date_created":"2024-11-11T08:40:45Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"has_accepted_license":"1","file":[{"access_level":"closed","file_id":"18551","file_size":26870629,"file_name":"AMrnjavac_thesis_library.docx","checksum":"3e48b163c22114ef5d5371f758668289","relation":"source_file","creator":"amrnjava","title":"Early stages of sex chromosome evolution","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2025-05-11T22:30:04Z","date_created":"2024-11-13T12:15:28Z"},{"date_created":"2024-11-13T12:15:54Z","date_updated":"2025-05-11T22:30:04Z","content_type":"application/pdf","title":"Early stages of sex chromosome evolution","creator":"amrnjava","relation":"main_file","file_name":"AMrnjavac_thesis_library.pdf","checksum":"3ead60c1b678e7dcf018043aef3b5db2","embargo":"2025-05-11","file_id":"18552","file_size":4228766,"access_level":"open_access"}],"doi":"10.15479/at:ista:18531","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"11","keyword":["Sex chromosomes","evolution","selection","sheltering"],"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"abstract":[{"lang":"eng","text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. "}],"status":"public","OA_place":"publisher","_id":"18531","date_updated":"2026-07-29T08:36:28Z","related_material":{"record":[{"id":"12521","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"18549","relation":"part_of_dissertation"}]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"ddc":["576"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"title":"Early stages of sex chromosome evolution","degree_awarded":"PhD","oa":1,"month":"11","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2025-05-11T22:30:04Z","author":[{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}],"publication_status":"published","citation":{"chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria."},"article_processing_charge":"No","year":"2024","page":"181","oa_version":"Published Version","corr_author":"1"},{"_id":"18549","type":"preprint","related_material":{"record":[{"relation":"later_version","status":"public","id":"19370"},{"id":"18531","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-08-30T22:31:09Z","OA_place":"repository","date_published":"2024-07-04T00:00:00Z","date_created":"2024-11-13T09:12:08Z","biorxivid":1,"external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"department":[{"_id":"BeVi"}],"oa":1,"doi":"10.1101/2024.07.02.601697","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"title":"Evidence of a Slower-Z effect in Schistosoma japonicum","publication_status":"draft","citation":{"mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.)."},"day":"04","publication":"bioRxiv","language":[{"iso":"eng"}],"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n"}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.07.02.601697","open_access":"1"}],"status":"public","oa_version":"Preprint","corr_author":"1","article_processing_charge":"No","year":"2024"},{"day":"17","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"supervisor":[{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"status":"public","date_published":"2024-12-17T00:00:00Z","date_created":"2024-12-16T10:53:39Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","file":[{"file_size":19161387,"file_id":"18671","access_level":"closed","checksum":"eca06497a29078558395455c890a32d9","file_name":"2024_msfa_thesis.zip","relation":"source_file","creator":"mamaral","embargo_to":"open_access","content_type":"application/zip","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:27:01Z"},{"content_type":"application/pdf","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:26:30Z","file_id":"18672","file_size":16530084,"access_level":"open_access","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","file_name":"2024_msfa_thesis.pdf","embargo":"2025-06-18","creator":"mamaral","relation":"main_file"}],"department":[{"_id":"GradSch"},{"_id":"AnSa"}],"has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/at:ista:18661","publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"}],"file_date_updated":"2025-06-18T22:30:03Z","citation":{"chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","ama":"Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes: In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.","apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes: In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>"},"publication_status":"published","article_processing_charge":"No","year":"2024","page":"57","oa_version":"Published Version","corr_author":"1","doi_confirm":"1","OA_place":"publisher","_id":"18661","date_updated":"2026-07-29T13:15:48Z","related_material":{"record":[{"status":"public","id":"18670","relation":"part_of_dissertation"}]},"tmp":{"image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)"},"ddc":["572","530"],"degree_awarded":"PhD","title":"Archaeal membranes: In silico modelling and design","month":"12","oa":1},{"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"has_accepted_license":"1","file":[{"file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","embargo":"2025-06-12","relation":"main_file","creator":"nmachnik","file_id":"18649","file_size":12845009,"access_level":"open_access","date_created":"2024-12-11T11:59:54Z","content_type":"application/pdf","date_updated":"2025-06-12T22:30:02Z"},{"relation":"source_file","creator":"nmachnik","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","file_name":"thesis.zip","file_size":14189810,"file_id":"18650","access_level":"closed","date_created":"2024-12-11T11:59:34Z","date_updated":"2025-06-12T22:30:02Z","embargo_to":"open_access","content_type":"application/zip"}],"doi":"10.15479/at:ista:18642","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","date_published":"2024-12-11T00:00:00Z","date_created":"2024-12-10T13:49:15Z","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"abstract":[{"text":"This thesis consists of two pieces of work in the broader field of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefficient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fine-map genetic effects, find the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal effect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe effects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specific genetic effects, and how the error rates of this recovery are influenced\r\nby missing data due to different censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size differences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand finally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n","lang":"eng"}],"status":"public","alternative_title":["ISTA Thesis"],"day":"11","oa":1,"month":"12","ddc":["576"],"title":"Algorithms for causal learning and comparative analysis for genomic data","degree_awarded":"PhD","_id":"18642","related_material":{"record":[{"relation":"part_of_dissertation","id":"18648","status":"public"},{"relation":"part_of_dissertation","id":"8707","status":"public"}]},"date_updated":"2026-07-29T13:02:44Z","doi_confirm":"1","OA_place":"publisher","acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","page":"138","project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","corr_author":"1","article_processing_charge":"No","year":"2024","publication_status":"published","citation":{"ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","apa":"Machnik, N. N. (2024). <i>Algorithms for causal learning and comparative analysis for genomic data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","mla":"Machnik, Nick N. <i>Algorithms for Causal Learning and Comparative Analysis for Genomic Data</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2025-06-12T22:30:02Z","author":[{"orcid":"0000-0001-6617-9742","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N","last_name":"Machnik"}]},{"corr_author":"1","oa_version":"Preprint","project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"},{"_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c","name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation","grant_number":"590359"}],"year":"2024","article_processing_charge":"No","publication":"bioRxiv","citation":{"ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. 2024. doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>","chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>.","mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” <i>BioRxiv</i>, 2024, doi:<a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>.","short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” <i>bioRxiv</i>. 2024.","apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., &#38; Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.12.06.570392\">https://doi.org/10.1101/2023.12.06.570392</a>","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, <a href=\"https://doi.org/10.1101/2023.12.06.570392\">10.1101/2023.12.06.570392</a>."},"publication_status":"published","author":[{"first_name":"Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N","last_name":"Machnik"},{"first_name":"Seyed Mahdi","id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","full_name":"Mahmoudi, Seyed Mahdi","last_name":"Mahmoudi"},{"first_name":"Malgorzata","full_name":"Borczyk, Malgorzata","last_name":"Borczyk"},{"last_name":"Krätschmer","full_name":"Krätschmer, Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse","orcid":"0000-0002-5636-9259"},{"full_name":"Bauer, Markus J.","last_name":"Bauer","first_name":"Markus J."},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"language":[{"iso":"eng"}],"month":"08","oa":1,"title":"Causal inference for multiple risk factors and diseases from genomics data","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18642"}]},"date_updated":"2026-08-30T22:31:12Z","_id":"18648","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","OA_place":"repository","OA_type":"free access","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.06.570392"}],"abstract":[{"lang":"eng","text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n"}],"day":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1101/2023.12.06.570392","department":[{"_id":"MaRo"}],"type":"preprint","date_created":"2024-12-11T10:42:59Z","date_published":"2024-08-10T00:00:00Z"},{"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.1101/2024.10.18.619072","department":[{"_id":"AnSa"}],"title":"Stability vs flexibility: Reshaping archaeal membranes in silico","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_updated":"2026-08-30T22:31:11Z","related_material":{"record":[{"relation":"dissertation_contains","id":"18661","status":"public"}]},"type":"preprint","_id":"18670","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","date_created":"2024-12-18T10:07:45Z","date_published":"2024-11-27T00:00:00Z","OA_place":"repository","ec_funded":1,"oa_version":"Preprint","corr_author":"1","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.18.619072","open_access":"1"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties.","lang":"eng"}],"year":"2024","article_processing_charge":"No","day":"27","publication":"bioRxiv","citation":{"ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>"},"publication_status":"draft","author":[{"first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","orcid":"0000-0001-8501-6017","last_name":"Frey","full_name":"Frey, Felix F"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"language":[{"iso":"eng"}]},{"external_id":{"arxiv":["2210.14182"],"isi":["001171652500001"]},"oa":1,"month":"02","volume":5,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"}],"title":"Emergent macroscopic bistability induced by a single superconducting qubit","intvolume":"         5","_id":"17183","date_updated":"2026-08-30T22:31:15Z","related_material":{"record":[{"id":"18978","status":"public","relation":"research_data"},{"id":"19533","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"OA_type":"gold","OA_place":"publisher","acknowledgement":"This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations.","project":[{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","call_identifier":"H2020","grant_number":"862644"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"APC_amount":"3782,54","corr_author":"1","oa_version":"Published Version","arxiv":1,"article_processing_charge":"Yes","year":"2024","publication_status":"published","article_number":"010327","citation":{"ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>.","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” <i>PRX Quantum</i>, vol. 5, no. 1. American Physical Society, 2024.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>"},"publication":"PRX Quantum","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2691-3399"]},"DOAJ_listed":"1","file_date_updated":"2024-06-28T12:04:43Z","author":[{"last_name":"Sett","full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya","orcid":"0000-0001-7641-8348"},{"orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","last_name":"Hassani"},{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"first_name":"Andras","last_name":"Vukics","full_name":"Vukics, Andras"},{"last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"department":[{"_id":"JoFi"},{"_id":"AnHi"}],"has_accepted_license":"1","article_type":"original","file":[{"date_updated":"2024-06-28T12:04:43Z","content_type":"application/pdf","date_created":"2024-06-28T12:04:43Z","success":1,"file_id":"17185","file_size":1443351,"access_level":"open_access","creator":"cchlebak","relation":"main_file","checksum":"0833880d47f74ad1deda93a1d8ffa5a7","file_name":"2024_PRXQuantum_Sett.pdf"}],"doi":"10.1103/prxquantum.5.010327","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"1","date_published":"2024-02-16T00:00:00Z","quality_controlled":"1","publisher":"American Physical Society","date_created":"2024-06-27T10:58:06Z","scopus_import":"1","abstract":[{"lang":"eng","text":"The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology."}],"status":"public","day":"16","isi":1},{"status":"public","oa_version":"Published Version","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.10518320"}],"abstract":[{"lang":"eng","text":"Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  "}],"year":"2024","article_processing_charge":"No","day":"16","citation":{"mla":"Sett, Riya, et al. <i>Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024)."},"author":[{"first_name":"Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid"},{"first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T","last_name":"Phan"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"},{"first_name":"Andras","last_name":"Vukics","full_name":"Vukics, Andras"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"oa":1,"doi":"10.5281/ZENODO.10518320","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"has_accepted_license":"1","title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"type":"research_data_reference","date_updated":"2026-08-30T22:31:15Z","related_material":{"record":[{"relation":"used_in_publication","id":"17183","status":"public"},{"id":"19533","status":"public","relation":"used_in_publication"}]},"_id":"18978","publisher":"Zenodo","date_created":"2025-01-30T08:30:03Z","date_published":"2024-01-16T00:00:00Z","OA_type":"gold","OA_place":"repository"},{"year":"2023","article_processing_charge":"No","corr_author":"1","oa_version":"None","page":"427-442","author":[{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","orcid":"0000-0001-8602-3083","first_name":"Bidyut B","last_name":"Goswami","full_name":"Goswami, Bidyut B"}],"publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"language":[{"iso":"eng"}],"publication":"Climate Dynamics","citation":{"mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>, vol. 60, Springer Nature, 2023, pp. 427–42, doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. 2023;60:427-442. doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” <i>Climate Dynamics</i>, vol. 60. Springer Nature, pp. 427–442, 2023."},"publication_status":"published","intvolume":"        60","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","volume":60,"month":"01","external_id":{"isi":["000803119400002"]},"acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","related_material":{"link":[{"url":" https://doi.org/10.1007/s00382-022-06401-2","relation":"erratum"}]},"date_updated":"2024-10-09T20:53:52Z","_id":"11434","status":"public","abstract":[{"lang":"eng","text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall."}],"isi":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00382-022-06337-7","article_type":"original","department":[{"_id":"CaMu"}],"scopus_import":"1","publisher":"Springer Nature","date_created":"2022-06-05T22:01:50Z","quality_controlled":"1","date_published":"2023-01-01T00:00:00Z","type":"journal_article"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["576"],"title":"Ten years of demographic modelling of divergence and speciation in the sea","intvolume":"        16","external_id":{"pmid":["36793688"],"isi":["000815663700001"]},"oa":1,"month":"02","volume":16,"pmid":1,"acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","_id":"11479","date_updated":"2025-04-23T08:49:14Z","article_processing_charge":"No","year":"2023","page":"542-559","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1752-4571"]},"file_date_updated":"2023-02-27T07:10:17Z","author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"publication_status":"published","citation":{"ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>"},"publication":"Evolutionary Applications","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file":[{"file_id":"12685","file_size":2269822,"access_level":"open_access","success":1,"file_name":"2023_EvolutionaryApplications_DeJode.pdf","checksum":"d4d6fa9ddf36643af994a6a757919afb","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z"}],"article_type":"original","doi":"10.1111/eva.13428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_published":"2023-02-01T00:00:00Z","publisher":"Wiley","date_created":"2022-07-03T22:01:33Z","scopus_import":"1","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"status":"public","isi":1,"day":"01"},{"date_updated":"2023-10-04T09:38:45Z","_id":"11706","acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","oa":1,"volume":62,"month":"07","external_id":{"isi":["000828530400001"]},"title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","intvolume":"        62","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"ddc":["510"],"publication":"Random Structures and Algorithms","publication_status":"published","citation":{"ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. 2023;62(4):1035-1055. doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>.","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>.","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” <i>Random Structures and Algorithms</i>, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., &#38; Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>","ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055."},"file_date_updated":"2023-10-04T09:37:26Z","author":[{"last_name":"Liebenau","full_name":"Liebenau, Anita","first_name":"Anita"},{"last_name":"Mattos","full_name":"Mattos, Letícia","first_name":"Letícia"},{"first_name":"Walner","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","full_name":"Mendonca Dos Santos, Walner","last_name":"Mendonca Dos Santos"},{"last_name":"Skokan","full_name":"Skokan, Jozef","first_name":"Jozef"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"oa_version":"Published Version","page":"1035-1055","year":"2023","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","issue":"4","date_created":"2022-07-31T22:01:49Z","publisher":"Wiley","scopus_import":"1","quality_controlled":"1","date_published":"2023-07-01T00:00:00Z","doi":"10.1002/rsa.21106","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"MaKw"}],"article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2023-10-04T09:37:26Z","date_created":"2023-10-04T09:37:26Z","file_size":1362334,"file_id":"14389","access_level":"open_access","success":1,"checksum":"3a5969d0c512aef01c30f3dc81c6d59b","file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","relation":"main_file","creator":"dernst"}],"day":"01","isi":1,"status":"public","abstract":[{"lang":"eng","text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. "}]},{"day":"01","isi":1,"abstract":[{"lang":"eng","text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble."}],"status":"public","type":"journal_article","date_published":"2023-04-01T00:00:00Z","quality_controlled":"1","date_created":"2022-08-07T22:02:00Z","publisher":"Springer Nature","scopus_import":"1","department":[{"_id":"LaEr"}],"has_accepted_license":"1","file":[{"file_id":"14054","file_size":782278,"access_level":"open_access","success":1,"checksum":"b9247827dae5544d1d19c37abe547abc","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_updated":"2023-08-14T12:47:32Z","date_created":"2023-08-14T12:47:32Z"}],"article_type":"original","doi":"10.1007/s00440-022-01156-7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2023;185:1183–1218. doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 185. Springer Nature, pp. 1183–1218, 2023.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>"},"publication":"Probability Theory and Related Fields","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"file_date_updated":"2023-08-14T12:47:32Z","author":[{"orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"page":"1183–1218","oa_version":"Published Version","corr_author":"1","arxiv":1,"article_processing_charge":"Yes (via OA deal)","year":"2023","_id":"11741","date_updated":"2024-10-09T21:03:02Z","acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"oa":1,"volume":185,"month":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"title":"Quenched universality for deformed Wigner matrices","intvolume":"       185"},{"quality_controlled":"1","date_published":"2023-04-01T00:00:00Z","publisher":"Springer Nature","date_created":"2022-08-28T22:02:01Z","scopus_import":"1","type":"journal_article","department":[{"_id":"UlWa"}],"has_accepted_license":"1","file":[{"file_id":"12006","file_size":1002218,"access_level":"open_access","success":1,"checksum":"def7ae3b28d9fd6aec16450e40090302","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","relation":"main_file","creator":"alisjak","content_type":"application/pdf","date_updated":"2022-08-29T11:23:15Z","date_created":"2022-08-29T11:23:15Z"}],"article_type":"original","doi":"10.1007/s00454-022-00394-9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"day":"01","abstract":[{"lang":"eng","text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles."}],"status":"public","ec_funded":1,"acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","_id":"11999","date_updated":"2025-04-14T07:43:59Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Inserting one edge into a simple drawing is hard","intvolume":"        69","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"oa":1,"volume":69,"month":"04","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"file_date_updated":"2022-08-29T11:23:15Z","author":[{"last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","orcid":"0000-0003-2401-8670"},{"full_name":"Klute, Fabian","last_name":"Klute","first_name":"Fabian"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"full_name":"Seidel, Raimund","last_name":"Seidel","first_name":"Raimund"},{"last_name":"Wiedera","full_name":"Wiedera, Tilo","first_name":"Tilo"}],"publication_status":"published","citation":{"mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 745–770, doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. 2023;69:745–770. doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>.","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., &#38; Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” <i>Discrete and Computational Geometry</i>, vol. 69. Springer Nature, pp. 745–770, 2023."},"publication":"Discrete and Computational Geometry","article_processing_charge":"Yes (in subscription journal)","year":"2023","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"page":"745–770","oa_version":"Published Version","arxiv":1},{"doi":"10.1007/s00453-022-01027-6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"HeEd"}],"file":[{"creator":"dernst","relation":"main_file","checksum":"71685ca5121f4c837f40c3f8eb50c915","file_name":"2023_Algorithmica_Edelsbrunner.pdf","success":1,"file_size":911017,"file_id":"12322","access_level":"open_access","date_created":"2023-01-20T10:02:48Z","date_updated":"2023-01-20T10:02:48Z","content_type":"application/pdf"}],"article_type":"original","publisher":"Springer Nature","date_created":"2022-09-11T22:01:57Z","scopus_import":"1","quality_controlled":"1","date_published":"2023-01-01T00:00:00Z","type":"journal_article","status":"public","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"isi":1,"day":"01","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","intvolume":"        85","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"oa":1,"month":"01","volume":85,"external_id":{"isi":["000846967100001"],"pmid":["36687803"]},"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","pmid":1,"ec_funded":1,"date_updated":"2025-04-23T08:46:48Z","_id":"12086","year":"2023","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","corr_author":"1","page":"277-295","project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"file_date_updated":"2023-01-20T10:02:48Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"publication":"Algorithmica","publication_status":"published","citation":{"ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. 2023;85:277-295. doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 277–95, doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 277–295, 2023.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."}},{"publication":"Annales Henri Poincare","citation":{"apa":"Wirth, M., &#38; Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 717–750, 2023.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 717–50, doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. 2023;24:717-750. doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>."},"publication_status":"published","author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"last_name":"Zhang","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan"}],"file_date_updated":"2023-08-14T11:38:28Z","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"arxiv":1,"corr_author":"1","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"},{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"page":"717-750","year":"2023","article_processing_charge":"Yes (via OA deal)","date_updated":"2025-04-23T08:53:05Z","_id":"12087","pmid":1,"acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","ec_funded":1,"volume":24,"month":"03","oa":1,"external_id":{"isi":["000837499800002"],"pmid":["36950223"],"arxiv":["2105.08303"]},"intvolume":"        24","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","isi":1,"status":"public","abstract":[{"text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.","lang":"eng"}],"type":"journal_article","scopus_import":"1","publisher":"Springer Nature","date_created":"2022-09-11T22:01:57Z","quality_controlled":"1","date_published":"2023-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00023-022-01220-x","file":[{"file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","checksum":"8c7b185eba5ccd92ef55c120f654222c","creator":"dernst","relation":"main_file","file_id":"14051","file_size":554871,"access_level":"open_access","success":1,"date_created":"2023-08-14T11:38:28Z","content_type":"application/pdf","date_updated":"2023-08-14T11:38:28Z"}],"article_type":"original","has_accepted_license":"1","department":[{"_id":"JaMa"}]},{"ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","intvolume":"        23","external_id":{"pmid":["36597554"],"isi":["000906214600004"]},"oa":1,"volume":23,"month":"01","ec_funded":1,"acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","pmid":1,"_id":"12104","date_updated":"2025-04-23T08:45:56Z","article_processing_charge":"Yes (via OA deal)","year":"2023","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208"},{"_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N"}],"oa_version":"Published Version","corr_author":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"file_date_updated":"2023-01-20T10:45:06Z","author":[{"orcid":"0000-0002-9881-6870","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo"},{"full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"publication_status":"published","article_number":"9","citation":{"short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” <i>Journal of Evolution Equations</i>, vol. 23, no. 1. Springer Nature, 2023.","apa":"Dello Schiavo, L., &#38; Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. 2023;23(1). doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>, vol. 23, no. 1, 9, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>."},"publication":"Journal of Evolution Equations","has_accepted_license":"1","department":[{"_id":"JaMa"}],"file":[{"date_updated":"2023-01-20T10:45:06Z","content_type":"application/pdf","date_created":"2023-01-20T10:45:06Z","success":1,"file_size":422612,"file_id":"12325","access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","checksum":"1f34f3e2cb521033de6154f274ea3a4e"}],"article_type":"original","doi":"10.1007/s00028-022-00859-7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_published":"2023-01-01T00:00:00Z","publisher":"Springer Nature","date_created":"2023-01-08T23:00:53Z","scopus_import":"1","type":"journal_article","issue":"1","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"status":"public","isi":1,"day":"01"}]
