[{"year":"2022","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10077"},{"status":"public","relation":"part_of_dissertation","id":"6194"}]},"author":[{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin"}],"date_updated":"2023-09-05T12:02:14Z","date_created":"2022-08-19T08:52:30Z","ec_funded":1,"file_date_updated":"2023-06-20T22:30:04Z","oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.15479/at:ista:11932","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"08","_id":"11932","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"On the encoding, transfer, and consolidation of spatial memories","ddc":["573"],"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"11935","date_created":"2022-08-19T16:31:34Z","date_updated":"2023-06-20T22:30:04Z","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","embargo_to":"open_access","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","access_level":"closed","content_type":"application/zip","file_size":13515457,"creator":"mnardin"},{"embargo":"2023-06-19","file_id":"11941","relation":"main_file","checksum":"0ec94035ea35a47a9f589ed168e60b48","date_updated":"2023-06-20T22:30:04Z","date_created":"2022-08-22T09:43:50Z","access_level":"open_access","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","creator":"mnardin","file_size":9906458,"content_type":"application/pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"citation":{"apa":"Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","mla":"Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932."},"page":"136","date_published":"2022-08-19T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"19"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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.","lang":"eng"}],"status":"public","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","ddc":["570"],"_id":"12378","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Gloria_Colombo_Thesis.docx","embargo_to":"open_access","creator":"cchlebak","file_size":23890382,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12379","relation":"source_file","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","date_updated":"2023-04-12T22:30:03Z","date_created":"2023-01-25T14:31:32Z"},{"creator":"cchlebak","content_type":"application/pdf","file_size":13802421,"access_level":"open_access","file_name":"Gloria_Colombo_Thesis.pdf","checksum":"8af4319c18b516e8758e9a6cb02b103b","date_created":"2023-01-25T14:31:36Z","date_updated":"2023-04-12T22:30:03Z","embargo":"2023-04-11","file_id":"12380","relation":"main_file"}],"article_processing_charge":"No","has_accepted_license":"1","day":"11","page":"142","citation":{"ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378."},"date_published":"2022-11-11T00:00:00Z","ec_funded":1,"file_date_updated":"2023-04-12T22:30:03Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publication_status":"published","year":"2022","date_created":"2023-01-25T14:27:43Z","date_updated":"2023-08-04T09:40:37Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12244"}]},"author":[{"full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","first_name":"Gloria","last_name":"Colombo"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra"}],"doi":"10.15479/at:ista:12378"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"ddc":["576"],"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","status":"public","_id":"11388","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"sbelohla","file_size":8247240,"content_type":"application/pdf","access_level":"open_access","file_name":"thesis_sb_final_pdfa.pdf","checksum":"4d75e6a619df7e8a9d6e840aee182380","date_created":"2022-05-19T13:03:13Z","date_updated":"2023-05-20T22:30:03Z","file_id":"11398","embargo":"2023-05-19","relation":"main_file"},{"file_name":"thesis_sb_final.zip","embargo_to":"open_access","access_level":"closed","creator":"sbelohla","content_type":"application/x-zip-compressed","file_size":7094,"file_id":"11399","relation":"source_file","date_created":"2022-05-19T13:07:47Z","date_updated":"2023-05-20T22:30:03Z","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0"}],"oa_version":"Published Version","day":"18","has_accepted_license":"1","article_processing_charge":"No","page":"98","citation":{"ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388."},"date_published":"2022-05-18T00:00:00Z","file_date_updated":"2023-05-20T22:30:03Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2022","date_created":"2022-05-16T16:49:18Z","date_updated":"2023-08-29T06:41:51Z","author":[{"full_name":"Belohlavy, Stefanie","first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6713"}]},"month":"05","publication_identifier":{"isbn":["978-3-99078-018-3"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11388"},{"day":"22","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-12-22T00:00:00Z","citation":{"chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","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.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401"},"page":"105","abstract":[{"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.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"embargo":"2023-12-20","file_id":"12402","relation":"main_file","date_created":"2023-01-26T11:58:14Z","date_updated":"2023-12-21T23:30:03Z","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":42059787},{"relation":"source_file","file_id":"12403","date_updated":"2023-12-21T23:30:03Z","date_created":"2023-01-26T12:00:10Z","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","embargo_to":"open_access","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","access_level":"closed","file_size":261256696,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12401","status":"public","ddc":["610"],"title":"Role of microenvironment heterogeneity in cancer cell invasion","month":"12","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12401","degree_awarded":"PhD","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2023-12-21T23:30:03Z","author":[{"first_name":"Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren"}],"related_material":{"record":[{"id":"679","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"9429","relation":"part_of_dissertation","status":"public"},{"id":"7885","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-12-21T23:30:04Z","date_created":"2023-01-26T11:55:16Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria"},{"citation":{"ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","apa":"Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193","mla":"Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193."},"page":"170","date_published":"2022-04-20T00:00:00Z","day":"20","article_processing_charge":"No","has_accepted_license":"1","_id":"11193","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"status":"public","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":8820951,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","checksum":"999ab16884c4522486136ebc5ae8dbff","date_updated":"2023-04-21T22:30:03Z","date_created":"2022-04-20T09:03:57Z","embargo":"2023-04-20","file_id":"11195","relation":"main_file"},{"checksum":"fd92b1e38d53bdf8b458213882d41383","date_created":"2022-04-22T12:41:00Z","date_updated":"2023-04-21T22:30:03Z","relation":"source_file","file_id":"11329","content_type":"application/x-zip-compressed","file_size":65864612,"creator":"cchlebak","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Stephanie_Wachner_20200414.zip"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"doi":"10.15479/at:ista:11193","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"}],"language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2663-337X"]},"year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Wachner, Stephanie","first_name":"Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10614","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"date_updated":"2023-09-19T10:15:54Z","date_created":"2022-04-20T08:59:07Z","file_date_updated":"2023-04-21T22:30:03Z"},{"year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"author":[{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"3","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11160"}]},"date_updated":"2023-11-16T13:10:22Z","date_created":"2023-01-24T13:09:57Z","file_date_updated":"2023-09-20T22:30:03Z","ec_funded":1,"oa":1,"project":[{"grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:12094","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"_id":"12364","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","status":"public","ddc":["570"],"file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":20457465,"file_name":"220923_Thesis_CDotter_Final.pdf","access_level":"open_access","date_created":"2023-01-24T13:15:45Z","date_updated":"2023-09-20T22:30:03Z","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_id":"12365","embargo":"2023-09-19","relation":"main_file"},{"creator":"cchlebak","file_size":22433512,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"latex_source_CDotter_Thesis_2022.zip","embargo_to":"open_access","checksum":"ad01bb20da163be6893b7af832e58419","date_created":"2023-02-02T09:15:35Z","date_updated":"2023-09-20T22:30:03Z","file_id":"12482","relation":"source_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"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."}],"citation":{"apa":"Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094","ieee":"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.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094."},"page":"152","date_published":"2022-09-19T00:00:00Z","day":"19","has_accepted_license":"1","article_processing_charge":"No"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"ddc":["006","514","516"],"title":"Multi-cover persistence and Delaunay mosaics","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9056","file":[{"access_level":"closed","file_name":"thesis_source.zip","content_type":"application/zip","file_size":13446994,"creator":"patrickd","relation":"source_file","file_id":"9063","checksum":"bcf27986147cab0533b6abadd74e7629","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z"},{"content_type":"application/pdf","file_size":5210329,"creator":"patrickd","access_level":"open_access","file_name":"thesis_pdfA2b.pdf","checksum":"9cc8af266579a464385bbe2aff6af606","success":1,"date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","relation":"main_file","file_id":"9064"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"134","citation":{"ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021."},"date_published":"2021-02-01T00:00:00Z","place":"Klosterneuburg","file_date_updated":"2021-02-03T10:37:28Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publication_status":"published","year":"2021","date_updated":"2023-09-07T13:29:01Z","date_created":"2021-02-02T14:11:06Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"187"},{"relation":"part_of_dissertation","status":"public","id":"8703"}]},"author":[{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"}],"publication_identifier":{"issn":["2663-337X"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:9056"},{"citation":{"chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022"},"page":"380","date_published":"2021-01-25T00:00:00Z","day":"25","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9022","status":"public","title":"Fluctuations in the spectrum of random matrices","ddc":["510"],"oa_version":"Published Version","file":[{"date_created":"2021-01-25T14:19:03Z","date_updated":"2021-01-25T14:19:03Z","success":1,"checksum":"5a93658a5f19478372523ee232887e2b","file_id":"9043","relation":"main_file","creator":"gcipollo","content_type":"application/pdf","file_size":4127796,"file_name":"thesis.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"9044","date_created":"2021-01-25T14:19:10Z","date_updated":"2021-01-25T14:19:10Z","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","file_name":"Thesis_files.zip","access_level":"closed","content_type":"application/zip","file_size":12775206,"creator":"gcipollo"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"doi":"10.15479/AT:ISTA:9022","supervisor":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"}],"date_created":"2021-01-21T18:16:54Z","date_updated":"2023-09-07T13:29:32Z","file_date_updated":"2021-01-25T14:19:10Z","ec_funded":1},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"year":"2021","date_updated":"2023-09-07T13:30:45Z","date_created":"2021-09-13T11:12:34Z","author":[{"full_name":"Hensel, Sebastian","first_name":"Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072"}],"related_material":{"record":[{"id":"10012","relation":"part_of_dissertation","status":"public"},{"id":"10013","status":"public","relation":"part_of_dissertation"},{"id":"7489","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-09-15T14:37:30Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"oa":1,"supervisor":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10007","month":"09","publication_identifier":{"issn":["2663-337X"]},"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","ddc":["515"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10007","oa_version":"Published Version","file":[{"content_type":"application/x-zip-compressed","file_size":15022154,"creator":"shensel","file_name":"thesis_final_Hensel.zip","access_level":"closed","date_updated":"2021-09-15T14:37:30Z","date_created":"2021-09-13T11:03:24Z","checksum":"c8475faaf0b680b4971f638f1db16347","relation":"source_file","file_id":"10008"},{"file_name":"thesis_final_Hensel.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6583638,"creator":"shensel","relation":"main_file","file_id":"10014","date_created":"2021-09-13T14:18:56Z","date_updated":"2021-09-14T09:52:47Z","checksum":"1a609937aa5275452822f45f2da17f07"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"page":"300","citation":{"short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria."},"date_published":"2021-09-14T00:00:00Z","day":"14","has_accepted_license":"1","article_processing_charge":"No"},{"day":"22","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-09-22T00:00:00Z","citation":{"mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030"},"abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"content_type":"application/x-zip-compressed","file_size":3876668,"creator":"cchlebak","access_level":"closed","file_name":"tex_and_pictures.zip","checksum":"8cd60dcb8762e8f21867e21e8001e183","date_updated":"2022-03-10T12:14:42Z","date_created":"2021-09-21T09:17:34Z","relation":"source_file","file_id":"10032"},{"relation":"main_file","file_id":"10047","date_created":"2021-09-27T11:14:31Z","date_updated":"2021-09-27T11:14:31Z","checksum":"9789e9d967c853c1503ec7f307170279","file_name":"thesis_portinale_Final (1).pdf","access_level":"open_access","content_type":"application/pdf","file_size":2532673,"creator":"cchlebak"}],"oa_version":"Published Version","ddc":["515"],"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10030","month":"09","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10030","project":[{"call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2022-03-10T12:14:42Z","date_created":"2021-09-21T09:14:15Z","date_updated":"2023-09-07T13:31:06Z","author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10022"},{"id":"9792","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7573"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","year":"2021"},{"file_date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:44:09Z","date_updated":"2023-09-07T13:31:22Z","related_material":{"record":[{"id":"9928","status":"public","relation":"part_of_dissertation"},{"id":"8755","relation":"part_of_dissertation","status":"public"}]},"author":[{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"doi":"10.15479/at:ista:9920","oa":1,"abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"content_type":"application/x-zip-compressed","file_size":151387283,"creator":"mperuzzo","access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip","checksum":"3cd1986efde5121d7581f6fcf9090da8","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-16T09:33:21Z","relation":"source_file","file_id":"9924"},{"content_type":"application/pdf","file_size":17596344,"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","access_level":"open_access","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:06Z","checksum":"50928c621cdf0775d7a5906b9dc8602c","relation":"main_file","file_id":"9939"},{"date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:09Z","checksum":"37f486aa1b622fe44af00d627ec13f6c","relation":"other","file_id":"9940","content_type":"application/pdf","file_size":17592425,"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","description":"Extra copy of the thesis as PDF/A-2b","access_level":"closed"}],"oa_version":"Published Version","status":"public","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","ddc":["539"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9920","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["quantum computing","superinductor","quantum metrology"],"date_published":"2021-08-19T00:00:00Z","page":"149","citation":{"mla":"Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920"}},{"article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2791-4585"]},"day":"07","month":"12","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"degree_awarded":"MS","date_published":"2021-12-07T00:00:00Z","doi":"10.15479/at:ista:10422","oa":1,"citation":{"short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria."},"file_date_updated":"2022-03-10T12:10:25Z","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"alternative_title":["ISTA Master's Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"10424","checksum":"114e8f4b2c002c6c352416c12de2c695","date_updated":"2022-03-10T12:10:25Z","date_created":"2021-12-07T11:13:52Z","access_level":"closed","file_name":"Thesis.zip","file_size":394018,"content_type":"application/x-zip-compressed","creator":"cchlebak"},{"creator":"cchlebak","file_size":47638,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Preliminary_pages_Piankov.docx","access_level":"closed","date_updated":"2022-03-10T12:10:25Z","date_created":"2021-12-07T11:14:01Z","checksum":"cd15ae991ced352a9959815f794e657c","file_id":"10425","relation":"source_file"},{"creator":"cchlebak","content_type":"application/pdf","file_size":484965,"file_name":"2021_Piankov_combined.pdf","access_level":"open_access","date_created":"2021-12-07T11:20:35Z","date_updated":"2021-12-07T11:20:35Z","success":1,"checksum":"e6899c798b75ba42fab9822bce309050","file_id":"10426","relation":"main_file"}],"oa_version":"Published Version","date_created":"2021-12-07T10:48:06Z","date_updated":"2023-09-07T13:34:12Z","author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","first_name":"Anton","last_name":"Piankov","full_name":"Piankov, Anton"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"publication_status":"published","title":"Towards designer materials using customizable particle shape","status":"public","ddc":["530"],"year":"2021","_id":"10422","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"05","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:9418","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-05-24T11:56:02Z","year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"}],"related_material":{"record":[{"status":"deleted","relation":"part_of_dissertation","id":"7435"},{"id":"7481","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9416"},{"relation":"part_of_dissertation","status":"public","id":"7479"}]},"date_updated":"2023-09-08T11:11:12Z","date_created":"2021-05-24T13:06:23Z","day":"30","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418."},"page":"125","date_published":"2021-05-30T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9418","title":"Underspecification in deep learning","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"success":1,"checksum":"4f0abe64114cfed264f9d36e8d1197e3","date_updated":"2021-05-24T11:22:29Z","date_created":"2021-05-24T11:22:29Z","file_id":"9419","relation":"main_file","creator":"bphuong","content_type":"application/pdf","file_size":2673905,"access_level":"open_access","file_name":"mph-thesis-v519-pdfimages.pdf"},{"creator":"bphuong","content_type":"application/zip","file_size":92995100,"file_name":"thesis.zip","access_level":"closed","date_created":"2021-05-24T11:56:02Z","date_updated":"2021-05-24T11:56:02Z","checksum":"f5699e876bc770a9b0df8345a77720a2","file_id":"9420","relation":"source_file"}]},{"degree_awarded":"PhD","supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10199","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"month":"10","publication_identifier":{"issn":["2663-337X"]},"date_created":"2021-10-29T20:09:01Z","date_updated":"2023-09-19T09:59:54Z","author":[{"full_name":"Toman, Viktor","first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X"}],"related_material":{"record":[{"id":"10190","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10191"},{"relation":"part_of_dissertation","status":"public","id":"9987"},{"id":"141","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","year":"2021","file_date_updated":"2021-11-09T09:00:50Z","ec_funded":1,"date_published":"2021-10-31T00:00:00Z","page":"166","citation":{"mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199"},"day":"31","has_accepted_license":"1","article_processing_charge":"No","keyword":["concurrency","verification","model checking"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10225","checksum":"4f412a1ee60952221b499a4b1268df35","date_created":"2021-11-08T14:12:22Z","date_updated":"2021-11-08T14:12:22Z","access_level":"open_access","file_name":"toman_th_final.pdf","file_size":2915234,"content_type":"application/pdf","creator":"vtoman"},{"file_size":8616056,"content_type":"application/zip","creator":"vtoman","file_name":"toman_thesis.zip","access_level":"closed","date_created":"2021-11-08T14:12:46Z","date_updated":"2021-11-09T09:00:50Z","checksum":"9584943f99127be2dd2963f6784c37d4","relation":"source_file","file_id":"10226"}],"title":"Improved verification techniques for concurrent systems","status":"public","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10199","abstract":[{"text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"has_accepted_license":"1","article_processing_charge":"No","day":"23","date_published":"2021-09-23T00:00:00Z","citation":{"ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035."},"page":"276","abstract":[{"lang":"eng","text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c])."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"thesis_pdfa.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":2104726,"file_id":"10082","relation":"main_file","date_created":"2021-10-04T12:22:33Z","date_updated":"2021-10-04T12:22:33Z","success":1,"checksum":"73a44345c683e81f3e765efbf86fdcc5"},{"relation":"source_file","file_id":"10085","date_created":"2021-10-05T07:04:37Z","date_updated":"2022-03-10T12:15:18Z","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_name":"thesis_final (1).zip","access_level":"closed","file_size":9538359,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"oa_version":"Published Version","_id":"10035","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["519"],"title":"On the adaptive security of graph-based games","publication_identifier":{"issn":["2663-337X"]},"month":"09","doi":"10.15479/at:ista:10035","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"ec_funded":1,"file_date_updated":"2022-03-10T12:15:18Z","related_material":{"record":[{"id":"10044","status":"public","relation":"part_of_dissertation"},{"id":"10049","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"637"},{"status":"public","relation":"part_of_dissertation","id":"10041"},{"id":"6430","status":"public","relation":"part_of_dissertation"},{"id":"10048","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"}],"date_created":"2021-09-23T07:31:44Z","date_updated":"2023-10-17T09:24:07Z","year":"2021","acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published"},{"abstract":[{"lang":"eng","text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"creator":"gnadirad","file_size":2370859,"content_type":"application/pdf","file_name":"Thesis_Final_09_12_2021.pdf","access_level":"open_access","date_created":"2021-12-09T17:47:49Z","date_updated":"2021-12-09T17:47:49Z","success":1,"checksum":"6bf14e9a523387328f016c0689f5e10e","file_id":"10436","relation":"main_file"},{"relation":"source_file","file_id":"10437","checksum":"914d6c5ca86bd0add471971a8f4c4341","date_updated":"2022-03-28T12:55:12Z","date_created":"2021-12-09T17:47:49Z","access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip","file_size":2596924,"content_type":"application/zip","creator":"gnadirad"}],"oa_version":"Published Version","title":"On achieving scalability through relaxation","ddc":["000"],"status":"public","_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"09","has_accepted_license":"1","article_processing_charge":"No","date_published":"2021-12-09T00:00:00Z","page":"132","citation":{"ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429."},"file_date_updated":"2022-03-28T12:55:12Z","ec_funded":1,"date_updated":"2023-10-17T11:48:55Z","date_created":"2021-12-08T21:52:28Z","author":[{"full_name":"Nadiradze, Giorgi","first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731"}],"related_material":{"record":[{"id":"10432","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6673"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"relation":"part_of_dissertation","status":"public","id":"10435"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria","year":"2021","month":"12","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10429","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"oa":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"20","date_published":"2021-08-20T00:00:00Z","page":"180","citation":{"ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733."},"abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_FeliciangeliA.pdf","content_type":"application/pdf","file_size":1958710,"creator":"dfelicia","relation":"main_file","file_id":"9944","checksum":"e88bb8ca43948abe060eb2d2fa719881","date_updated":"2021-09-06T09:28:56Z","date_created":"2021-08-19T14:03:48Z"},{"file_name":"thesis.7z","access_level":"closed","file_size":3771669,"content_type":"application/octet-stream","creator":"dfelicia","relation":"source_file","file_id":"9945","date_updated":"2022-03-10T12:13:57Z","date_created":"2021-08-19T14:06:35Z","checksum":"72810843abee83705853505b3f8348aa"}],"status":"public","ddc":["515","519","539"],"title":"The polaron at strong coupling","_id":"9733","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"},{"last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9733","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"file_date_updated":"2022-03-10T12:13:57Z","date_updated":"2024-03-06T12:30:44Z","date_created":"2021-07-27T15:48:30Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"id":"9792","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9225"},{"id":"9781","status":"public","relation":"part_of_dissertation"},{"id":"9791","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:9992","project":[{"grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_created":"2021-09-09T07:37:20Z","date_updated":"2023-09-07T13:38:33Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6351"},{"id":"6943","relation":"part_of_dissertation","status":"public"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2021","ec_funded":1,"file_date_updated":"2021-09-15T22:30:26Z","date_published":"2021-09-13T00:00:00Z","page":"168","citation":{"chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992"},"article_processing_charge":"No","has_accepted_license":"1","day":"13","file":[{"creator":"lhoermaye","file_size":25179004,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_vupload.docx","embargo_to":"open_access","access_level":"closed","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","checksum":"c763064adaa720e16066c1a4f9682bbb","file_id":"9993","relation":"source_file"},{"file_name":"Thesis_vfinal_pdfa.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6246900,"creator":"lhoermaye","relation":"main_file","file_id":"9996","embargo":"2021-09-09","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f"}],"oa_version":"Published Version","status":"public","ddc":["575"],"title":"Wound healing in the Arabidopsis root meristem","_id":"9992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"date_created":"2021-07-01T14:50:17Z","date_updated":"2023-09-07T13:33:27Z","related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"id":"9006","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","file_date_updated":"2022-07-02T22:30:06Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9623","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"month":"07","file":[{"file_name":"PhDThesis_SCM.docx","embargo_to":"open_access","access_level":"closed","creator":"scaballe","file_size":131946790,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"9624","relation":"source_file","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:48:54Z","checksum":"e039225a47ef32666d59bf35ddd30ecf"},{"creator":"scaballe","file_size":17094958,"content_type":"application/pdf","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:46:25Z","embargo":"2022-07-01","file_id":"9625","relation":"main_file"}],"oa_version":"Published Version","status":"public","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9623","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-07-01T00:00:00Z","page":"111","citation":{"ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623."},"has_accepted_license":"1","article_processing_charge":"No"},{"month":"10","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:10058","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"supervisor":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"}],"file_date_updated":"2022-12-20T23:30:07Z","author":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec","full_name":"Jirovec, Daniel"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8831"},{"id":"10065","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10066"},{"relation":"part_of_dissertation","status":"public","id":"8909"},{"status":"public","relation":"part_of_dissertation","id":"5816"}]},"date_created":"2021-09-30T07:53:49Z","date_updated":"2023-09-08T11:41:08Z","year":"2021","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","day":"05","has_accepted_license":"1","article_processing_charge":"No","keyword":["qubits","quantum computing","holes"],"date_published":"2021-10-05T00:00:00Z","citation":{"ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058."},"page":"151","abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_id":"10061","relation":"source_file","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-09-30T14:29:14Z","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_name":"PHD_Thesis_Jirovec_Source.zip","embargo_to":"open_access","access_level":"closed","creator":"djirovec","content_type":"application/x-zip-compressed","file_size":32397600},{"file_size":26910829,"content_type":"application/pdf","creator":"djirovec","access_level":"open_access","file_name":"PHD_Thesis_pdfa2b_1.pdf","checksum":"5fbe08d4f66d1153e04c47971538fae8","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-10-05T07:56:49Z","relation":"main_file","embargo":"2022-10-06","file_id":"10087"}],"_id":"10058","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["621","539"],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","status":"public"},{"page":"101","citation":{"ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021."},"date_published":"2021-05-18T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"18","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","status":"public","ddc":["571"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9397","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","access_level":"closed","embargo_to":"open_access","file_name":"KHuljev_Thesis_corrections.docx","file_size":47799741,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"khuljev"},{"file_name":"new_KHuljev_Thesis_corrections.pdf","access_level":"open_access","content_type":"application/pdf","file_size":16542131,"creator":"khuljev","relation":"main_file","embargo":"2022-05-20","file_id":"9401","date_created":"2021-05-18T14:50:28Z","date_updated":"2022-05-21T22:30:04Z","checksum":"bf512f8a1e572a543778fc4b227c01ba"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:9397","publication_identifier":{"issn":["2663-337X"]},"month":"05","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-07T13:32:32Z","date_created":"2021-05-17T12:31:30Z","author":[{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"}],"file_date_updated":"2022-05-21T22:30:04Z"},{"publication_identifier":{"issn":["2663-337X"]},"month":"06","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"doi":"10.15479/at:ista:9562","oa":1,"file_date_updated":"2022-07-02T22:30:04Z","date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","related_material":{"record":[{"id":"9756","status":"public","relation":"part_of_dissertation"},{"id":"9437","relation":"part_of_dissertation","status":"public"},{"id":"8532","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2021-06-01T00:00:00Z","page":"124","citation":{"short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria."},"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"659df5518db495f679cb1df9e9bd1d94","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z","relation":"main_file","embargo":"2022-07-01","file_id":"9563","content_type":"application/pdf","file_size":77299142,"creator":"dkleindienst","access_level":"open_access","file_name":"Thesis.pdf"},{"embargo_to":"open_access","file_name":"Thesis_source.zip","access_level":"closed","file_size":369804895,"content_type":"application/zip","creator":"dkleindienst","relation":"source_file","file_id":"9564","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:04:30Z","checksum":"3bcf63a2b19e5b6663be051bea332748"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","_id":"9562","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria."},"page":"278","date_published":"2021-01-01T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8934","status":"public","ddc":["005"],"title":"Parameterized and algebro-geometric advances in static program analysis","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2021-12-22","file_id":"8969","checksum":"d1b9db3725aed34dadd81274aeb9426c","date_updated":"2021-12-23T23:30:04Z","date_created":"2020-12-22T20:08:44Z","access_level":"open_access","file_name":"Thesis-pdfa.pdf","file_size":5251507,"content_type":"application/pdf","creator":"akafshda"},{"relation":"source_file","file_id":"8970","date_created":"2020-12-22T20:08:50Z","date_updated":"2021-03-04T23:30:04Z","checksum":"1661df7b393e6866d2460eba3c905130","embargo_to":"open_access","file_name":"source.zip","access_level":"closed","file_size":10636756,"content_type":"application/zip","creator":"akafshda"}],"publication_identifier":{"issn":["2663-337X"]},"month":"01","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"doi":"10.15479/AT:ISTA:8934","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"file_date_updated":"2021-12-23T23:30:04Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","year":"2021","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1386"},{"status":"public","relation":"part_of_dissertation","id":"1437"},{"id":"311","relation":"part_of_dissertation","status":"public"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"6380","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"639"},{"id":"66","status":"public","relation":"part_of_dissertation"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6918"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"status":"public","relation":"part_of_dissertation","id":"6175"},{"status":"public","relation":"part_of_dissertation","id":"6378"},{"relation":"part_of_dissertation","status":"public","id":"6490"},{"relation":"part_of_dissertation","status":"public","id":"7014"},{"id":"8089","relation":"part_of_dissertation","status":"public"},{"id":"8728","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"status":"public","relation":"part_of_dissertation","id":"6009"},{"id":"6340","status":"public","relation":"part_of_dissertation"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"date_updated":"2023-09-22T10:03:21Z","date_created":"2020-12-10T12:17:07Z"},{"file_date_updated":"2022-12-20T23:30:05Z","related_material":{"record":[{"id":"10316","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek"}],"date_created":"2021-11-18T15:05:06Z","date_updated":"2023-09-07T13:34:38Z","year":"2021","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"11","doi":"10.15479/at:ista:10307","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"oa":1,"abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"relation":"main_file","embargo":"2022-11-18","file_id":"10308","checksum":"b39c9e0ef18d0484d537a67551effd02","date_created":"2021-11-18T15:07:31Z","date_updated":"2022-12-20T23:30:05Z","access_level":"open_access","file_name":"ThesisTomasekKathrin.pdf","file_size":13266088,"content_type":"application/pdf","creator":"ktomasek"},{"file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ktomasek","access_level":"closed","embargo_to":"open_access","file_name":"ThesisTomasekKathrin.docx","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:46Z","relation":"source_file","file_id":"10309"}],"oa_version":"Published Version","_id":"10307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Pathogenic Escherichia coli hijack the host immune response","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"18","date_published":"2021-11-18T00:00:00Z","citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307."},"page":"73"},{"day":"22","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-11-22T00:00:00Z","citation":{"ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303."},"page":"139","abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"checksum":"dea38b98aa4da1cea03dcd0f10862818","date_created":"2021-11-22T14:48:21Z","date_updated":"2022-12-20T23:30:06Z","embargo":"2022-11-23","file_id":"10331","relation":"main_file","creator":"rabualia","content_type":"application/pdf","file_size":28005730,"access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf"},{"creator":"rabualia","file_size":62841883,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"AbualiaPhDthesisfinalv3.docx","embargo_to":"open_access","access_level":"closed","date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_id":"10332","relation":"source_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10303","status":"public","title":"Role of hormones in nitrate regulated growth","ddc":["580","581"],"month":"11","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:10303","degree_awarded":"PhD","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2022-12-20T23:30:06Z","author":[{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"}],"related_material":{"record":[{"id":"9010","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9913"},{"id":"47","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-19T14:42:45Z","date_created":"2021-11-18T11:20:59Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}]},{"citation":{"chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962"},"page":"182","date_published":"2021-09-02T00:00:00Z","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"has_accepted_license":"1","article_processing_charge":"No","day":"02","_id":"9962","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","ddc":["570"],"status":"public","file":[{"creator":"ahansen","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":10629190,"access_level":"closed","file_name":"Thesis_Hansen.docx","embargo_to":"open_access","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","date_created":"2021-08-30T09:17:39Z","date_updated":"2022-09-03T22:30:04Z","file_id":"9971","relation":"source_file"},{"file_id":"9972","embargo":"2022-09-02","relation":"main_file","date_created":"2021-08-30T09:29:44Z","date_updated":"2022-09-03T22:30:04Z","checksum":"204fa40321a1c6289b68c473634c4bf3","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","creator":"ahansen","content_type":"application/pdf","file_size":13457469}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:9962","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"09","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publication_status":"published","related_material":{"record":[{"id":"8569","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"960"}]},"author":[{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H"}],"date_created":"2021-08-29T12:36:50Z","date_updated":"2023-09-22T09:58:30Z","file_date_updated":"2022-09-03T22:30:04Z"},{"_id":"10083","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["575"],"title":"Rapid cell growth regulation in Arabidopsis","status":"public","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","content_type":"application/pdf","file_size":8616142,"creator":"cchlebak","relation":"main_file","file_id":"10138","embargo":"2022-10-14","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:07Z"},{"file_id":"10139","relation":"source_file","checksum":"f23ed258ca894f6aabf58b0c128bf242","date_created":"2021-10-14T08:00:13Z","date_updated":"2022-12-20T23:30:03Z","access_level":"closed","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","embargo_to":"open_access","creator":"cchlebak","file_size":15058499,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"citation":{"mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021."},"date_published":"2021-10-06T00:00:00Z","day":"06","has_accepted_license":"1","article_processing_charge":"No","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"author":[{"first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"}],"related_material":{"record":[{"id":"442","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8283"},{"status":"public","relation":"part_of_dissertation","id":"8986"},{"relation":"part_of_dissertation","status":"public","id":"6627"},{"relation":"part_of_dissertation","status":"public","id":"10095"},{"relation":"part_of_dissertation","status":"public","id":"10015"}]},"date_updated":"2023-10-31T19:30:02Z","date_created":"2021-10-04T13:33:10Z","file_date_updated":"2022-12-20T23:30:03Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:10083","degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10293","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","status":"public","ddc":["519","576"],"oa_version":"Published Version","file":[{"date_created":"2021-11-18T12:41:46Z","date_updated":"2022-12-20T23:30:08Z","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","relation":"source_file","file_id":"10305","content_type":"application/zip","file_size":29703124,"creator":"lschmid","embargo_to":"open_access","file_name":"submission_new.zip","access_level":"closed"},{"relation":"main_file","file_id":"10306","embargo":"2022-10-18","checksum":"d940af042e94660c6b6a7b4f0b184d47","date_created":"2021-11-18T12:59:15Z","date_updated":"2022-12-20T23:30:08Z","access_level":"open_access","file_name":"thesis_new_upload.pdf","file_size":8320985,"content_type":"application/pdf","creator":"lschmid"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"citation":{"chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293"},"page":"171","date_published":"2021-11-17T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"17","year":"2021","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"9997","relation":"part_of_dissertation","status":"public"},{"id":"2","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9402"}]},"author":[{"last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura"}],"date_updated":"2023-11-07T08:28:29Z","date_created":"2021-11-15T17:12:57Z","ec_funded":1,"file_date_updated":"2022-12-20T23:30:08Z","oa":1,"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"doi":"10.15479/at:ista:10293","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11"},{"year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"author":[{"full_name":"Semerádová, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","last_name":"Semerádová"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9160"}]},"date_created":"2021-10-13T13:42:48Z","date_updated":"2024-01-25T10:53:29Z","file_date_updated":"2022-12-20T23:30:05Z","oa":1,"project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."}],"doi":"10.15479/at:ista:10135","supervisor":[{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10135","status":"public","ddc":["570"],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","oa_version":"Published Version","file":[{"creator":"cziletti","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28508629,"access_level":"closed","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","embargo_to":"open_access","checksum":"ce7108853e6cec6224f17cd6429b51fe","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:37Z","file_id":"10186","relation":"source_file"},{"access_level":"open_access","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","file_size":10623525,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"10187","embargo":"2022-10-28","checksum":"0d7afb846e8e31ec794de47bf44e12ef","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"citation":{"mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135"},"date_published":"2021-10-13T00:00:00Z","day":"13","has_accepted_license":"1","article_processing_charge":"No"},{"file_date_updated":"2022-07-29T22:30:05Z","author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal","last_name":"Agrawal","full_name":"Agrawal, Nishchal"}],"related_material":{"record":[{"id":"6189","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-07-27T13:40:30Z","date_updated":"2024-02-28T13:14:39Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9728","supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2021-07-28T13:32:02Z","date_updated":"2022-07-29T22:30:05Z","checksum":"77436be3563a90435024307b1b5ee7e8","relation":"source_file","file_id":"9744","file_size":22859658,"content_type":"application/x-zip-compressed","creator":"nagrawal","embargo_to":"open_access","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","access_level":"closed"},{"checksum":"72a891d7daba85445c29b868c22575ed","date_created":"2021-07-28T13:32:05Z","date_updated":"2022-07-29T22:30:05Z","file_id":"9745","embargo":"2022-07-28","relation":"main_file","creator":"nagrawal","file_size":18658048,"content_type":"application/pdf","access_level":"open_access","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf"}],"oa_version":"Published Version","_id":"9728","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","status":"public","ddc":["532"],"day":"29","article_processing_charge":"No","has_accepted_license":"1","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"date_published":"2021-07-29T00:00:00Z","citation":{"ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728."},"page":"118"},{"file_date_updated":"2020-07-14T12:48:01Z","ec_funded":1,"year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JaMa"}],"author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","last_name":"Forkert","full_name":"Forkert, Dominik L"}],"date_created":"2020-04-02T06:40:23Z","date_updated":"2023-09-07T13:03:12Z","month":"03","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"doi":"10.15479/AT:ISTA:7629","supervisor":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"_id":"7629","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["510"],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","status":"public","file":[{"creator":"dernst","file_size":3297129,"content_type":"application/pdf","file_name":"Thesis_Forkert_PDFA.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T10:47:59Z","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_id":"7657","relation":"main_file"},{"file_id":"7658","relation":"source_file","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T10:47:59Z","access_level":"closed","file_name":"Thesis_Forkert_source.zip","creator":"dernst","file_size":1063908,"content_type":"application/x-zip-compressed"}],"oa_version":"Published Version","day":"31","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629."},"page":"154","date_published":"2020-03-31T00:00:00Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8574","title":"Local adaptation in metapopulations","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"8575","relation":"main_file","date_updated":"2020-09-28T07:25:35Z","date_created":"2020-09-28T07:25:35Z","success":1,"checksum":"20e71f015fbbd78fea708893ad634ed0","file_name":"thesis_EnikoSzep_final.pdf","access_level":"open_access","creator":"dernst","file_size":6354833,"content_type":"application/pdf"},{"file_name":"thesisFiles_EnikoSzep.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":23020401,"creator":"dernst","relation":"source_file","file_id":"8576","date_created":"2020-09-28T07:25:37Z","date_updated":"2020-09-28T07:25:37Z","checksum":"a8de2c14a1bb4e53c857787efbb289e1"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"citation":{"ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574."},"page":"158","date_published":"2020-09-20T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"20","year":"2020","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:11:39Z","date_created":"2020-09-28T07:33:38Z","file_date_updated":"2020-09-28T07:25:37Z","oa":1,"doi":"10.15479/AT:ISTA:8574","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"degree_awarded":"PhD","publication_identifier":{"eissn":["2663-337X"]},"month":"09"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z","year":"2020","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"7524","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon"}],"date_created":"2020-02-24T09:17:27Z","date_updated":"2023-09-07T13:12:42Z","publication_identifier":{"issn":["2663-337X"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:7514","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7514","status":"public","title":"The free energy of a dilute two-dimensional Bose gas","ddc":["510"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1563429,"creator":"dernst","access_level":"open_access","file_name":"thesis.pdf","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-24T09:15:06Z","relation":"main_file","file_id":"7515"},{"access_level":"closed","file_name":"thesis_source.zip","creator":"dernst","file_size":2028038,"content_type":"application/x-zip-compressed","file_id":"7516","relation":"source_file","checksum":"ad7425867b52d7d9e72296e87bc9cb67","date_created":"2020-02-24T09:15:16Z","date_updated":"2020-07-14T12:47:59Z"}],"article_processing_charge":"No","has_accepted_license":"1","day":"24","citation":{"ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020."},"page":"148","date_published":"2020-02-24T00:00:00Z"},{"date_published":"2020-09-09T00:00:00Z","page":"191","citation":{"ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353."},"article_processing_charge":"No","has_accepted_license":"1","day":"09","file":[{"access_level":"open_access","file_name":"Thesis_Julia_Steiner_pdfA.pdf","file_size":117547589,"content_type":"application/pdf","creator":"jsteiner","relation":"main_file","file_id":"8354","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","date_created":"2020-09-09T14:22:35Z"},{"date_created":"2020-09-09T14:23:25Z","date_updated":"2020-09-15T08:48:37Z","checksum":"ba112f957b7145462d0ab79044873ee9","relation":"source_file","file_id":"8355","file_size":223328668,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jsteiner","file_name":"Thesis_Julia_Steiner.docx","access_level":"closed"}],"oa_version":"None","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","ddc":["572"],"status":"public","_id":"8353","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"supervisor":[{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8353","project":[{"grant_number":"24741","_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_updated":"2023-09-07T13:14:09Z","date_created":"2020-09-09T14:27:01Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8284"}]},"author":[{"full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner","first_name":"Julia"}],"department":[{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","file_date_updated":"2021-09-16T12:40:56Z"},{"oa_version":"Published Version","file":[{"file_size":49198118,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","access_level":"closed","file_name":"2020_Han_Thesis.docx","checksum":"c4bda1947d4c09c428ac9ce667b02327","date_created":"2020-09-30T14:50:20Z","date_updated":"2020-09-30T14:50:20Z","relation":"source_file","file_id":"8590"},{"file_size":15513963,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_Han_Thesis.pdf","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","date_updated":"2021-10-01T13:33:02Z","date_created":"2020-09-30T14:49:59Z","relation":"main_file","file_id":"8591"}],"status":"public","ddc":["580"],"title":"Novel insights into PIN polarity regulation during Arabidopsis development","_id":"8589","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-09-30T00:00:00Z","page":"164","citation":{"chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589"},"has_accepted_license":"1","article_processing_charge":"No","day":"30","date_created":"2020-09-30T14:50:51Z","date_updated":"2023-09-07T13:13:05Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7643"}]},"author":[{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin"}],"department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","file_date_updated":"2021-10-01T13:33:02Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"doi":"10.15479/AT:ISTA:8589","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","content_type":"application/pdf","file_size":16638998,"creator":"rgrah","relation":"main_file","file_id":"8176","success":1,"date_created":"2020-07-27T12:00:07Z","date_updated":"2020-07-27T12:00:07Z"},{"file_size":347459978,"content_type":"application/zip","creator":"rgrah","file_name":"Thesis_new.zip","access_level":"closed","date_updated":"2020-07-30T13:04:55Z","date_created":"2020-07-27T12:02:23Z","relation":"main_file","file_id":"8177"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","status":"public","ddc":["530","570"],"_id":"8155","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-07-24T00:00:00Z","page":"310","citation":{"ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155."},"day":"24","has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-09-07T13:13:27Z","date_created":"2020-07-23T09:51:28Z","author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok"}],"related_material":{"record":[{"id":"7675","relation":"part_of_dissertation","status":"public"},{"id":"7569","status":"public","relation":"part_of_dissertation"},{"id":"7652","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","year":"2020","file_date_updated":"2020-07-30T13:04:55Z","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8155","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"oa":1,"month":"07","publication_identifier":{"issn":["2663-337X"]}},{"date_published":"2020-02-10T00:00:00Z","page":"155","citation":{"ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460."},"day":"10","has_accepted_license":"1","article_processing_charge":"No","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"file":[{"relation":"main_file","file_id":"7461","date_created":"2020-02-06T14:43:54Z","date_updated":"2020-07-14T12:47:58Z","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_name":"thesis_ist-final_noack.pdf","access_level":"open_access","content_type":"application/pdf","file_size":76195184,"creator":"koelsboe"},{"date_created":"2020-02-06T14:52:45Z","date_updated":"2020-07-14T12:47:58Z","checksum":"7a52383c812b0be64d3826546509e5a4","relation":"source_file","file_id":"7462","content_type":"application/x-zip-compressed","file_size":122103715,"creator":"koelsboe","description":"latex source files, figures","file_name":"latex-files.zip","access_level":"closed"}],"oa_version":"Published Version","status":"public","ddc":["514"],"title":"The hole system of triangulated shapes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7460","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7460","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"month":"02","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T13:15:30Z","date_created":"2020-02-06T14:56:53Z","author":[{"full_name":"Ölsböck, Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297","first_name":"Katharina","last_name":"Ölsböck"}],"related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"year":"2020","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:58Z"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"title":"On the average-case hardness of total search problems","status":"public","ddc":["000"],"_id":"7896","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2020_Thesis_Kamath.pdf","access_level":"open_access","creator":"dernst","file_size":1622742,"content_type":"application/pdf","file_id":"7897","relation":"main_file","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:13Z","checksum":"b39e2e1c376f5819b823fb7077491c64"},{"file_id":"7898","relation":"source_file","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:23Z","access_level":"closed","file_name":"Thesis_Kamath.zip","creator":"dernst","content_type":"application/x-zip-compressed","file_size":15301529}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"25","page":"126","citation":{"ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020."},"date_published":"2020-05-25T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_updated":"2023-09-07T13:15:55Z","date_created":"2020-05-26T14:08:55Z","related_material":{"record":[{"id":"6677","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"doi":"10.15479/AT:ISTA:7896"},{"publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"month":"06","doi":"10.15479/AT:ISTA:7944","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"file_date_updated":"2020-07-14T12:48:05Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7950"},{"status":"public","relation":"part_of_dissertation","id":"5986"}]},"author":[{"full_name":"Masárová, Zuzana","last_name":"Masárová","first_name":"Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:17:37Z","date_created":"2020-06-08T00:49:46Z","year":"2020","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"09","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"date_published":"2020-06-09T00:00:00Z","citation":{"chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944"},"page":"160","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_name":"THESIS_Zuzka_Masarova.pdf","access_level":"open_access","file_size":13661779,"content_type":"application/pdf","creator":"zmasarov","relation":"main_file","file_id":"7945","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T00:34:00Z","checksum":"df688bc5a82b50baee0b99d25fc7b7f0"},{"creator":"zmasarov","content_type":"application/zip","file_size":32184006,"file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","access_level":"closed","date_created":"2020-06-08T00:35:30Z","date_updated":"2020-07-14T12:48:05Z","checksum":"45341a35b8f5529c74010b7af43ac188","file_id":"7946","relation":"source_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7944","title":"Reconfiguration problems","ddc":["516","514"],"status":"public"},{"file_date_updated":"2021-09-16T12:49:12Z","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaLo"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7580"}]},"author":[{"full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","last_name":"Bezeljak","first_name":"Urban"}],"date_created":"2020-09-08T08:53:53Z","date_updated":"2023-09-07T13:17:06Z","publication_identifier":{"issn":["2663-337X"]},"month":"09","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"doi":"10.15479/AT:ISTA:8341","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8341","title":"In vitro reconstitution of a Rab activation switch","status":"public","ddc":["570"],"file":[{"creator":"dernst","content_type":"application/x-zip-compressed","file_size":65246782,"access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","date_created":"2020-09-08T09:00:29Z","file_id":"8342","relation":"source_file"},{"access_level":"open_access","file_name":"2020_Urban_Bezeljak_Thesis.pdf","content_type":"application/pdf","file_size":31259058,"creator":"dernst","relation":"main_file","file_id":"8343","checksum":"59a62275088b00b7241e6ff4136434c7","date_created":"2020-09-08T09:00:27Z","date_updated":"2021-09-16T12:49:12Z"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"08","citation":{"ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020."},"page":"215","date_published":"2020-09-08T00:00:00Z"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"title":"Combinatorial width parameters for 3-dimensional manifolds","ddc":["514"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8032","oa_version":"Published Version","file":[{"file_name":"Kristof_Huszar-Thesis.pdf","access_level":"open_access","creator":"khuszar","file_size":2637562,"content_type":"application/pdf","file_id":"8034","relation":"main_file","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-26T10:03:58Z","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3"},{"creator":"khuszar","content_type":"application/x-zip-compressed","file_size":7163491,"file_name":"Kristof_Huszar-Thesis-source.zip","access_level":"closed","date_created":"2020-06-26T10:10:06Z","date_updated":"2020-07-14T12:48:08Z","checksum":"d5f8456202b32f4a77552ef47a2837d1","file_id":"8035","relation":"source_file"}],"has_accepted_license":"1","article_processing_charge":"No","day":"26","page":"xviii+120","citation":{"chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032"},"date_published":"2020-06-26T00:00:00Z","file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_updated":"2023-09-07T13:18:27Z","date_created":"2020-06-26T10:00:36Z","related_material":{"record":[{"id":"6556","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"7093"}]},"author":[{"full_name":"Huszár, Kristóf","last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-006-0"]},"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"doi":"10.15479/AT:ISTA:8032"},{"_id":"8358","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","ddc":["572"],"status":"public","file":[{"creator":"pcaldas","content_type":"application/pdf","file_size":141602462,"access_level":"open_access","file_name":"phd_thesis_pcaldas.pdf","success":1,"checksum":"882f93fe9c351962120e2669b84bf088","date_updated":"2020-09-10T12:11:29Z","date_created":"2020-09-10T12:11:29Z","file_id":"8364","relation":"main_file"},{"relation":"source_file","file_id":"8365","date_updated":"2020-09-11T07:48:10Z","date_created":"2020-09-10T12:18:17Z","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_name":"phd_thesis_latex_pcaldas.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":450437458,"creator":"pcaldas"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"citation":{"chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358"},"page":"135","date_published":"2020-09-10T00:00:00Z","day":"10","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","year":"2020","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7572"},{"status":"public","relation":"part_of_dissertation","id":"7197"}]},"date_updated":"2023-09-07T13:18:51Z","date_created":"2020-09-10T09:26:49Z","file_date_updated":"2020-09-11T07:48:10Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:8358","acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-009-1"]}},{"author":[{"full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"133"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"id":"8195","relation":"part_of_dissertation","status":"public"},{"id":"160","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-13T08:45:08Z","date_created":"2020-09-04T12:24:12Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","doi":"10.15479/AT:ISTA:8332","supervisor":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","file":[{"file_id":"8333","relation":"main_file","checksum":"26fe261550f691280bda4c454bf015c7","date_updated":"2020-09-04T12:17:47Z","date_created":"2020-09-04T12:17:47Z","access_level":"open_access","file_name":"kragl-thesis.pdf","creator":"bkragl","content_type":"application/pdf","file_size":1348815},{"creator":"bkragl","content_type":"application/zip","file_size":372312,"file_name":"kragl-thesis.zip","access_level":"closed","date_updated":"2020-09-04T13:00:17Z","date_created":"2020-09-04T13:00:17Z","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","relation":"source_file"}],"_id":"8332","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","abstract":[{"lang":"eng","text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-03T00:00:00Z","citation":{"chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332"},"page":"120","day":"03","article_processing_charge":"No","has_accepted_license":"1"},{"publication_identifier":{"issn":["2663-337X"]},"month":"12","oa":1,"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"doi":"10.15479/AT:ISTA:8958","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"ec_funded":1,"file_date_updated":"2020-12-30T07:18:03Z","year":"2020","department":[{"_id":"MiLe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"5886","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8587"},{"relation":"part_of_dissertation","status":"public","id":"1120"}]},"author":[{"full_name":"Li, Xiang","first_name":"Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-12-21T09:44:30Z","date_updated":"2023-09-20T11:30:58Z","article_processing_charge":"No","has_accepted_license":"1","day":"21","citation":{"ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958."},"page":"125","date_published":"2020-12-21T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.","lang":"eng"}],"_id":"8958","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Rotation of coupled cold molecules in the presence of a many-body environment","status":"public","ddc":["539"],"file":[{"access_level":"open_access","file_name":"THESIS_Xiang_Li.pdf","file_size":3622305,"content_type":"application/pdf","creator":"xli","relation":"main_file","file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"date_created":"2020-12-22T10:55:56Z","date_updated":"2020-12-22T10:55:56Z"},{"file_name":"THESIS_Xiang_Li.zip","access_level":"closed","creator":"xli","file_size":4018859,"content_type":"application/x-zip-compressed","file_id":"8968","relation":"source_file","date_created":"2020-12-22T10:56:03Z","date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00"}],"oa_version":"Published Version"},{"oa":1,"project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:8386","supervisor":[{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","year":"2020","publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Zhang, Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X","first_name":"Ran","last_name":"Zhang"}],"related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"id":"1002","status":"public","relation":"part_of_dissertation"}]},"date_created":"2020-09-14T01:04:53Z","date_updated":"2023-09-22T09:49:31Z","file_date_updated":"2020-09-15T12:51:53Z","ec_funded":1,"citation":{"ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386."},"page":"148","date_published":"2020-09-14T00:00:00Z","day":"14","has_accepted_license":"1","article_processing_charge":"No","_id":"8386","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["003"],"status":"public","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","file":[{"relation":"source_file","file_id":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","date_updated":"2020-09-14T12:18:43Z","date_created":"2020-09-14T01:02:59Z","access_level":"closed","file_name":"Thesis_Ran.zip","content_type":"application/x-zip-compressed","file_size":1245800191,"creator":"rzhang"},{"file_id":"8396","relation":"main_file","date_updated":"2020-09-15T12:51:53Z","date_created":"2020-09-15T12:51:53Z","success":1,"checksum":"817e20c33be9247f906925517c56a40d","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","access_level":"open_access","creator":"rzhang","content_type":"application/pdf","file_size":161385316}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}]},{"citation":{"chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996"},"page":"178","date_published":"2020-06-22T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"22","_id":"7996","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7997","date_created":"2020-06-22T09:22:04Z","date_updated":"2020-07-14T12:48:07Z","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","file_name":"JK_thesis_latex_source_files.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":392794743,"creator":"dernst"},{"checksum":"1de716bf110dbd77d383e479232bf496","date_created":"2020-06-22T09:21:29Z","date_updated":"2020-07-14T12:48:07Z","relation":"main_file","file_id":"7998","file_size":28453247,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"PhD_thesis_JK_pdfa.pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.","lang":"eng"}],"oa":1,"doi":"10.15479/AT:ISTA:7996","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"publication_identifier":{"issn":["2663-337X"]},"month":"06","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1328"},{"id":"7541","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"77"},{"relation":"part_of_dissertation","status":"public","id":"23"},{"status":"public","relation":"part_of_dissertation","id":"840"}]},"author":[{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"}],"date_updated":"2023-09-26T15:50:22Z","date_created":"2020-06-22T09:22:23Z","file_date_updated":"2020-07-14T12:48:07Z"},{"abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"date_updated":"2020-09-14T13:39:14Z","date_created":"2020-09-14T13:39:14Z","success":1,"checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","relation":"main_file","creator":"dernst","file_size":30224591,"content_type":"application/pdf","file_name":"2020_Thesis_Royer.pdf","access_level":"open_access"},{"checksum":"ae98fb35d912cff84a89035ae5794d3c","date_updated":"2020-09-14T13:39:17Z","date_created":"2020-09-14T13:39:17Z","file_id":"8392","relation":"main_file","creator":"dernst","file_size":74227627,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"thesis_sources.zip"}],"oa_version":"Published Version","status":"public","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8390","day":"14","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-09-14T00:00:00Z","page":"197","citation":{"ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390."},"file_date_updated":"2020-09-14T13:39:17Z","date_updated":"2023-10-16T10:04:02Z","date_created":"2020-09-14T13:42:09Z","author":[{"first_name":"Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7936"},{"id":"7937","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8193"},{"id":"8092","relation":"part_of_dissertation","status":"public"},{"id":"911","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"year":"2020","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","month":"09","publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8390","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"}},{"author":[{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7210"},{"id":"5751","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"7212"}]},"date_updated":"2023-10-17T12:29:46Z","date_created":"2019-12-20T12:26:36Z","year":"2020","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:52Z","doi":"10.15479/AT:ISTA:7196","supervisor":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"01","publication_identifier":{"eissn":["2663-337X"]},"file":[{"relation":"source_file","file_id":"7255","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","access_level":"closed","file_name":"thesis.zip","file_size":21100497,"content_type":"application/zip","creator":"jtkadlec"},{"creator":"dernst","file_size":11670983,"content_type":"application/pdf","file_name":"2020_Tkadlec_Thesis.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-28T07:32:42Z","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_id":"7367","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7196","title":"A role of graphs in evolutionary processes","ddc":["519"],"status":"public","abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-01-12T00:00:00Z","citation":{"mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020."},"page":"144","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2020-07-24T00:00:00Z","citation":{"ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020."},"page":"119","day":"24","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"8178","relation":"source_file","date_created":"2020-07-27T12:44:51Z","date_updated":"2020-07-27T12:44:51Z","file_name":"source.zip","access_level":"closed","creator":"savvakum","file_size":1061740,"content_type":"application/zip"},{"content_type":"application/pdf","file_size":1336501,"creator":"savvakum","file_name":"thesis_pdfa.pdf","access_level":"open_access","date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-27T12:46:53Z","success":1,"relation":"main_file","file_id":"8179"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8156","title":"Topological methods in geometry and discrete mathematics","status":"public","ddc":["514"],"abstract":[{"lang":"eng","text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:8156","supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"07","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov"}],"related_material":{"record":[{"id":"8182","relation":"part_of_dissertation","status":"public"},{"id":"8183","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8185"},{"status":"public","relation":"part_of_dissertation","id":"8184"},{"status":"public","relation":"part_of_dissertation","id":"6355"},{"id":"75","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-12-18T10:51:01Z","date_created":"2020-07-23T09:51:29Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-27T12:46:53Z"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop.","lang":"eng"}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","status":"public","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8366","file":[{"date_created":"2020-09-10T16:11:49Z","date_updated":"2020-09-10T16:11:49Z","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","file_id":"8367","relation":"main_file","creator":"rguseino","content_type":"application/pdf","file_size":70950442,"file_name":"thesis_rguseinov.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"8374","checksum":"e8fd944c960c20e0e27e6548af69121d","date_created":"2020-09-11T09:39:48Z","date_updated":"2020-09-16T15:11:01Z","access_level":"closed","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","file_size":76207597,"creator":"rguseino"}],"oa_version":"Published Version","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"article_processing_charge":"No","has_accepted_license":"1","day":"21","page":"118","citation":{"ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366."},"date_published":"2020-09-21T00:00:00Z","ec_funded":1,"file_date_updated":"2020-09-16T15:11:01Z","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","year":"2020","date_created":"2020-09-10T16:19:55Z","date_updated":"2024-02-21T12:44:29Z","related_material":{"record":[{"relation":"research_data","status":"deleted","id":"7151"},{"id":"7262","status":"public","relation":"part_of_dissertation"},{"id":"8562","relation":"part_of_dissertation","status":"public"},{"id":"1001","relation":"part_of_dissertation","status":"public"},{"id":"8375","status":"public","relation":"research_data"}]},"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"month":"09","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.15479/AT:ISTA:8366"}]