[{"alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"}],"month":"01","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"oa_version":"Published Version","day":"09","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"cchlebak","file_size":41771714,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"12471","file_name":"20230109_PhD_thesis_JM_final.pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","embargo":"2023-07-09","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z"},{"embargo_to":"open_access","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_size":66983464,"file_name":"20230109_PhD_thesis_JM_final.docx","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_id":"12472","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z"}],"language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-08-31T12:26:58Z","article_processing_charge":"No","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","has_accepted_license":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"date_published":"2023-01-09T00:00:00Z","page":"201","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publication_status":"published","ddc":["610"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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"}],"file_date_updated":"2023-07-27T22:30:54Z","_id":"12470","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.15479/at:ista:12470","year":"2023","citation":{"apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>","mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","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.","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."},"date_created":"2023-01-31T15:10:53Z","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11943"},{"status":"public","relation":"part_of_dissertation","id":"11950"}]},"degree_awarded":"PhD"},{"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"_id":"12491","file_date_updated":"2024-02-08T23:30:04Z","doi":"10.15479/at:ista:12491","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"],"date_created":"2023-02-02T14:50:20Z","citation":{"apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>"},"year":"2023","related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"page":"187","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"date_published":"2023-02-02T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","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"}],"ddc":["570"],"language":[{"iso":"eng"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","article_processing_charge":"No","oa":1,"date_updated":"2024-02-08T23:30:05Z","has_accepted_license":"1","status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Zens, Bettina","first_name":"Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_created":"2023-02-07T13:07:38Z","date_updated":"2024-02-08T23:30:04Z","embargo":"2024-02-07","file_id":"12527","file_name":"PhDThesis_BettinaZens_2023_final.pdf","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"bzens"},{"file_name":"PhDThesis_BettinaZens_2023_final.docx","checksum":"8c66ed203495d6e078ed1002a866520c","file_id":"12528","date_created":"2023-02-07T13:09:05Z","date_updated":"2024-02-08T23:30:04Z","creator":"bzens","embargo_to":"open_access","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":106169509,"access_level":"closed"}],"day":"02","oa_version":"Published Version","month":"02","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]}},{"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","article_processing_charge":"No","date_updated":"2023-04-05T10:59:04Z","oa":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-8937-410X","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","first_name":"Laura"}],"file":[{"creator":"lburnett","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":23029260,"checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_name":"Burnett_Thesis_2023.docx","file_id":"12717","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z"},{"success":1,"file_name":"Burnett_Thesis_2023_pdfA.pdf","checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","creator":"lburnett","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":11959869}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","day":"10","publication_identifier":{"issn":["2663-337X"]},"month":"03","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"date_created":"2023-03-08T15:19:45Z","citation":{"apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>."},"year":"2023","degree_awarded":"PhD","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"_id":"12716","file_date_updated":"2023-03-08T15:08:46Z","doi":"10.15479/at:ista:12716","publication_status":"published","abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"ddc":["599","573"],"project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"page":"178","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"date_published":"2023-03-10T00:00:00Z","publisher":"Institute of Science and Technology Austria"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"_id":"12726","file_date_updated":"2023-11-24T11:57:46Z","doi":"10.15479/at:ista:12726","date_created":"2023-03-15T13:22:13Z","citation":{"short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>"},"year":"2023","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"status":"public","id":"10791","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7932","status":"public"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"new_edition","id":"14530"}]},"page":"260","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_published":"2023-03-23T00:00:00Z","supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"ddc":["530"],"language":[{"iso":"eng"}],"title":"Synchronization in collectively moving active matter","article_processing_charge":"No","date_updated":"2023-11-30T10:55:13Z","has_accepted_license":"1","status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"author":[{"first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"file":[{"description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_id":"12745","file_name":"Thesis_Riedl_2023.pdf","date_created":"2023-03-23T12:49:23Z","date_updated":"2023-11-24T11:57:46Z","creator":"cchlebak","content_type":"application/pdf","relation":"main_file","file_size":63734746,"access_level":"closed"},{"content_type":"application/octet-stream","access_level":"closed","file_size":339473651,"relation":"source_file","embargo_to":"open_access","creator":"cchlebak","date_updated":"2023-09-24T22:30:03Z","date_created":"2023-03-23T12:54:34Z","file_name":"Thesis_Riedl_2023_source.rar","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_id":"12746"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"23","oa_version":"None","month":"03","publication_identifier":{"issn":["2663-337X"]}},{"acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"12732","file_date_updated":"2023-03-23T16:43:14Z","doi":"10.15479/at:ista:12732","date_created":"2023-03-17T13:30:48Z","citation":{"apa":"Brighi, P. (2023). <i>Ergodicity breaking in disordered and kinetically constrained quantum many-body systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","mla":"Brighi, Pietro. <i>Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>.","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023."},"year":"2023","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"11470","status":"public"},{"id":"8308","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"11469","status":"public"},{"relation":"part_of_dissertation","id":"12750","status":"public"}]},"ec_funded":1,"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"page":"158","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"date_published":"2023-03-21T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons 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Pietro","first_name":"Pietro"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_id":"12753","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_name":"Thesis_sub_PBrighi.zip","date_updated":"2023-03-23T16:42:56Z","date_created":"2023-03-23T16:42:56Z","creator":"pbrighi","file_size":42167561,"access_level":"closed","content_type":"application/zip","relation":"source_file"},{"date_updated":"2023-03-23T16:43:14Z","date_created":"2023-03-23T16:43:14Z","checksum":"7caa153d4a5b0873a79358787d2dfe1e","file_name":"Thesis_PBrighi.pdf","file_id":"12754","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":13977000,"creator":"pbrighi"}],"oa_version":"None","day":"21","publication_identifier":{"issn":["2663-337X"]},"month":"03"},{"citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>"},"date_created":"2023-03-31T12:24:42Z","year":"2023","ec_funded":1,"degree_awarded":"PhD","related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"file_date_updated":"2023-04-20T07:02:59Z","_id":"12781","doi":"10.15479/at:ista:12781","publication_status":"published","abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"ddc":["570","572"],"project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"page":"127","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-03-23T00:00:00Z","supervisor":[{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","date_updated":"2023-08-04T08:54:51Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","day":"23","file":[{"access_level":"closed","relation":"main_file","content_type":"application/pdf","file_size":6071553,"embargo_to":"local","creator":"vkravchu","date_updated":"2023-04-19T14:33:41Z","date_created":"2023-04-19T14:33:41Z","file_id":"12852","checksum":"5ebb6345cb4119f93460c81310265a6d","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo":"2024-04-20"},{"relation":"source_file","access_level":"closed","file_size":19468766,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vkravchu","embargo_to":"local","date_created":"2023-04-19T14:33:52Z","date_updated":"2023-04-20T07:02:59Z","embargo":"2024-04-20","checksum":"c12055c48411d030d2afa51de2166221","file_id":"12853","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"month":"03","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public"},{"doi":"10.15479/at:ista:12885","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"12885","file_date_updated":"2023-05-02T07:43:18Z","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"10806","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10042","status":"public"},{"id":"12237","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9118"},{"relation":"part_of_dissertation","id":"10123","status":"public"}]},"ec_funded":1,"date_created":"2023-05-02T07:58:57Z","citation":{"apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023."},"year":"2023","page":"82","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"supervisor":[{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"}],"date_published":"2023-04-28T00:00:00Z","publisher":"Institute of Science and Technology Austria","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"ddc":["546","541"],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","article_processing_charge":"No","date_updated":"2023-08-14T07:25:26Z","oa":1,"status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"12887","checksum":"9347b0e09425f56fdcede5d3528404dc","file_name":"Thesis_Calcabrini.docx","date_updated":"2023-05-02T07:43:18Z","date_created":"2023-05-02T07:43:18Z","creator":"mcalcabr","access_level":"closed","relation":"source_file","file_size":99627036,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2023-05-02T07:42:45Z","date_updated":"2023-05-02T07:42:45Z","success":1,"file_name":"Thesis_Calcabrini_pdfa.pdf","checksum":"2d188b76621086cd384f0b9264b0a576","file_id":"12888","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":8742220,"creator":"mcalcabr"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","day":"28","month":"04","publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"author":[{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","first_name":"Mariano"}]},{"alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"first_name":"Christian","full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"month":"05","publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"day":"05","oa_version":"Published Version","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"thesis-hafner-2023may11-a2b.pdf","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","file_id":"12942","embargo":"2023-12-07","date_updated":"2023-12-08T23:30:04Z","date_created":"2023-05-11T10:43:20Z","creator":"chafner","relation":"main_file","content_type":"application/pdf","file_size":50714445,"access_level":"open_access"},{"date_created":"2023-05-11T10:43:44Z","date_updated":"2023-12-08T23:30:04Z","checksum":"a6b51334be2b81672357b1549afab40c","file_id":"12943","file_name":"thesis-release-form.pdf","relation":"source_file","access_level":"closed","file_size":265319,"content_type":"application/pdf","creator":"chafner","embargo_to":"open_access"}],"language":[{"iso":"eng"}],"oa":1,"date_updated":"2024-01-29T10:47:51Z","article_processing_charge":"No","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","has_accepted_license":"1","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd"}],"date_published":"2023-05-05T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"page":"180","publication_status":"published","ddc":["516","004","518","531"],"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."}],"file_date_updated":"2023-12-08T23:30:04Z","_id":"12897","acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.15479/at:ista:12897","year":"2023","citation":{"ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","short":"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). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>"},"date_created":"2023-05-05T10:40:14Z","ec_funded":1,"related_material":{"record":[{"id":"9817","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7117"},{"status":"public","id":"13188","relation":"dissertation_contains"}]},"degree_awarded":"PhD"},{"doi":"10.15479/at:ista:12964","file_date_updated":"2023-05-19T07:04:25Z","_id":"12964","ec_funded":1,"related_material":{"record":[{"id":"8602","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","date_created":"2023-05-15T14:52:36Z","citation":{"apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023."},"year":"2023","page":"146","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"date_published":"2023-05-17T00:00:00Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"ddc":["530"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","title":"Mechanochemical pattern formation across biological scales","date_updated":"2023-08-04T11:02:40Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","oa_version":"Published Version","day":"17","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_updated":"2023-05-19T07:04:25Z","date_created":"2023-05-17T13:39:54Z","file_id":"12988","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","file_name":"thesis_boocock.pdf","embargo":"2024-05-17","access_level":"closed","content_type":"application/pdf","relation":"main_file","file_size":40414730,"embargo_to":"open_access","creator":"dboocock"},{"file_size":34338567,"content_type":"application/zip","relation":"source_file","access_level":"closed","creator":"dboocock","date_updated":"2023-05-17T14:35:13Z","date_created":"2023-05-17T13:39:53Z","checksum":"581a2313ffeb40fe77e8a122a25a7795","file_id":"12989","file_name":"thesis_boocock.zip"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"month":"05","author":[{"orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","first_name":"Daniel R","full_name":"Boocock, Daniel R"}]},{"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11458"},{"status":"public","relation":"part_of_dissertation","id":"13053"},{"status":"public","relation":"part_of_dissertation","id":"12299"}]},"ec_funded":1,"year":"2023","citation":{"apa":"Peste, E.-A. (2023). <i>Efficiency and generalization of sparse neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>.","mla":"Peste, Elena-Alexandra. <i>Efficiency and Generalization of Sparse Neural Networks</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023."},"date_created":"2023-05-23T17:07:53Z","doi":"10.15479/at:ista:13074","_id":"13074","file_date_updated":"2023-05-24T16:12:59Z","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["000"],"abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"publication_status":"published","date_published":"2023-05-23T00:00:00Z","supervisor":[{"first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"publisher":"Institute of Science and Technology Austria","page":"147","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-08-04T10:33:27Z","oa":1,"title":"Efficiency and generalization of sparse neural networks","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","file":[{"file_id":"13087","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"date_updated":"2023-05-24T16:11:16Z","date_created":"2023-05-24T16:11:16Z","creator":"epeste","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2152072},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_size":1658293,"creator":"epeste","date_created":"2023-05-24T16:12:59Z","date_updated":"2023-05-24T16:12:59Z","file_name":"PhD_Thesis_APeste.zip","checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_id":"13088"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"23","oa_version":"Published Version","author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra"}],"type":"dissertation","status":"public","alternative_title":["ISTA Thesis"]},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_published":"2023-08-15T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"page":"230","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"ddc":["576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"publication_status":"published","doi":"10.15479/at:ista:14058","file_date_updated":"2023-08-18T10:47:55Z","_id":"14058","ec_funded":1,"degree_awarded":"PhD","related_material":{"record":[{"id":"9803","relation":"research_data","status":"public"},{"relation":"research_data","id":"12933","status":"public"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14077","status":"public"}]},"year":"2023","citation":{"apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>."},"date_created":"2023-08-15T10:20:40Z","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"month":"08","oa_version":"Published Version","day":"15","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"relation":"source_file","content_type":"application/zip","access_level":"closed","file_size":10891454,"creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z","file_name":"Thesis_latex_forpdfa.zip","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_id":"14075"},{"date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-18T10:47:55Z","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","file_id":"14079","file_name":"PhDThesis_PuixeuG.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":19856686,"creator":"gpuixeus"}],"author":[{"first_name":"Gemma","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","date_updated":"2023-12-13T12:15:36Z","oa":1,"article_processing_charge":"No","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation"},{"year":"2023","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"date_created":"2023-09-06T10:58:25Z","citation":{"mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>"},"related_material":{"record":[{"relation":"part_of_dissertation","id":"11373","status":"public"},{"id":"7387","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10934","relation":"research_data"}]},"degree_awarded":"PhD","ec_funded":1,"_id":"14280","file_date_updated":"2023-10-04T10:28:35Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:14280","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["572"],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin"}],"date_published":"2023-09-25T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"page":"156","article_processing_charge":"No","date_updated":"2024-02-21T12:35:18Z","title":"Spatiotemporal signaling during assembly of the bacterial divisome","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Radler, Philipp","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler"}],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"month":"09","file":[{"creator":"pradler","relation":"source_file","access_level":"closed","file_size":114932847,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14390","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_updated":"2023-10-04T10:28:35Z","date_created":"2023-10-04T10:11:53Z"},{"file_name":"PhD Thesis_Philipp Radler_20231004.pdf","checksum":"3253e099b7126469d941fd9419d68b4f","file_id":"14391","embargo":"2024-10-04","date_updated":"2023-10-04T10:28:35Z","date_created":"2023-10-04T10:11:21Z","embargo_to":"open_access","creator":"pradler","file_size":37838778,"access_level":"closed","content_type":"application/pdf","relation":"main_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","day":"25","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"]},{"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"page":"180","supervisor":[{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin"}],"date_published":"2023-11-10T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"14510","file_date_updated":"2023-11-23T13:10:55Z","doi":"10.15479/at:ista:14510","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"citation":{"ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>.","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>"},"date_created":"2023-11-10T09:10:06Z","year":"2023","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14591"},{"status":"public","id":"9887","relation":"part_of_dissertation"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","ec_funded":1,"status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"author":[{"first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509"}],"file":[{"creator":"ngnyliuk","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20824903,"relation":"source_file","access_level":"closed","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","file_id":"14567","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z"},{"embargo_to":"open_access","creator":"ngnyliuk","access_level":"closed","file_size":24871844,"relation":"main_file","content_type":"application/pdf","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo":"2024-11-23","date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-20T09:23:11Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"10","oa_version":"Published Version","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"month":"11","language":[{"iso":"eng"}],"title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","article_processing_charge":"No","date_updated":"2024-03-25T23:30:25Z","has_accepted_license":"1"},{"acknowledged_ssus":[{"_id":"SSU"}],"_id":"12358","file_date_updated":"2023-02-02T09:39:25Z","doi":"10.15479/at:ista:12103","date_created":"2023-01-24T10:49:46Z","citation":{"chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>"},"year":"2022","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"11736","relation":"part_of_dissertation"},{"id":"9818","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8385","status":"public"}]},"ec_funded":1,"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"page":"138","date_published":"2022-09-22T00:00:00Z","supervisor":[{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","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"}],"ddc":["000","620"],"language":[{"iso":"eng"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","article_processing_charge":"No","oa":1,"date_updated":"2024-02-28T12:57:46Z","has_accepted_license":"1","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg","full_name":"Sperl, Georg"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"relation":"main_file","content_type":"application/pdf","file_size":104497530,"access_level":"open_access","creator":"cchlebak","title":"Thesis","date_created":"2023-01-25T12:04:41Z","date_updated":"2023-02-02T09:29:57Z","description":"This is the main PDF file of the thesis. File size: 105 MB","file_name":"thesis_gsperl.pdf","checksum":"083722acbb8115e52e3b0fdec6226769","file_id":"12371"},{"description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","checksum":"511f82025e5fcb70bff4731d6896ca07","file_id":"12483","file_name":"thesis_gsperl_compressed.pdf","date_created":"2023-02-02T09:33:37Z","title":"Thesis (compressed 23MB)","date_updated":"2023-02-02T09:33:37Z","creator":"cchlebak","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":23183710},{"date_created":"2023-02-02T09:39:25Z","date_updated":"2023-02-02T09:39:25Z","file_id":"12484","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_name":"thesis-source.zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":98382247,"relation":"source_file","creator":"cchlebak"}],"oa_version":"Published Version","day":"22","month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]}},{"author":[{"full_name":"Dotter, Christoph","first_name":"Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":20457465,"creator":"cchlebak","date_updated":"2023-09-20T22:30:03Z","date_created":"2023-01-24T13:15:45Z","file_name":"220923_Thesis_CDotter_Final.pdf","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_id":"12365","embargo":"2023-09-19"},{"date_created":"2023-02-02T09:15:35Z","date_updated":"2023-09-20T22:30:03Z","file_name":"latex_source_CDotter_Thesis_2022.zip","file_id":"12482","checksum":"ad01bb20da163be6893b7af832e58419","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_size":22433512,"creator":"cchlebak","embargo_to":"open_access"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"19","oa_version":"Published Version","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_updated":"2023-11-16T13:10:22Z","oa":1,"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570"],"abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence."}],"project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205","call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia"}],"date_published":"2022-09-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"page":"152","year":"2022","date_created":"2023-01-24T13:09:57Z","citation":{"ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>"},"related_material":{"record":[{"status":"public","id":"3","relation":"part_of_dissertation"},{"status":"public","id":"11160","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","ec_funded":1,"_id":"12364","file_date_updated":"2023-09-20T22:30:03Z","doi":"10.15479/at:ista:12094"},{"doi":"10.15479/at:ista:12132","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"_id":"12366","file_date_updated":"2023-01-26T23:30:44Z","degree_awarded":"PhD","ec_funded":1,"date_created":"2023-01-25T09:17:02Z","citation":{"apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>."},"year":"2022","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"page":"168","date_published":"2022-09-26T00:00:00Z","supervisor":[{"orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"publisher":"Institute of Science and Technology Austria","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"ddc":["530"],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","title":"Controllable states of superconducting Qubit ensembles","article_processing_charge":"No","oa":1,"date_updated":"2024-08-07T07:11:56Z","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"Final_Thesis_ES_Redchenko.pdf","checksum":"39eabb1e006b41335f17f3b29af09648","file_id":"12367","embargo":"2022-12-28","date_updated":"2023-01-26T23:30:44Z","date_created":"2023-01-25T09:41:49Z","creator":"cchlebak","relation":"main_file","file_size":56076868,"access_level":"open_access","content_type":"application/pdf"}],"day":"26","oa_version":"Published Version","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"month":"09","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"}]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-025-1 "]},"day":"29","oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":14581024,"creator":"cchlebak","date_updated":"2023-01-25T10:52:46Z","date_created":"2023-01-25T10:52:46Z","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","checksum":"e54a3e69b83ebf166544164afd25608e","file_id":"12369","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","orcid":"0000-0001-5809-9566","first_name":"Feyza N","full_name":"Arslan, Feyza N"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","date_updated":"2023-08-08T13:14:10Z","oa":1,"article_processing_charge":"No","title":"Remodeling of E-cadherin-mediated contacts via cortical  flows","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"date_published":"2022-09-29T00:00:00Z","page":"113","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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"}],"publication_status":"published","doi":"10.15479/at:ista:12153","file_date_updated":"2023-01-25T10:52:46Z","_id":"12368","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"ec_funded":1,"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"9350","status":"public"}]},"year":"2022","citation":{"apa":"Arslan, F. N. (2022). <i>Remodeling of E-cadherin-mediated contacts via cortical  flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>.","mla":"Arslan, Feyza N. <i>Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>"},"date_created":"2023-01-25T10:43:24Z"},{"supervisor":[{"full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-11-11T00:00:00Z","publisher":"Institute of Science and Technology Austria","page":"142","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"publication_status":"published","doi":"10.15479/at:ista:12378","_id":"12378","file_date_updated":"2023-04-12T22:30:03Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"related_material":{"record":[{"id":"12244","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","ec_funded":1,"year":"2022","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>"},"date_created":"2023-01-25T14:27:43Z","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"month":"11","publication_identifier":{"issn":["2663-337X"]},"file":[{"checksum":"8cd3ddfe9b53381dcf086023d8d8893a","file_name":"Gloria_Colombo_Thesis.docx","file_id":"12379","date_updated":"2023-04-12T22:30:03Z","date_created":"2023-01-25T14:31:32Z","embargo_to":"open_access","creator":"cchlebak","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23890382},{"date_created":"2023-01-25T14:31:36Z","date_updated":"2023-04-12T22:30:03Z","embargo":"2023-04-11","file_name":"Gloria_Colombo_Thesis.pdf","checksum":"8af4319c18b516e8758e9a6cb02b103b","file_id":"12380","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":13802421,"creator":"cchlebak"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"11","author":[{"full_name":"Colombo, Gloria","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-08-04T09:40:37Z","oa":1,"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes"},{"publication_status":"published","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"}],"ddc":["500"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"page":"196","publisher":"Institute of Science and Technology Austria","date_published":"2022-12-15T00:00:00Z","supervisor":[{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert"}],"date_created":"2023-01-26T10:00:42Z","citation":{"apa":"Brooks, M. (2022). <i>Translation-invariant quantum systems with effectively broken symmetry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","mla":"Brooks, Morris. <i>Translation-Invariant Quantum Systems with Effectively Broken Symmetry</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022."},"year":"2022","ec_funded":1,"related_material":{"record":[{"id":"9005","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","file_date_updated":"2023-01-26T10:02:42Z","_id":"12390","doi":"10.15479/at:ista:12390","author":[{"orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","first_name":"Morris","full_name":"Brooks, Morris"}],"oa_version":"Published Version","day":"15","file":[{"creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_size":3095225,"access_level":"open_access","success":1,"file_id":"12391","checksum":"b31460e937f33b557abb40ebef02b567","file_name":"Brooks_Thesis.pdf","date_created":"2023-01-26T10:02:34Z","date_updated":"2023-01-26T10:02:34Z"},{"checksum":"9751869fa5e7981588ad4228f4fd4bd6","file_name":"Brooks_Thesis.tex","file_id":"12392","date_created":"2023-01-26T10:02:42Z","date_updated":"2023-01-26T10:02:42Z","creator":"cchlebak","content_type":"application/octet-stream","access_level":"closed","file_size":809842,"relation":"source_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"month":"12","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","title":"Translation-invariant quantum systems with effectively broken symmetry","date_updated":"2023-08-07T13:32:09Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"title":"Role of microenvironment heterogeneity in cancer cell invasion","oa":1,"date_updated":"2024-09-10T12:04:26Z","article_processing_charge":"No","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"full_name":"Tasciyan, Saren","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","orcid":"0000-0003-1671-393X"}],"day":"22","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","file_id":"12402","embargo":"2023-12-20","date_updated":"2023-12-21T23:30:03Z","date_created":"2023-01-26T11:58:14Z","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_size":42059787,"access_level":"open_access"},{"content_type":"application/x-zip-compressed","file_size":261256696,"access_level":"closed","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","date_updated":"2023-12-21T23:30:03Z","date_created":"2023-01-26T12:00:10Z","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","file_id":"12403"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12","file_date_updated":"2023-12-21T23:30:03Z","_id":"12401","doi":"10.15479/at:ista:12401","citation":{"ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","mla":"Tasciyan, Saren. <i>Role of Microenvironment Heterogeneity in Cancer Cell Invasion</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>.","apa":"Tasciyan, S. (2022). <i>Role of microenvironment heterogeneity in cancer cell invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>"},"date_created":"2023-01-26T11:55:16Z","year":"2022","degree_awarded":"PhD","related_material":{"record":[{"id":"679","relation":"part_of_dissertation","status":"public"},{"id":"10703","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7885"},{"status":"public","id":"9429","relation":"part_of_dissertation"}]},"page":"105","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"}],"date_published":"2022-12-22T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening."}],"ddc":["610"]}]