[{"date_published":"2023-11-21T00:00:00Z","citation":{"short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria."},"page":"228","article_processing_charge":"No","has_accepted_license":"1","day":"21","file":[{"success":1,"checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","date_updated":"2023-11-29T09:09:31Z","date_created":"2023-11-29T09:09:31Z","file_id":"14626","relation":"main_file","creator":"amarvegg","content_type":"application/pdf","file_size":2881100,"access_level":"open_access","file_name":"thesis_Marveggio.pdf"},{"content_type":"application/zip","file_size":10189696,"creator":"amarvegg","file_name":"Thesis_Marveggio.zip","access_level":"closed","date_updated":"2024-03-20T12:28:32Z","date_created":"2023-11-29T09:10:19Z","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","relation":"source_file","file_id":"14627"}],"oa_version":"Published Version","_id":"14587","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","ddc":["515"],"abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:14587","language":[{"iso":"eng"}],"supervisor":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"publication_identifier":{"issn":["2663 - 337X"]},"month":"11","related_material":{"record":[{"id":"11842","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14597"}]},"author":[{"full_name":"Marveggio, Alice","last_name":"Marveggio","first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425"}],"date_updated":"2024-03-22T13:21:28Z","date_created":"2023-11-21T11:41:05Z","year":"2023","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2024-03-20T12:28:32Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"citation":{"apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491."},"page":"187","date_published":"2023-02-02T00:00:00Z","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"day":"02","article_processing_charge":"No","has_accepted_license":"1","_id":"12491","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"status":"public","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","file":[{"content_type":"application/pdf","file_size":23082464,"creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.pdf","access_level":"open_access","date_created":"2023-02-07T13:07:38Z","date_updated":"2024-02-08T23:30:04Z","checksum":"069d87f025e0799bf9e3c375664264f2","relation":"main_file","file_id":"12527","embargo":"2024-02-07"},{"relation":"source_file","file_id":"12528","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z","checksum":"8c66ed203495d6e078ed1002a866520c","embargo_to":"open_access","file_name":"PhDThesis_BettinaZens_2023_final.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":106169509,"creator":"bzens"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"oa":1,"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.15479/at:ista:12491","supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8586"}]},"date_updated":"2024-03-25T23:30:05Z","date_created":"2023-02-02T14:50:20Z","file_date_updated":"2024-02-08T23:30:04Z"},{"abstract":[{"lang":"eng","text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes."}],"alternative_title":["ISTA Master's Thesis"],"type":"dissertation","file":[{"content_type":"application/x-zip-compressed","file_size":15501411,"creator":"cchlebak","access_level":"closed","embargo_to":"open_access","file_name":"documents-export-2023-08-24.zip","checksum":"453caf851d75c3478c10ed09bd242a91","date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:02:49Z","relation":"source_file","file_id":"14227"},{"file_name":"thesis_pdf_a.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":6854783,"file_id":"14228","embargo":"2024-02-25","relation":"main_file","date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:03:42Z","checksum":"7349d29963d6695e555e171748648d9a"}],"oa_version":"Published Version","ddc":["500"],"status":"public","title":"Generalizing medial axes with homology switches","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14226","day":"24","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-08-24T00:00:00Z","page":"43","citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226"},"file_date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:01:18Z","date_updated":"2024-02-26T23:30:04Z","author":[{"orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"year":"2023","month":"08","publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","supervisor":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14226","oa":1},{"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","ddc":["610"],"status":"public","_id":"12470","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"content_type":"application/pdf","file_size":41771714,"creator":"cchlebak","access_level":"open_access","file_name":"20230109_PhD_thesis_JM_final.pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","date_created":"2023-01-31T15:11:42Z","date_updated":"2023-07-27T22:30:54Z","relation":"main_file","embargo":"2023-07-09","file_id":"12471"},{"file_id":"12472","relation":"source_file","checksum":"0bebbdee0773443959e1f6ab8caf281f","date_created":"2023-01-31T15:11:51Z","date_updated":"2023-07-10T22:30:04Z","access_level":"closed","file_name":"20230109_PhD_thesis_JM_final.docx","embargo_to":"open_access","creator":"cchlebak","file_size":66983464,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"page":"201","citation":{"apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470."},"date_published":"2023-01-09T00:00:00Z","day":"09","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"year":"2023","date_updated":"2023-08-31T12:26:58Z","date_created":"2023-01-31T15:10:53Z","author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","last_name":"Michalska"}],"related_material":{"record":[{"id":"11943","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-07-27T22:30:54Z","ec_funded":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12470","month":"01","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]}},{"abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"alternative_title":["ISTA Master's Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_created":"2023-02-09T08:03:32Z","date_updated":"2024-02-09T23:30:03Z","embargo":"2024-02-08","file_id":"12532","relation":"main_file","creator":"cchlebak","file_size":8369317,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf"},{"embargo_to":"open_access","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":11204408,"creator":"cchlebak","relation":"source_file","file_id":"12535","date_updated":"2024-02-09T23:30:03Z","date_created":"2023-02-10T09:32:06Z","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f"}],"title":"Panoramic functional gradients across the mouse retina","status":"public","ddc":["570"],"_id":"12531","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"08","date_published":"2023-02-08T00:00:00Z","page":"46","citation":{"ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531."},"file_date_updated":"2024-02-09T23:30:03Z","date_created":"2023-02-09T07:45:05Z","date_updated":"2024-02-09T23:30:04Z","author":[{"last_name":"Kirillova","first_name":"Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","full_name":"Kirillova, Kseniia"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","publication_identifier":{"issn":["2791-4585"]},"month":"02","language":[{"iso":"eng"}],"degree_awarded":"MS","supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:12531","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"}},{"doi":"10.15479/at:ista:12800","degree_awarded":"MS","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa":1,"month":"04","publication_identifier":{"issn":["2791-4585"]},"author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth","first_name":"Mara","full_name":"Julseth, Mara"}],"date_updated":"2023-06-02T22:30:05Z","date_created":"2023-04-04T18:57:11Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-06-02T22:30:04Z","date_published":"2023-04-05T00:00:00Z","citation":{"ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800."},"page":"21","day":"05","article_processing_charge":"No","has_accepted_license":"1","file":[{"checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T06:09:40Z","relation":"supplementary_material","file_id":"12805","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":52795,"creator":"mjulseth","access_level":"closed","embargo_to":"open_access","file_name":"Dispersaldata.xlsx"},{"relation":"supplementary_material","file_id":"12806","embargo":"2023-06-01","checksum":"5a13b6d204371572e249f03795bc0d04","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T06:11:27Z","access_level":"open_access","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","content_type":"application/vnd.wolfram.nb","file_size":787239,"creator":"mjulseth"},{"embargo_to":"open_access","file_name":"ThesisMaraJulseth_04_23.docx","access_level":"closed","file_size":1061763,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mjulseth","relation":"source_file","file_id":"12812","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:12Z","checksum":"c3ec842839ed1e66bf2618ae33047df8"},{"access_level":"open_access","file_name":"ThesisMaraJulseth_04_23.pdf","file_size":1741364,"content_type":"application/pdf","creator":"mjulseth","relation":"main_file","embargo":"2023-06-01","file_id":"12813","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:37Z"}],"oa_version":"Published Version","_id":"12800","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","ddc":["576"],"status":"public","abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20824903,"creator":"ngnyliuk","access_level":"closed","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","date_created":"2023-11-20T09:18:51Z","date_updated":"2023-11-20T09:18:51Z","relation":"source_file","file_id":"14567"},{"date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-20T09:23:11Z","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","embargo":"2024-11-23","relation":"main_file","creator":"ngnyliuk","file_size":24871844,"content_type":"application/pdf","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","access_level":"closed"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","_id":"14510","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"10","has_accepted_license":"1","article_processing_charge":"No","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"date_published":"2023-11-10T00:00:00Z","page":"180","citation":{"chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510"},"file_date_updated":"2023-11-23T13:10:55Z","ec_funded":1,"date_created":"2023-11-10T09:10:06Z","date_updated":"2024-03-28T23:30:46Z","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14591"},{"status":"public","relation":"part_of_dissertation","id":"9887"},{"relation":"part_of_dissertation","status":"public","id":"8139"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","year":"2023","month":"11","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14510","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"page":"180","citation":{"ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897."},"date_published":"2023-05-05T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"05","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","ddc":["516","004","518","531"],"status":"public","_id":"12897","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"embargo":"2023-12-07","file_id":"12942","relation":"main_file","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","date_created":"2023-05-11T10:43:20Z","date_updated":"2023-12-08T23:30:04Z","access_level":"open_access","file_name":"thesis-hafner-2023may11-a2b.pdf","creator":"chafner","content_type":"application/pdf","file_size":50714445},{"content_type":"application/pdf","file_size":265319,"creator":"chafner","embargo_to":"open_access","file_name":"thesis-release-form.pdf","access_level":"closed","date_created":"2023-05-11T10:43:44Z","date_updated":"2023-12-08T23:30:04Z","checksum":"a6b51334be2b81672357b1549afab40c","relation":"source_file","file_id":"12943"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.15479/at:ista:12897","publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"month":"05","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","date_updated":"2024-01-29T10:47:51Z","date_created":"2023-05-05T10:40:14Z","related_material":{"record":[{"id":"9817","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7117"},{"relation":"dissertation_contains","status":"public","id":"13188"}]},"author":[{"first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"}],"ec_funded":1,"file_date_updated":"2023-12-08T23:30:04Z"},{"status":"public","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","ddc":["512"],"_id":"12072","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"12073","relation":"main_file","date_updated":"2022-09-08T21:50:34Z","date_created":"2022-09-08T21:50:34Z","success":1,"checksum":"bf073344320e05d92c224786cec2e92d","file_name":"Thesis_final_draft.pdf","access_level":"open_access","creator":"ashute","file_size":1907386,"content_type":"application/pdf"},{"checksum":"b054ac6baa09f70e8235403a4abbed80","date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-08T21:50:42Z","relation":"source_file","file_id":"12074","file_size":495393,"content_type":"application/octet-stream","creator":"ashute","access_level":"closed","file_name":"athesis.tex"},{"file_size":944534,"content_type":"application/x-zip-compressed","creator":"ashute","access_level":"closed","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","checksum":"0a31e905f1cff5eb8110978cc90e1e79","date_created":"2022-09-09T12:05:00Z","date_updated":"2022-09-12T11:24:21Z","relation":"source_file","file_id":"12078"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. ","lang":"eng"}],"page":"208","citation":{"ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072."},"date_published":"2022-09-08T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"08","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"publication_status":"published","acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","year":"2022","date_created":"2022-09-08T21:53:03Z","date_updated":"2023-02-21T16:37:35Z","related_material":{"record":[{"id":"12076","relation":"part_of_dissertation","status":"public"},{"id":"12077","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Shute, Alec L","first_name":"Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810"}],"ec_funded":1,"file_date_updated":"2022-09-12T11:24:21Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"}],"doi":"10.15479/at:ista:12072","publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"month":"09"},{"day":"11","has_accepted_license":"1","article_processing_charge":"No","page":"170","citation":{"chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.","apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777"},"date_published":"2022-08-11T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"title":"High-dimensional expansion and crossing numbers of simplicial complexes","ddc":["500","516","514"],"status":"public","_id":"11777","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","file_name":"flags.py","access_level":"open_access","file_size":16828,"content_type":"text/x-python","creator":"pwild","relation":"supplementary_material","file_id":"11780","date_updated":"2022-08-10T15:34:04Z","date_created":"2022-08-10T15:34:04Z","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4"},{"file_id":"11781","relation":"supplementary_material","date_updated":"2022-08-10T15:34:10Z","date_created":"2022-08-10T15:34:10Z","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","description":"Code for proof of Lemma 8.20 in Thesis","file_name":"lowerbound.cpp","access_level":"open_access","creator":"pwild","content_type":"text/x-c++src","file_size":12226},{"access_level":"open_access","description":"Code for proof of Proposition 7.9 in Thesis","file_name":"upperbound.py","file_size":3240,"content_type":"text/x-python","creator":"pwild","relation":"supplementary_material","file_id":"11782","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","date_created":"2022-08-10T15:34:17Z","date_updated":"2022-08-10T15:34:17Z"},{"creator":"pwild","file_size":5086282,"content_type":"application/pdf","access_level":"open_access","file_name":"finalthesisPascalWildPDFA.pdf","checksum":"4e96575b10cbe4e0d0db2045b2847774","date_updated":"2022-08-11T16:08:33Z","date_created":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","file_id":"11809","relation":"main_file"},{"date_updated":"2022-08-11T16:09:19Z","date_created":"2022-08-11T16:09:19Z","checksum":"92d94842a1fb6dca5808448137573b2e","file_id":"11810","relation":"source_file","creator":"pwild","content_type":"application/zip","file_size":18150068,"file_name":"ThesisSubmission.zip","access_level":"closed"}],"oa_version":"Published Version","month":"08","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"oa":1,"supervisor":[{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11777","file_date_updated":"2022-08-11T16:09:19Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"publisher":"Institute of Science and Technology","year":"2022","date_created":"2022-08-10T15:51:19Z","date_updated":"2023-06-22T09:56:36Z","author":[{"first_name":"Pascal","last_name":"Wild","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","full_name":"Wild, Pascal"}]},{"file_date_updated":"2022-04-07T08:11:51Z","date_updated":"2023-06-23T06:26:41Z","date_created":"2022-04-07T08:19:54Z","author":[{"last_name":"Matejovicova","first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","full_name":"Matejovicova, Lenka"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"year":"2022","month":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11128","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"creator":"cchlebak","file_size":11906472,"content_type":"application/pdf","file_name":"LenkaPhD_Official_PDFA.pdf","access_level":"open_access","date_updated":"2022-04-07T08:11:34Z","date_created":"2022-04-07T08:11:34Z","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","file_id":"11129","relation":"main_file"},{"access_level":"closed","file_name":"LenkaPhD Official_source.zip","content_type":"application/x-zip-compressed","file_size":23036766,"creator":"cchlebak","relation":"source_file","file_id":"11130","checksum":"99d67040432fd07a225643a212ee8588","date_created":"2022-04-07T08:11:51Z","date_updated":"2022-04-07T08:11:51Z"}],"oa_version":"Published Version","ddc":["576","582"],"title":"Genetic basis of flower colour as a model for adaptive evolution","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11128","day":"06","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-04-06T00:00:00Z","page":"112","citation":{"ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022."}},{"file_date_updated":"2022-08-25T09:33:31Z","author":[{"full_name":"Schulz, Rouven","first_name":"Rouven","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11995"}]},"date_created":"2022-08-23T11:33:11Z","date_updated":"2023-08-03T13:02:26Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publisher":"Institute of Science and Technology Austria","month":"08","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11945","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","creator":"rschulz","content_type":"application/pdf","file_size":28079331,"file_id":"11970","relation":"main_file","success":1,"checksum":"61b1b666a210ff7cdd0e95ea75207a13","date_updated":"2022-08-25T08:59:57Z","date_created":"2022-08-25T08:59:57Z"},{"file_size":27226963,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rschulz","file_name":"Thesis_Rouven_Schulz_2022_final.docx","access_level":"closed","date_created":"2022-08-25T09:00:11Z","date_updated":"2022-08-25T09:33:31Z","checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","relation":"source_file","file_id":"11971"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11945","ddc":["570"],"title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","status":"public","day":"23","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-08-23T00:00:00Z","citation":{"short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria."},"page":"133"},{"file_date_updated":"2023-01-26T10:02:42Z","ec_funded":1,"date_created":"2023-01-26T10:00:42Z","date_updated":"2023-08-07T13:32:09Z","author":[{"full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","first_name":"Morris"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9005"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"year":"2022","month":"12","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12390","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"abstract":[{"lang":"eng","text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"success":1,"checksum":"b31460e937f33b557abb40ebef02b567","date_created":"2023-01-26T10:02:34Z","date_updated":"2023-01-26T10:02:34Z","file_id":"12391","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":3095225,"access_level":"open_access","file_name":"Brooks_Thesis.pdf"},{"relation":"source_file","file_id":"12392","date_updated":"2023-01-26T10:02:42Z","date_created":"2023-01-26T10:02:42Z","checksum":"9751869fa5e7981588ad4228f4fd4bd6","file_name":"Brooks_Thesis.tex","access_level":"closed","content_type":"application/octet-stream","file_size":809842,"creator":"cchlebak"}],"oa_version":"Published Version","status":"public","ddc":["500"],"title":"Translation-invariant quantum systems with effectively broken symmetry","_id":"12390","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"15","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-12-15T00:00:00Z","page":"196","citation":{"ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390."}},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"year":"2022","date_created":"2023-01-25T10:43:24Z","date_updated":"2023-08-08T13:14:10Z","author":[{"full_name":"Arslan, Feyza N","first_name":"Feyza N","last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566"}],"related_material":{"record":[{"id":"9350","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2023-01-25T10:52:46Z","ec_funded":1,"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12153","month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-025-1 "]},"ddc":["570"],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows","status":"public","_id":"12368","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"e54a3e69b83ebf166544164afd25608e","success":1,"date_created":"2023-01-25T10:52:46Z","date_updated":"2023-01-25T10:52:46Z","relation":"main_file","file_id":"12369","content_type":"application/pdf","file_size":14581024,"creator":"cchlebak","access_level":"open_access","file_name":"THESIS_FINAL_FArslan_pdfa.pdf"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"page":"113","citation":{"mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153"},"date_published":"2022-09-29T00:00:00Z","day":"29","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2022-05-12T00:00:00Z","citation":{"short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria."},"page":"124","day":"12","has_accepted_license":"1","article_processing_charge":"No","keyword":["neural networks","verification","machine learning"],"oa_version":"Published Version","file":[{"file_name":"src.zip","access_level":"closed","file_size":13210143,"content_type":"application/zip","creator":"mlechner","relation":"source_file","file_id":"11378","date_created":"2022-05-13T12:33:26Z","date_updated":"2022-05-13T12:49:00Z","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645"},{"content_type":"application/pdf","file_size":2732536,"creator":"mlechner","access_level":"open_access","file_name":"thesis_main-a2.pdf","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","date_created":"2022-05-16T08:02:28Z","date_updated":"2022-05-17T15:19:39Z","relation":"main_file","file_id":"11382"}],"_id":"11362","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Learning verifiable representations","ddc":["004"],"status":"public","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:11362","supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"month":"05","publication_identifier":{"isbn":["978-3-99078-017-6"]},"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10665","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10667"},{"status":"public","relation":"part_of_dissertation","id":"11366"},{"id":"7808","status":"public","relation":"part_of_dissertation"},{"id":"10666","status":"public","relation":"part_of_dissertation"}]},"date_created":"2022-05-12T07:14:01Z","date_updated":"2023-08-17T06:58:38Z","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2022-05-17T15:19:39Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/"},{"abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_size":1830973,"content_type":"application/pdf","creator":"kmysliwy","access_level":"open_access","file_name":"thes1_no_isbn_2_1b.pdf","checksum":"7970714a20a6052f75fb27a6c3e9976e","success":1,"date_created":"2022-07-05T08:12:56Z","date_updated":"2022-07-05T08:12:56Z","relation":"main_file","file_id":"11486"},{"date_updated":"2022-07-05T08:17:12Z","date_created":"2022-07-05T08:15:52Z","checksum":"647a2011fdf56277096c9350fefe1097","file_id":"11487","relation":"source_file","creator":"kmysliwy","file_size":5831060,"content_type":"application/zip","file_name":"thes_source.zip","access_level":"closed"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"11473","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","ddc":["515","539"],"status":"public","day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-07-01T00:00:00Z","citation":{"short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria."},"page":"138","file_date_updated":"2022-07-05T08:17:12Z","ec_funded":1,"author":[{"full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10564"},{"relation":"part_of_dissertation","status":"public","id":"8705"}]},"date_updated":"2023-09-07T13:43:52Z","date_created":"2022-06-30T12:15:03Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publisher":"Institute of Science and Technology Austria","month":"07","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11473","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}]},{"publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"month":"03","language":[{"iso":"eng"}],"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10799","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"ec_funded":1,"file_date_updated":"2022-03-10T12:11:48Z","date_updated":"2023-10-17T12:31:54Z","date_created":"2022-02-28T13:03:49Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8724"},{"id":"10803","relation":"part_of_dissertation","status":"public"},{"id":"10802","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6590"}]},"author":[{"first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publication_status":"published","year":"2022","article_processing_charge":"No","has_accepted_license":"1","day":"08","keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"date_published":"2022-03-08T00:00:00Z","page":"176","citation":{"chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799.","mla":"Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022.","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","apa":"Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799"},"abstract":[{"text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"access_level":"open_access","file_name":"thesis.pdf","creator":"nkonstan","file_size":4204905,"content_type":"application/pdf","file_id":"10823","relation":"main_file","success":1,"checksum":"626bc523ae8822d20e635d0e2d95182e","date_updated":"2022-03-06T11:42:54Z","date_created":"2022-03-06T11:42:54Z"},{"file_name":"thesis.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":22841103,"creator":"nkonstan","relation":"source_file","file_id":"10824","date_created":"2022-03-06T11:42:57Z","date_updated":"2022-03-10T12:11:48Z","checksum":"e2ca2b88350ac8ea1515b948885cbcb1"}],"oa_version":"Published Version","status":"public","ddc":["000"],"title":"Robustness and fairness in machine learning","_id":"10799","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2022-07-20T00:00:00Z","page":"248","citation":{"chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626"},"has_accepted_license":"1","article_processing_charge":"No","day":"20","oa_version":"Published Version","file":[{"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","date_updated":"2022-07-25T09:08:47Z","date_created":"2022-07-25T09:08:47Z","file_id":"11645","relation":"main_file","creator":"mgallei","file_size":9730864,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Gallei.pdf"},{"file_id":"11646","relation":"source_file","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","date_created":"2022-07-25T09:09:09Z","date_updated":"2022-07-25T09:39:58Z","access_level":"closed","file_name":"Thesis_Gallei_source.docx","creator":"mgallei","file_size":19560720,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"access_level":"closed","description":"This is the print version of the thesis including the full appendix","file_name":"Thesis_Gallei_to_print.pdf","content_type":"application/pdf","file_size":24542837,"creator":"mgallei","relation":"source_file","file_id":"11647","checksum":"3994f7f20058941b5bb8a16886b21e71","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:32Z"},{"file_id":"11650","relation":"main_file","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_created":"2022-07-25T11:48:45Z","date_updated":"2022-07-25T11:48:45Z","access_level":"open_access","file_name":"Thesis_Gallei_Appendix.pdf","creator":"mgallei","file_size":15435966,"content_type":"application/pdf"}],"status":"public","ddc":["575"],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","_id":"11626","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:11626","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"oa":1,"publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"month":"07","date_updated":"2023-11-07T08:20:13Z","date_created":"2022-07-20T11:21:53Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8931"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7142"},{"id":"7465","status":"public","relation":"part_of_dissertation"},{"id":"8138","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6260"},{"id":"10411","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2022","ec_funded":1,"file_date_updated":"2022-07-25T11:48:45Z"},{"month":"09","publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12103","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2023-02-02T09:39:25Z","ec_funded":1,"date_updated":"2024-02-28T12:57:46Z","date_created":"2023-01-24T10:49:46Z","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11736"},{"id":"9818","status":"public","relation":"part_of_dissertation"},{"id":"8385","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"year":"2022","day":"22","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-09-22T00:00:00Z","page":"138","citation":{"ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103."},"abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"083722acbb8115e52e3b0fdec6226769","date_updated":"2023-02-02T09:29:57Z","date_created":"2023-01-25T12:04:41Z","title":"Thesis","file_id":"12371","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":104497530,"access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB","file_name":"thesis_gsperl.pdf"},{"creator":"cchlebak","content_type":"application/pdf","file_size":23183710,"access_level":"open_access","file_name":"thesis_gsperl_compressed.pdf","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","checksum":"511f82025e5fcb70bff4731d6896ca07","date_created":"2023-02-02T09:33:37Z","date_updated":"2023-02-02T09:33:37Z","file_id":"12483","title":"Thesis (compressed 23MB)","relation":"main_file"},{"file_id":"12484","relation":"source_file","date_updated":"2023-02-02T09:39:25Z","date_created":"2023-02-02T09:39:25Z","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_name":"thesis-source.zip","access_level":"open_access","creator":"cchlebak","file_size":98382247,"content_type":"application/x-zip-compressed"}],"oa_version":"Published Version","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","status":"public","ddc":["000","620"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12358"},{"abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_id":"10785","date_updated":"2022-02-22T07:20:12Z","date_created":"2022-02-21T13:58:16Z","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_name":"Rzadkowski_thesis_final_source.zip","access_level":"closed","content_type":"application/zip","file_size":17668233,"creator":"wrzadkow"},{"content_type":"application/pdf","file_size":13307331,"creator":"wrzadkow","access_level":"open_access","file_name":"Rzadkowski_thesis_final.pdf","checksum":"22d2d7af37ca31f6b1730c26cac7bced","success":1,"date_updated":"2022-02-21T14:02:54Z","date_created":"2022-02-21T14:02:54Z","relation":"main_file","file_id":"10786"}],"oa_version":"Published Version","_id":"10759","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Analytic and machine learning approaches to composite quantum impurities","status":"public","ddc":["530"],"day":"21","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-02-21T00:00:00Z","citation":{"apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759."},"page":"120","file_date_updated":"2022-02-22T07:20:12Z","ec_funded":1,"author":[{"first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech"}],"related_material":{"record":[{"id":"10762","status":"public","relation":"part_of_dissertation"},{"id":"8644","status":"public","relation":"part_of_dissertation"},{"id":"7956","status":"public","relation":"part_of_dissertation"},{"id":"415","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2024-02-28T13:01:59Z","date_created":"2022-02-16T13:27:37Z","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"month":"02","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:10759","supervisor":[{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}]}]