[{"volume":13,"publication_identifier":{"issn":["2010-3263"],"eissn":["2010-3271"]},"researchdata_availability":"unclear","publisher":"World Scientific Publishing","supplementarymaterial":"unclear","arxiv":1,"language":[{"iso":"eng"}],"oa":1,"author":[{"last_name":"Dubach","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137","full_name":"Dubach, Guillaume","first_name":"Guillaume"},{"full_name":"Reker, Jana","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","first_name":"Jana","last_name":"Reker"}],"citation":{"chicago":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>.","apa":"Dubach, G., &#38; Reker, J. (2024). Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>","ista":"Dubach G, Reker J. 2024. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. 13(2), 2450007.","mla":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2, 2450007, World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>.","short":"G. Dubach, J. Reker, Random Matrices: Theory and Applications 13 (2024).","ama":"Dubach G, Reker J. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. 2024;13(2). doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>","ieee":"G. Dubach and J. Reker, “Dynamics of a rank-one multiplicative perturbation of a unitary matrix,” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2. World Scientific Publishing, 2024."},"article_number":"2450007","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2212.14638"}],"issue":"2","type":"journal_article","das_tickbox":"0","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1142/s2010326324500072","doi":"10.1142/s2010326324500072","publication_status":"published","date_created":"2024-05-23T08:31:57Z","article_type":"original","year":"2024","date_updated":"2026-10-02T11:31:29Z","quality_controlled":"1","intvolume":"        13","date_published":"2024-04-01T00:00:00Z","publication":"Random Matrices: Theory and Applications","abstract":[{"text":"We provide a dynamical study of a model of multiplicative perturbation of a unitary matrix introduced by Fyodorov. In particular, we identify a flow of deterministic domains that bound the spectrum with high probability, separating the outlier from the typical eigenvalues at all sub-critical timescales. These results are obtained under generic assumptions on U that hold for a variety of unitary random matrix models.","lang":"eng"}],"_id":"17047","ec_funded":1,"oa_version":"Preprint","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"external_id":{"isi":["001229295200002"],"arxiv":["2212.14638"]},"OA_type":"green","OA_place":"repository","title":"Dynamics of a rank-one multiplicative perturbation of a unitary matrix","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","month":"04","related_material":{"record":[{"id":"17164","relation":"dissertation_contains","status":"public"}]},"day":"01","isi":1,"status":"public"},{"alternative_title":["ISTA Thesis"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"oa_version":"Published Version","ec_funded":1,"_id":"18568","abstract":[{"text":"Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the  optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males\r\nengaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion.","lang":"eng"}],"status":"public","month":"11","related_material":{"record":[{"id":"18444","relation":"part_of_dissertation","status":"public"}]},"day":"20","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster","degree_awarded":"PhD","OA_place":"publisher","has_accepted_license":"1","year":"2024","publication_status":"published","date_created":"2024-11-19T12:34:30Z","doi":"10.15479/at:ista:18568","fulldoi":"https://doi.org/10.15479/at:ista:18568","article_processing_charge":"No","supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2024-11-20T00:00:00Z","date_updated":"2026-10-02T11:33:28Z","doi_confirm":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"tmp":{"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","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"citation":{"ama":"Satapathy RK. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>","ieee":"R. K. Satapathy, “Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria, 2024.","short":"R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria, 2024.","ista":"Satapathy RK. 2024. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.","mla":"Satapathy, Roshan K. <i>Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>.","apa":"Satapathy, R. K. (2024). <i>Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>","chicago":"Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>."},"file_date_updated":"2024-12-13T10:27:25Z","author":[{"first_name":"Roshan K","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0006-2974-5075","full_name":"Satapathy, Roshan K","last_name":"Satapathy"}],"das_tickbox":"0","type":"dissertation","acknowledgement":"I am incredibly thankful for the outstanding support provided by ISTA, especially the Machine Shop team, who made conducting research much easier and more efficient. I am also grateful for the funding provided by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization of neuronal processing”.","file":[{"date_created":"2024-11-19T12:39:55Z","content_type":"application/pdf","access_level":"open_access","checksum":"340f2bfe882c8a85e11ec0687ca15f5e","relation":"main_file","creator":"rsatapat","file_id":"18570","success":1,"file_size":10960975,"date_updated":"2024-11-19T12:39:55Z","file_name":"Roshan PhD thesis-Final.pdf"},{"access_level":"closed","date_created":"2024-11-19T12:46:47Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"0f846fce60d6ea511e07f77eff59a6a1","creator":"rsatapat","file_id":"18571","date_updated":"2024-12-13T10:27:25Z","file_name":"Roshan PhD thesis-Final.docx","file_size":36695917}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-047-3"]},"language":[{"iso":"eng"}],"oa":1,"page":"114","publisher":"Institute of Science and Technology Austria","supplementarymaterial":"no","ddc":["573"],"researchdata_availability":"no"},{"author":[{"first_name":"Daniel","full_name":"Beaglehole, Daniel","last_name":"Beaglehole"},{"first_name":"Peter","full_name":"Súkeník, Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník"},{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"},{"first_name":"Mikhail","full_name":"Belkin, Mikhail","last_name":"Belkin"}],"citation":{"apa":"Beaglehole, D., Súkeník, P., Mondelli, M., &#38; Belkin, M. (2024). Average gradient outer product as a mechanism for deep neural collapse. In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","mla":"Beaglehole, Daniel, et al. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ista":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. 2024. Average gradient outer product as a mechanism for deep neural collapse. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","chicago":"Beaglehole, Daniel, Peter Súkeník, Marco Mondelli, and Mikhail Belkin. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","ieee":"D. Beaglehole, P. Súkeník, M. Mondelli, and M. Belkin, “Average gradient outer product as a mechanism for deep neural collapse,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","ama":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. Average gradient outer product as a mechanism for deep neural collapse. In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","short":"D. Beaglehole, P. Súkeník, M. Mondelli, M. Belkin, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024."},"conference":{"end_date":"2024-12-16","location":"Vancouver, Canada","start_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems"},"main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=lJ1jdl2K9k"}],"das_tickbox":"0","type":"conference","acknowledgement":"We acknowledge support from the National Science Foundation (NSF) and the Simons Foundation for the Collaboration on the Theoretical Foundations of Deep Learning through awards DMS-2031883 and #814639 as well as the TILOS institute (NSF CCF-2112665). This work used the programs (1) XSEDE (Extreme science and engineering discovery environment) which is supported by NSF grant numbers ACI-1548562, and (2) ACCESS (Advanced cyberinfrastructure coordination ecosystem: services & support) which is supported by NSF grants numbers #2138259, #2138286, #2138307, #2137603, and #2138296. Specifically, we used the resources from SDSC Expanse GPU compute nodes, and NCSA Delta system, via allocations TG-CIS220009. Marco Mondelli is supported by the 2019 Lopez-Loreta prize. We also acknowledge useful feedback from anonymous reviewers. ","volume":37,"publication_identifier":{"eissn":["1049-5258"]},"language":[{"iso":"eng"}],"oa":1,"arxiv":1,"researchdata_availability":"no","publisher":"Neural Information Processing Systems Foundation","supplementarymaterial":"no","alternative_title":["Advances in Neural Information Processing Systems"],"external_id":{"arxiv":["2402.13728"]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Deep Neural Collapse (DNC) refers to the surprisingly rigid structure of the data representations in the final layers of Deep Neural Networks (DNNs). Though the phenomenon has been measured in a variety of settings, its emergence is typically explained via data-agnostic approaches, such as the unconstrained features model. In this work, we introduce a data-dependent setting where DNC forms due to feature learning through the average gradient outer product (AGOP). The AGOP is defined with respect to a learned predictor and is equal to the uncentered covariance matrix of its input-output gradients averaged over the training dataset. The Deep Recursive Feature Machine (Deep RFM) is a method that constructs a neural network by iteratively mapping the data with the AGOP and applying an untrained random feature map. We demonstrate empirically that DNC occurs in Deep RFM across standard settings as a consequence of the projection with the AGOP matrix computed at each layer. Further, we theoretically explain DNC in Deep RFM in an asymptotic setting and as a result of kernel learning. We then provide evidence that this mechanism holds for neural networks more generally. In particular, we show that the right singular vectors and values of the weights can be responsible for the majority of within-class variability collapse for DNNs trained in the feature learning regime. As observed in recent work, this singular structure is highly correlated with that of the AGOP."}],"_id":"18890","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"department":[{"_id":"GradSch"},{"_id":"MaMo"}],"corr_author":"1","status":"public","day":"01","month":"12","OA_type":"green","OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Average gradient outer product as a mechanism for deep neural collapse","publication_status":"published","date_created":"2025-01-27T11:11:40Z","year":"2024","scopus_import":"1","article_processing_charge":"No","date_published":"2024-12-01T00:00:00Z","publication":"38th Annual Conference on Neural Information Processing Systems","quality_controlled":"1","date_updated":"2026-10-02T11:34:14Z","intvolume":"        37"},{"external_id":{"arxiv":["2405.14468"]},"alternative_title":["Advances in Neural Information Processing Systems"],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"_id":"18891","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent."}],"oa_version":"Published Version","day":"01","month":"12","status":"public","corr_author":"1","title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"gold","has_accepted_license":"1","OA_place":"publisher","year":"2024","date_created":"2025-01-27T11:15:18Z","publication_status":"published","article_processing_charge":"No","publication":"38th Annual Conference on Neural Information Processing Systems","date_published":"2024-12-01T00:00:00Z","intvolume":"        37","quality_controlled":"1","date_updated":"2026-10-02T11:34:35Z","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024."},"conference":{"location":"Vancouver, Canada","start_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems","end_date":"2024-12-16"},"author":[{"first_name":"Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","full_name":"Súkeník, Peter","last_name":"Súkeník"},{"last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"file_date_updated":"2025-02-04T08:11:25Z","type":"conference","das_tickbox":"0","acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","file":[{"content_type":"application/pdf","date_created":"2025-02-04T08:11:25Z","access_level":"open_access","relation":"main_file","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","success":1,"file_id":"18989","creator":"dernst","date_updated":"2025-02-04T08:11:25Z","file_name":"2024_NeurIPS_Sukenik.pdf","file_size":1784118}],"volume":37,"arxiv":1,"language":[{"iso":"eng"}],"oa":1,"publisher":"Neural Information Processing Systems Foundation","supplementarymaterial":"no","researchdata_availability":"no","ddc":["000"]},{"status":"public","day":"07","month":"11","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","OA_type":"gold","OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations."}],"_id":"18515","date_published":"2024-11-07T00:00:00Z","date_updated":"2026-10-02T11:36:48Z","doi_confirm":"1","year":"2024","date_created":"2024-11-06T21:25:37Z","publication_status":"published","doi":"10.15479/at:ista:18515","fulldoi":"https://doi.org/10.15479/at:ista:18515","article_processing_charge":"No","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"das_tickbox":"1","type":"dissertation","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"citation":{"chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024."},"file_date_updated":"2024-11-07T10:59:42Z","author":[{"last_name":"Surendranadh","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"}],"oa":1,"language":[{"iso":"eng"}],"page":"219","supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","researchdata_availability":"yes","ddc":["576"],"acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-11-07T10:59:29Z","relation":"main_file","checksum":"c32cf7bc75748d9c551d8eb70178bbec","success":1,"file_id":"18519","creator":"psurendr","date_updated":"2024-11-07T10:59:29Z","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","file_size":37019760},{"date_created":"2024-11-07T10:59:42Z","access_level":"closed","content_type":"application/zip","relation":"source_file","checksum":"4417e02d54084d89e75734e18caaa96d","file_id":"18520","creator":"psurendr","date_updated":"2024-11-07T10:59:42Z","file_name":"PhD Thesis- Parvathy_071124.zip","file_size":41198857}],"publication_identifier":{"issn":["2663-337X"]}},{"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"ec_funded":1,"_id":"17208","abstract":[{"text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"title":"Exploring the optimization landscape of variational quantum algorithms","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","month":"07","related_material":{"record":[{"id":"10545","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10067","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17222"},{"relation":"part_of_dissertation","id":"13125","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11471"}]},"day":"09","status":"public","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:17208","doi":"10.15479/at:ista:17208","article_processing_charge":"No","supervisor":[{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"year":"2024","date_created":"2024-07-09T09:14:24Z","publication_status":"published","doi_confirm":"1","date_updated":"2026-10-02T11:36:07Z","date_published":"2024-07-09T00:00:00Z","citation":{"apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"}],"file_date_updated":"2024-07-17T09:23:24Z","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"dissertation","das_tickbox":"0","publication_identifier":{"issn":["2663-337X"]},"file":[{"creator":"rmedinar","file_id":"17212","date_updated":"2024-07-10T11:34:09Z","file_name":"Raimel_Thesis-Final.zip","file_size":"14218691","date_created":"2024-07-09T09:21:44Z","access_level":"closed","content_type":"application/zip","relation":"source_file","checksum":"6f45273d04f4418bc2adc018baed0525"},{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-07-17T09:23:24Z","checksum":"6724a95bec772dbabc0111b9f08a805e","relation":"main_file","file_id":"17275","creator":"rmedinar","success":1,"file_size":11253627,"file_name":"Raimel_Thesis-20_pdfa.pdf","date_updated":"2024-07-17T09:23:24Z"}],"supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","ddc":["539"],"researchdata_availability":"no","oa":1,"language":[{"iso":"eng"}],"page":"133"},{"ddc":["530"],"researchdata_availability":"no","publisher":"American Physical Society","supplementarymaterial":"yes","arxiv":1,"language":[{"iso":"eng"}],"oa":1,"volume":6,"APC_amount":"3028,31 EUR","publication_identifier":{"eissn":["2643-1564"]},"file":[{"date_updated":"2024-09-23T09:46:20Z","file_name":"2024_PhysicalReviewResearch_Maslov.pdf","file_size":1563824,"success":1,"creator":"dernst","file_id":"18125","relation":"main_file","checksum":"8f744d94956a1683b473b1cf9b411a37","content_type":"application/pdf","date_created":"2024-09-23T09:46:20Z","access_level":"open_access"}],"acknowledgement":"We are grateful to Emilio Pisanty and Philipp Lunt for valuable discussions. This research was funded wholly or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). O.H.H. acknowledges support by the Austrian Science Fund (FWF) [10.55776/P36040]. Furthermore, the financial support by the Austrian Federal Ministry for Digital and Economic Affairs, the National Foundation for Research, Technology and Development, and the Christian Doppler Research Association is gratefully acknowledged.","article_number":"033277","issue":"3","type":"journal_article","das_tickbox":"0","author":[{"last_name":"Maslov","first_name":"Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail"},{"last_name":"Koutentakis","full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios"},{"last_name":"Hrast","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","full_name":"Hrast, Mateja","first_name":"Mateja"},{"full_name":"Heckl, Oliver H.","first_name":"Oliver H.","last_name":"Heckl"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko"}],"file_date_updated":"2024-09-23T09:46:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"M. Maslov, G. Koutentakis, M. Hrast, O.H. Heckl, M. Lemeshko, Physical Review Research 6 (2024).","ama":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. 2024;6(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>","ieee":"M. Maslov, G. Koutentakis, M. Hrast, O. H. Heckl, and M. Lemeshko, “Theory of angular momentum transfer from light to molecules,” <i>Physical Review Research</i>, vol. 6, no. 3. American Physical Society, 2024.","chicago":"Maslov, Mikhail, Georgios Koutentakis, Mateja Hrast, Oliver H. Heckl, and Mikhail Lemeshko. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>.","apa":"Maslov, M., Koutentakis, G., Hrast, M., Heckl, O. H., &#38; Lemeshko, M. (2024). Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>","ista":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. 2024. Theory of angular momentum transfer from light to molecules. Physical Review Research. 6(3), 033277.","mla":"Maslov, Mikhail, et al. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>, vol. 6, no. 3, 033277, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>."},"DOAJ_listed":"1","date_updated":"2026-10-02T11:36:24Z","quality_controlled":"1","intvolume":"         6","date_published":"2024-09-10T00:00:00Z","publication":"Physical Review Research","scopus_import":"1","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.1103/physrevresearch.6.033277","doi":"10.1103/physrevresearch.6.033277","date_created":"2024-09-18T11:43:16Z","publication_status":"published","article_type":"original","year":"2024","OA_place":"publisher","has_accepted_license":"1","OA_type":"gold","title":"Theory of angular momentum transfer from light to molecules","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","day":"10","month":"09","related_material":{"record":[{"relation":"dissertation_contains","id":"19048","status":"public"}]},"status":"public","_id":"18087","abstract":[{"text":"We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","project":[{"name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403","_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3"},{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"external_id":{"arxiv":["2310.00095"]}},{"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_id":"15021","creator":"mhledik","success":1,"file_size":7102089,"file_name":"hledik thesis pdfa 2b.pdf","date_updated":"2024-02-23T13:50:53Z","access_level":"open_access","content_type":"application/pdf","date_created":"2024-02-23T13:50:53Z","checksum":"b2d3da47c98d481577a4baf68944fe41","relation":"main_file"},{"date_updated":"2024-02-23T14:20:16Z","file_name":"hledik thesis source.zip","file_size":14014790,"creator":"mhledik","file_id":"15022","relation":"source_file","checksum":"eda9b9430da2610fee7ce1c1419a479a","content_type":"application/zip","date_created":"2024-02-23T13:50:54Z","access_level":"closed"}],"publisher":"Institute of Science and Technology Austria","supplementarymaterial":"no","ddc":["576","519"],"researchdata_availability":"no","oa":1,"language":[{"iso":"eng"}],"page":"158","citation":{"short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>."},"file_date_updated":"2024-02-23T14:20:16Z","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"das_tickbox":"0","type":"dissertation","doi":"10.15479/at:ista:15020","fulldoi":"https://doi.org/10.15479/at:ista:15020","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"article_processing_charge":"No","year":"2024","publication_status":"published","date_created":"2024-02-23T14:02:04Z","date_updated":"2026-10-02T11:40:30Z","doi_confirm":"1","date_published":"2024-02-23T00:00:00Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Published Version","_id":"15020","ec_funded":1,"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Genetic information and biological optimization","degree_awarded":"PhD","has_accepted_license":"1","OA_place":"publisher","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7606"},{"status":"public","relation":"part_of_dissertation","id":"12081"},{"status":"public","relation":"part_of_dissertation","id":"7553"}]},"day":"23","month":"02","keyword":["Theoretical biology","Optimality","Evolution","Information"],"corr_author":"1"},{"doi_confirm":"1","date_updated":"2026-10-02T11:41:41Z","date_published":"2024-07-11T00:00:00Z","article_processing_charge":"No","supervisor":[{"last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X"}],"fulldoi":"https://doi.org/10.15479/at:ista:17225","doi":"10.15479/at:ista:17225","publication_status":"published","date_created":"2024-07-11T09:46:48Z","year":"2024","OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","title":"Towards a quantum entanglement enhanced atom interferomter","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","month":"07","day":"11","related_material":{"record":[{"status":"public","id":"11438","relation":"part_of_dissertation"}]},"status":"public","abstract":[{"text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence.","lang":"eng"}],"_id":"17225","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"project":[{"grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"alternative_title":["ISTA Thesis"],"researchdata_availability":"no","ddc":["530"],"supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","page":"79","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"open_access","date_created":"2024-07-11T10:26:22Z","content_type":"application/pdf","relation":"main_file","checksum":"15b2dbe8d2c9ed7ca5dd413827928077","success":1,"file_id":"17228","creator":"vli","date_updated":"2024-07-11T10:26:22Z","file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","file_size":6729761},{"date_created":"2024-07-11T10:26:22Z","content_type":"application/x-zip-compressed","access_level":"closed","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","relation":"source_file","file_id":"17229","creator":"vli","file_size":9542859,"date_updated":"2024-07-11T10:26:22Z","file_name":"PhD Thesis Vyacheslav Li.zip"}],"type":"dissertation","das_tickbox":"0","author":[{"id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Vyacheslav","first_name":"Vyacheslav","last_name":"Li"}],"file_date_updated":"2024-07-11T10:26:22Z","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"citation":{"ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>","short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>.","apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>."}},{"date_updated":"2026-10-02T11:43:01Z","doi_confirm":"1","date_published":"2024-09-23T00:00:00Z","doi":"10.15479/at:ista:18135","fulldoi":"https://doi.org/10.15479/at:ista:18135","supervisor":[{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"article_processing_charge":"No","year":"2024","date_created":"2024-09-24T10:56:25Z","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Energies of dilute Fermi gases and universalities in BCS theory","has_accepted_license":"1","OA_place":"publisher","degree_awarded":"PhD","status":"public","related_material":{"record":[{"status":"public","id":"11732","relation":"part_of_dissertation"},{"id":"17240","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"14931","status":"public"},{"relation":"part_of_dissertation","id":"14542","status":"public"},{"relation":"part_of_dissertation","id":"18107","status":"public"}]},"month":"09","day":"23","corr_author":"1","project":[{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$."}],"_id":"18135","ec_funded":1,"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supplementarymaterial":"no","researchdata_availability":"no","ddc":["515","539"],"language":[{"iso":"eng"}],"oa":1,"page":"353","publication_identifier":{"isbn":["978-3-99078-042-8"],"issn":["2663-337X"]},"file":[{"date_created":"2024-09-26T13:11:24Z","access_level":"open_access","content_type":"application/pdf","checksum":"c7bc3b31e430d57c65393051ca439575","relation":"main_file","creator":"alaurits","file_id":"18147","success":1,"file_size":3648831,"file_name":"Lauritsen-thesis-final.pdf","date_updated":"2024-09-26T13:11:24Z"},{"content_type":"application/x-zip-compressed","access_level":"closed","date_created":"2024-09-26T13:12:55Z","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","relation":"source_file","file_id":"18148","creator":"alaurits","file_size":1625888,"file_name":"Lauritsen-thesis-source.zip","date_updated":"2024-09-26T13:12:55Z"}],"das_tickbox":"0","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024."},"file_date_updated":"2024-09-26T13:12:55Z","author":[{"last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard"}]},{"acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges  partial  financial  support  by  the  ERC  Advanced  Grant  “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","file":[{"relation":"main_file","checksum":"2b053a4223b4db14b90520999ec56054","date_created":"2025-01-09T07:56:28Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-01-09T07:56:28Z","file_name":"2024_ReviewsmathPhysics_Henheik.pdf","file_size":503910,"success":1,"creator":"dernst","file_id":"18786"}],"publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"volume":36,"language":[{"iso":"eng"}],"oa":1,"arxiv":1,"publisher":"World Scientific Publishing","supplementarymaterial":"no","researchdata_availability":"no","ddc":["510"],"citation":{"ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. 2024;36(9). doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” <i>Reviews in Mathematical Physics</i>, vol. 36, no. 9. World Scientific Publishing, 2024.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics 36 (2024).","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>, vol. 36, no. 9, 2360005, World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2024. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 36(9), 2360005.","apa":"Henheik, S. J., Lauritsen, A. B., &#38; Roos, B. (2024). Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2025-01-09T07:56:28Z","author":[{"last_name":"Henheik","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha"},{"orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen"},{"last_name":"Roos","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","first_name":"Barbara"}],"das_tickbox":"0","issue":"9","type":"journal_article","article_number":"2360005 ","year":"2024","publication_status":"published","date_created":"2023-11-15T23:48:14Z","article_type":"original","doi":"10.1142/s0129055x2360005x","fulldoi":"https://doi.org/10.1142/s0129055x2360005x","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","publication":"Reviews in Mathematical Physics","date_published":"2024-10-01T00:00:00Z","intvolume":"        36","quality_controlled":"1","date_updated":"2026-10-02T11:43:00Z","external_id":{"isi":["001099640300002"],"arxiv":["2301.05621"]},"department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"oa_version":"Published Version","_id":"14542","ec_funded":1,"abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"isi":1,"status":"public","day":"01","related_material":{"record":[{"relation":"dissertation_contains","id":"19540","status":"public"},{"relation":"dissertation_contains","id":"18135","status":"public"}]},"month":"10","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Universality in low-dimensional BCS theory","OA_place":"publisher","OA_type":"hybrid","has_accepted_license":"1"},{"date_published":"2024-09-09T00:00:00Z","publication":"Forum of Mathematics, Sigma","quality_controlled":"1","date_updated":"2026-10-02T11:43:00Z","intvolume":"        12","date_created":"2024-09-20T12:25:25Z","publication_status":"published","article_type":"original","year":"2024","scopus_import":"1","article_processing_charge":"Yes","doi":"10.1017/fms.2024.56","fulldoi":"https://doi.org/10.1017/fms.2024.56","corr_author":"1","status":"public","isi":1,"day":"09","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18135"}]},"month":"09","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Pressure of a dilute spin-polarized Fermi gas: Lower bound","external_id":{"arxiv":["2407.05990"],"isi":["001307817400001"]},"oa_version":"Published Version","abstract":[{"text":"We consider a dilute fully spin-polarized Fermi gas at positive temperature in dimensions  d∈{1,2,3} . We show that the pressure of the interacting gas is bounded from below by that of the free gas plus, to leading order, an explicit term of order  adρ2+2/d, where a is the p-wave scattering length of the repulsive interaction and  ρ  is the particle density. The results are valid for a wide range of repulsive interactions, including that of a hard core, and uniform in temperatures at most of the order of the Fermi temperature. A central ingredient in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin, Gillespie and Ripka (Nucl. Phys. A, 176.2 (1971), pp. 237–260).","lang":"eng"}],"_id":"18107","project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"oa":1,"language":[{"iso":"eng"}],"arxiv":1,"researchdata_availability":"no","ddc":["510"],"publisher":"Cambridge University Press","supplementarymaterial":"no","file":[{"file_name":"2024_ForumMath_Lauritsen.pdf","date_updated":"2024-09-23T09:56:17Z","file_size":599886,"success":1,"creator":"dernst","file_id":"18126","relation":"main_file","checksum":"330b881240013213a8e08538fec13d29","content_type":"application/pdf","access_level":"open_access","date_created":"2024-09-23T09:56:17Z"}],"acknowledgement":"Financial support by the Austrian Science Fund (FWF) through grant DOI: 10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged.","volume":12,"publication_identifier":{"issn":["2050-5094"]},"article_number":"e78","das_tickbox":"0","type":"journal_article","file_date_updated":"2024-09-23T09:56:17Z","author":[{"orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"A.B. Lauritsen, R. Seiringer, Forum of Mathematics, Sigma 12 (2024).","ieee":"A. B. Lauritsen and R. Seiringer, “Pressure of a dilute spin-polarized Fermi gas: Lower bound,” <i>Forum of Mathematics, Sigma</i>, vol. 12. Cambridge University Press, 2024.","ama":"Lauritsen AB, Seiringer R. Pressure of a dilute spin-polarized Fermi gas: Lower bound. <i>Forum of Mathematics, Sigma</i>. 2024;12. doi:<a href=\"https://doi.org/10.1017/fms.2024.56\">10.1017/fms.2024.56</a>","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute Spin-Polarized Fermi Gas: Lower Bound.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2024. <a href=\"https://doi.org/10.1017/fms.2024.56\">https://doi.org/10.1017/fms.2024.56</a>.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute Spin-Polarized Fermi Gas: Lower Bound.” <i>Forum of Mathematics, Sigma</i>, vol. 12, e78, Cambridge University Press, 2024, doi:<a href=\"https://doi.org/10.1017/fms.2024.56\">10.1017/fms.2024.56</a>.","ista":"Lauritsen AB, Seiringer R. 2024. Pressure of a dilute spin-polarized Fermi gas: Lower bound. Forum of Mathematics, Sigma. 12, e78.","apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Pressure of a dilute spin-polarized Fermi gas: Lower bound. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2024.56\">https://doi.org/10.1017/fms.2024.56</a>"}},{"author":[{"full_name":"Sisak, Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","first_name":"Maria A","last_name":"Sisak"}],"file_date_updated":"2024-10-24T08:09:13Z","citation":{"ieee":"M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024.","ama":"Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>","short":"M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024.","ista":"Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria.","mla":"Sisak, Maria A. <i>T-Dual Branes on Hyperkähler Manifolds</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>.","apa":"Sisak, M. A. (2024). <i>T-dual branes on hyperkähler manifolds</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>","chicago":"Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"type":"dissertation","das_tickbox":"0","publication_identifier":{"issn":["2663-337X"]},"file":[{"success":1,"file_id":"18467","creator":"msisak","file_name":"MASisak_dissertation.pdf","date_updated":"2024-10-23T14:42:45Z","file_size":1672547,"access_level":"open_access","content_type":"application/pdf","date_created":"2024-10-23T14:42:45Z","relation":"main_file","checksum":"8c4893e726aaa4b3efb82758da9b6851"},{"creator":"msisak","file_id":"18468","file_size":617913,"date_updated":"2024-10-24T08:09:13Z","file_name":"MASisak_source.zip","content_type":"application/x-zip-compressed","date_created":"2024-10-23T14:43:56Z","access_level":"closed","checksum":"1831b072e861a1e5481024ca9d02b036","relation":"source_file"}],"researchdata_availability":"no","ddc":["516"],"supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","page":"178","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n"}],"_id":"18443","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"project":[{"name":"Branes on hyperkähler manifolds","_id":"6286e8c4-2b32-11ec-9570-f5297902f67f","grant_number":"26069"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","degree_awarded":"PhD","has_accepted_license":"1","OA_type":"free access","title":"T-dual branes on hyperkähler manifolds","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","keyword":["hyperkaehler geometry","branes","mirror symmetry","T-duality"],"corr_author":"1","month":"10","day":"24","status":"public","supervisor":[{"first_name":"Tamás","orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/at:ista:18443","doi":"10.15479/at:ista:18443","date_created":"2024-10-19T12:00:37Z","publication_status":"published","year":"2024","doi_confirm":"1","date_updated":"2026-10-02T11:43:57Z","date_published":"2024-10-24T00:00:00Z"},{"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-3-031-75387-9_1","doi":"10.1007/978-3-031-75387-9_1","publication_status":"published","date_created":"2024-09-05T14:27:08Z","year":"2024","quality_controlled":"1","date_updated":"2026-10-02T11:44:52Z","intvolume":"     15222","date_published":"2024-10-26T00:00:00Z","publication":"12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation","_id":"17634","ec_funded":1,"abstract":[{"text":"System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems.","lang":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"alternative_title":["LNCS"],"external_id":{"arxiv":["2409.03569"],"isi":["001419008700001"]},"OA_type":"hybrid","has_accepted_license":"1","OA_place":"publisher","title":"QuAK: Quantitative Automata Kit","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"20147","status":"public"}]},"day":"26","month":"10","status":"public","isi":1,"volume":15222,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031753862"],"eissn":["1611-3349"]},"APC_amount":"2748 EUR","file":[{"date_created":"2024-09-05T14:26:02Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"43e432f82be376434b358f3dd7a94b71","success":1,"file_id":"17635","creator":"esarac","date_updated":"2024-09-05T14:26:02Z","file_name":"isola24.pdf","file_size":847422},{"relation":"main_file","checksum":"6bc04f07bb5612c0e7ea00ac121a69b6","access_level":"open_access","date_created":"2025-01-21T14:39:49Z","content_type":"application/pdf","file_name":"2024_LNCS_Chalupa.pdf","date_updated":"2025-01-21T14:39:49Z","file_size":1358706,"success":1,"file_id":"18865","creator":"dernst"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started.","ddc":["000"],"researchdata_availability":"no","publisher":"Springer Nature","supplementarymaterial":"no","page":"3-20","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien"},{"last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"}],"file_date_updated":"2025-01-21T14:39:49Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"mla":"Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>.","ista":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative Automata Kit. 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. ISoLA: International Symposium on Leveraging Applications, LNCS, vol. 15222, 3–20.","apa":"Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i> (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>","chicago":"Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, 15222:3–20. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>.","ama":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>. Vol 15222. Springer Nature; 2024:3-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>","ieee":"M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, Crete, Greece, 2024, vol. 15222, pp. 3–20.","short":"M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Springer Nature, 2024, pp. 3–20."},"conference":{"name":"ISoLA: International Symposium on Leveraging Applications","start_date":"2024-10-27","location":"Crete, Greece","end_date":"2024-10-31"},"type":"conference","das_tickbox":"0"},{"page":"195","language":[{"iso":"eng"}],"oa":1,"researchdata_availability":"no","ddc":["512"],"supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","file":[{"file_name":"PhDthesis (3).zip","date_updated":"2024-09-23T18:49:22Z","file_size":5382106,"creator":"jglas","file_id":"18133","relation":"source_file","checksum":"2f8cf5cefdab108b1979caa8146cae9a","date_created":"2024-09-23T18:49:22Z","content_type":"application/x-zip-compressed","access_level":"closed"},{"success":1,"creator":"jglas","file_id":"18140","file_name":"example-phd.pdf","date_updated":"2024-09-25T14:08:57Z","file_size":2380127,"content_type":"application/pdf","access_level":"open_access","date_created":"2024-09-25T14:08:57Z","relation":"main_file","checksum":"08bb6f14c42b47ff25882a2ce3ea0d8a"}],"publication_identifier":{"issn":["2663-337X"]},"das_tickbox":"0","type":"dissertation","file_date_updated":"2024-09-25T14:08:57Z","author":[{"id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","full_name":"Glas, Jakob","first_name":"Jakob","last_name":"Glas"}],"tmp":{"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)","image":"/images/cc_by_nc.png"},"citation":{"mla":"Glas, Jakob. <i>Counting Rational Points over Function Fields</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>.","ista":"Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria.","apa":"Glas, J. (2024). <i>Counting rational points over function fields</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>","chicago":"Glas, Jakob. “Counting Rational Points over Function Fields.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>.","ieee":"J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024.","ama":"Glas J. Counting rational points over function fields. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>","short":"J. Glas, Counting Rational Points over Function Fields, Institute of Science and Technology Austria, 2024."},"date_published":"2024-09-23T00:00:00Z","date_updated":"2026-10-02T11:44:29Z","doi_confirm":"1","publication_status":"published","date_created":"2024-09-23T18:58:08Z","year":"2024","article_processing_charge":"No","supervisor":[{"last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"}],"doi":"10.15479/at:ista:18132","fulldoi":"https://doi.org/10.15479/at:ista:18132","corr_author":"1","status":"public","related_material":{"record":[{"status":"public","id":"18173","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18295","status":"public"},{"relation":"part_of_dissertation","id":"18294","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18293"}]},"day":"23","month":"09","degree_awarded":"PhD","has_accepted_license":"1","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Counting rational points over function fields","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","_id":"18132","abstract":[{"text":"In this thesis, we are dealing with both arithmetic and geometric problems coming from the\r\nstudy of rational points with a particular focus on function fields over finite fields:\r\n(1) Using the circle method we produce upper bounds for the number of rational points of\r\nbounded height on diagonal cubic surfaces and fourfolds over Fq(t). This is based on\r\njoint work with Leonhard Hochfilzer.\r\n(2) We study rational points on smooth complete intersections X defined by cubic and\r\nquadratic hypersurfaces over Fq(t). We refine the Farey dissection of the “unit square”\r\ndeveloped by Vishe [202] and use the circle method with a Kloosterman refinement to\r\nestablish an asymptotic formula for the number of rational points of bounded height on\r\nX when dim(X) ≥ 23. Under the same hypotheses, we also verify weak approximation.\r\n(3) In joint work with Hochfilzer, we obtain upper bounds for the number of rational points of\r\nbounded height on del Pezzo surfaces of low degree over any global field. Our approach\r\nis to take hyperplane sections, which reduces the problem to uniform estimates for the\r\nnumber of rational points on curves.\r\n(4) We develop a version of the circle method capable of counting Fq-points on jet schemes\r\nof moduli spaces of rational curves on hypersurfaces. Combining this with a spreading\r\nout argument and a result of Mustaţă [150], this allows us to show that these moduli\r\nspaces only have canonical singularities under suitable assumptions on the degree and the\r\ndimension.\r\nIn addition, we give an overview of guiding questions and conjectures in the field of rational\r\npoints and explain the basic mechanism underlying the circle method.\r\n","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"TiBr"}],"project":[{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}]},{"date_published":"2024-12-17T00:00:00Z","doi_confirm":"1","date_updated":"2026-10-02T11:55:42Z","year":"2024","date_created":"2024-12-17T16:17:55Z","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18667","doi":"10.15479/at:ista:18667","article_processing_charge":"No","supervisor":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"day":"17","related_material":{"record":[{"status":"public","id":"10828","relation":"part_of_dissertation"},{"status":"public","id":"11440","relation":"part_of_dissertation"},{"id":"9345","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18673","relation":"part_of_dissertation"}]},"month":"12","status":"public","corr_author":"1","keyword":["persistent homology","topological data analysis","periodic","crystalline materials","images","fingerprint"],"title":"New methods for applying topological data analysis to materials science","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","degree_awarded":"PhD","has_accepted_license":"1","OA_place":"publisher","alternative_title":["ISTA Thesis"],"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"Many chemical and physical properties of materials are determined by the material’s shape,\r\nfor example the size of its pores and the width of its tunnels. This makes materials science\r\na prime application area for geometrical and topological methods. Nevertheless many\r\nmethods in topological data analysis have not been satisfyingly extended to the needs of\r\nmaterials science. This thesis provides new methods and new mathematical theorems\r\ntargeted at those specific needs by answering four different research questions. While the\r\nmotivation for each of the research questions arises from materials science, the methods\r\nare versatile and can be applied in different areas as well. \r\n\r\nThe first research question is concerned with image data, for example a three-dimensional\r\ncomputed tomography (CT) scan of a material, like sand or stone. There are two commonly\r\nused topologies for digital images and depending on the application either of them might be\r\nrequired. However, software for computing the topological data analysis method persistence\r\nhomology, usually supports only one of the two topologies. We answer the question how to\r\ncompute persistent homology of an image with respect to one of the two topologies using\r\nsoftware that is intended for the other topology. \r\n\r\nThe second research question is concerned with image data as well, and asks how much\r\nof the topological information of an image is lost when the resolution is coarsened. As\r\ncomputer tomography scanners are more expensive the higher the resolution, it is an\r\nimportant question in materials science to know which resolution is enough to get satisfying\r\npersistent homology. We give theoretical bounds on the information loss based on different\r\ngeometrical properties of the object to be scanned. In addition, we conduct experiments on\r\nsand and stone CT image data. \r\n\r\nThe third research question is motivated by comparing crystalline materials efficiently. As\r\nthe atoms within a crystal repeat periodically, crystalline materials are either modeled by\r\nunmanageable infinite periodic point sets, or by one of their fundamental domains, which is\r\nunstable under perturbation. Therefore a fingerprint of crystalline materials is needed, with\r\nappropriate properties such that comparing the crystals can be eased by comparing the\r\nfingerprints instead. We define the density fingerprint and prove the necessary properties. \r\n\r\nThe fourth research question is motivated by studying the hole-structure or connectedness,\r\ni.e. persistent homology or merge trees, of crystalline materials. A common way to deal\r\nwith periodicity is to take a fundamental domain and identify opposite boundaries to form a\r\ntorus. However, computing persistent homology or merge trees on that torus loses some\r\nof the information materials scientists are interested in and is additionally not stable under\r\ncertain noise. We therefore decorate the merge tree stemming from the torus with additional\r\ninformation describing the density and growth rate of the periodic copies of a component\r\nwithin a growing spherical window. We prove all desired properties, like stability and efficient\r\ncomputability."}],"_id":"18667","ec_funded":1,"oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"page":"111","publisher":"Institute of Science and Technology Austria","supplementarymaterial":"no","ddc":["514","516","004"],"researchdata_availability":"no","acknowledgement":"I was supported by the European Research Council (ERC) Horizon 2020 project\r\n“Alpha Shape Theory Extended” No. 788183 and by the Pöttinger Scholarship. In addition,\r\nI am very thankful for having been able to attend the second Workshop for Women in\r\nComputational Topology in July 2019, funded by the Mathematical Sciences Institute at\r\nANU, the US National Science Foundation through the award CCF-1841455, the Australian\r\nMathematical Sciences Institute and the Association for Women in Mathematics. Two of the\r\nprojects presented in this thesis started there. One of them reached completion thanks to\r\nfunding from the MSRI Summer Research in Mathematics program awarded to me and my\r\ncollaborators in 2020.","file":[{"file_size":7752253,"date_updated":"2024-12-19T10:24:46Z","file_name":"Teresa_Heiss_PhD_Thesis_final.pdf","file_id":"18686","creator":"theiss","success":1,"checksum":"247bb057aed2fba1cd4711917aaa2d77","relation":"main_file","access_level":"open_access","date_created":"2024-12-19T10:24:46Z","content_type":"application/pdf"},{"relation":"source_file","checksum":"9648b45c07a008ee11a07f99856a139d","content_type":"application/zip","access_level":"closed","date_created":"2024-12-19T10:24:50Z","date_updated":"2024-12-19T10:24:50Z","file_name":"PhD_Thesis.zip","file_size":17197731,"creator":"theiss","file_id":"18687"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-052-7"]},"type":"dissertation","das_tickbox":"0","citation":{"apa":"Heiss, T. (2024). <i>New methods for applying topological data analysis to materials science</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>","ista":"Heiss T. 2024. New methods for applying topological data analysis to materials science. Institute of Science and Technology Austria.","mla":"Heiss, Teresa. <i>New Methods for Applying Topological Data Analysis to Materials Science</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>.","chicago":"Heiss, Teresa. “New Methods for Applying Topological Data Analysis to Materials Science.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>.","ieee":"T. Heiss, “New methods for applying topological data analysis to materials science,” Institute of Science and Technology Austria, 2024.","ama":"Heiss T. New methods for applying topological data analysis to materials science. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>","short":"T. Heiss, New Methods for Applying Topological Data Analysis to Materials Science, Institute of Science and Technology Austria, 2024."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa","last_name":"Heiss"}],"file_date_updated":"2024-12-19T10:24:50Z"},{"citation":{"short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","mla":"Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>.","apa":"Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete geometric structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>"},"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"file_date_updated":"2024-03-14T14:14:35Z","author":[{"first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano"}],"das_tickbox":"0","type":"dissertation","file":[{"date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","file_size":4106872,"success":1,"creator":"scultrer","file_id":"15112","relation":"main_file","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","content_type":"application/pdf","date_created":"2024-03-14T08:55:07Z","access_level":"open_access"},{"access_level":"closed","date_created":"2024-03-14T08:56:24Z","content_type":"application/zip","relation":"source_file","checksum":"bcbd213490f5a7e68855a092bbce93f1","creator":"scultrer","file_id":"15113","file_name":"Thesis (1).zip","date_updated":"2024-03-14T14:14:35Z","file_size":4746234}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"language":[{"iso":"eng"}],"page":"108","publisher":"Institute of Science and Technology Austria","supplementarymaterial":"no","ddc":["514","500","516"],"researchdata_availability":"no","alternative_title":["ISTA Thesis"],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"name":"Persistent Homology, Algorithms and Stochastic Geometry","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"_id":"15094","ec_funded":1,"status":"public","day":"08","month":"03","related_material":{"record":[{"id":"15090","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11658"},{"relation":"part_of_dissertation","id":"11660","status":"public"},{"id":"13182","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"15091"},{"relation":"part_of_dissertation","id":"15093","status":"public"}]},"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Persistence and Morse theory for discrete geometric structures","OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","year":"2024","date_created":"2024-03-08T15:28:10Z","publication_status":"published","doi":"10.15479/at:ista:15094","fulldoi":"https://doi.org/10.15479/at:ista:15094","article_processing_charge":"No","supervisor":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"date_published":"2024-03-08T00:00:00Z","date_updated":"2026-10-02T11:57:31Z","doi_confirm":"1"},{"day":"31","month":"07","related_material":{"record":[{"relation":"part_of_dissertation","id":"17351","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17143"},{"relation":"part_of_dissertation","id":"17352","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17353"},{"status":"public","id":"17350","relation":"part_of_dissertation"}]},"status":"public","corr_author":"1","title":"Functional inequalities and convergence of stochastic processes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"abstract":[{"lang":"eng","text":"This thesis deals with the study of stochastic processes and their ergodicity properties. The\r\nvariety of problems encountered calls for a set of different approaches, ranging from classical to\r\nmodern ones: a special place is held by probabilistic methods based on couplings, by functional\r\ninequalities, and by the theory of gradient flows in the space of measures.\r\n\r\nThe material is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith a general presentation of some of the relevant topics. Section 1.1 is dedicated to the\r\ntheory of gradient flows in metric spaces, and introduces the first contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding with a brief description of our second contribution\r\n[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome related problems, concerning the regularization properties of the heat flow. It serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular stochastic model from quantitative genetics:\r\nthis is established via some functional inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n"}],"_id":"17336","ec_funded":1,"oa_version":"Published Version","date_published":"2024-07-31T00:00:00Z","doi_confirm":"1","date_updated":"2026-10-02T12:22:41Z","year":"2024","date_created":"2024-07-29T09:14:14Z","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:17336","doi":"10.15479/at:ista:17336","supervisor":[{"last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan"}],"article_processing_charge":"No","type":"dissertation","das_tickbox":"0","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"chicago":"Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic Processes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>.","mla":"Pedrotti, Francesco. <i>Functional Inequalities and Convergence of Stochastic Processes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>.","ista":"Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria.","apa":"Pedrotti, F. (2024). <i>Functional inequalities and convergence of stochastic processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>","short":"F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes, Institute of Science and Technology Austria, 2024.","ama":"Pedrotti F. Functional inequalities and convergence of stochastic processes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>","ieee":"F. Pedrotti, “Functional inequalities and convergence of stochastic processes,” Institute of Science and Technology Austria, 2024."},"author":[{"last_name":"Pedrotti","first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco"}],"file_date_updated":"2024-08-02T09:27:15Z","oa":1,"language":[{"iso":"eng"}],"page":"183","supplementarymaterial":"no","publisher":"Institute of Science and Technology Austria","ddc":["500","510","515","519"],"researchdata_availability":"no","file":[{"access_level":"open_access","date_created":"2024-08-02T09:23:26Z","content_type":"application/pdf","relation":"main_file","checksum":"11650bab714ef85ad43a287060850523","success":1,"file_id":"17366","creator":"fpedrott","file_name":"thesis_final.pdf","date_updated":"2024-08-02T09:23:26Z","file_size":2941599},{"file_name":"thesis_final_source.zip","date_updated":"2024-08-02T09:27:15Z","file_size":6293375,"file_id":"17367","creator":"fpedrott","relation":"source_file","checksum":"c30ba5611941226cf1bfc867c25b1e80","date_created":"2024-08-02T09:27:15Z","content_type":"application/x-zip-compressed","access_level":"closed"}],"publication_identifier":{"issn":["2663-337X"]}},{"file":[{"file_id":"15354","creator":"cchlebak","file_size":5936142,"file_name":"Murmann_Thesis_final_2024_2.pdf","date_updated":"2025-05-02T22:30:04Z","access_level":"open_access","content_type":"application/pdf","date_created":"2024-05-02T12:26:13Z","checksum":"095817a6c944954ac3f277e547031a33","embargo":"2025-05-02","relation":"main_file"},{"checksum":"43b632255372973a437ac87739cfd4db","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2024-05-02T12:37:56Z","file_size":20645510,"date_updated":"2025-05-02T22:30:04Z","file_name":"Murmann_Thesis_final_2024.zip","file_id":"15355","creator":"cchlebak","embargo_to":"open_access"}],"publication_identifier":{"issn":["2791-4585"]},"page":"54","oa":1,"language":[{"iso":"eng"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"author":[{"first_name":"Julie Stefanie","full_name":"Murmann, Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","last_name":"Murmann"}],"file_date_updated":"2025-05-02T22:30:04Z","citation":{"short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"type":"dissertation","date_created":"2024-05-02T08:31:38Z","publication_status":"published","year":"2024","supervisor":[{"last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/at:ista:15352","doi":"10.15479/at:ista:15352","date_published":"2024-05-02T00:00:00Z","date_updated":"2026-04-07T13:05:00Z","alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"_id":"15352","oa_version":"Published Version","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"corr_author":"1","day":"02","month":"05","status":"public","OA_place":"publisher","degree_awarded":"MS","has_accepted_license":"1","title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"fulldoi":"https://doi.org/10.1126/science.adi2982","doi":"10.1126/science.adi2982","scopus_import":"1","article_processing_charge":"No","year":"2024","date_created":"2024-01-14T23:00:56Z","article_type":"original","publication_status":"published","intvolume":"       383","date_updated":"2026-10-04T22:30:41Z","quality_controlled":"1","publication":"Science","pmid":1,"date_published":"2024-01-05T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"_id":"14796","oa_version":"Submitted Version","external_id":{"pmid":["38175895"],"isi":["001138156400003"]},"title":"The genetic basis of a recent transition to live-bearing in marine snails","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","OA_type":"green","day":"05","month":"01","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/"}],"record":[{"relation":"research_data","id":"14812","status":"public"},{"status":"public","relation":"research_data","id":"22905"},{"status":"public","id":"20694","relation":"dissertation_contains"}]},"isi":1,"status":"public","corr_author":"1","publication_identifier":{"eissn":["1095-9203"]},"volume":383,"acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","publisher":"American Association for the Advancement of Science","oa":1,"language":[{"iso":"eng"}],"page":"114-119","citation":{"ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>","ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>."},"author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"last_name":"Garlovsky","first_name":"Martin D.","full_name":"Garlovsky, Martin D."},{"last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","first_name":"Arka"},{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","last_name":"Shipilina"},{"last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"last_name":"Lifchitz","first_name":"Hila","full_name":"Lifchitz, Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"first_name":"Erica","full_name":"Leder, Erica","last_name":"Leder"},{"full_name":"Reeve, James","first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"issue":"6678","type":"journal_article","main_file_link":[{"url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241","open_access":"1"}]}]