[{"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publication_identifier":{"issn":["2663-337X"]},"day":"12","OA_place":"publisher","date_published":"2023-12-12T00:00:00Z","file_date_updated":"2023-12-14T08:58:18Z","type":"dissertation","doi":"10.15479/at:ista:14651","oa":1,"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"_id":"14651","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","file":[{"file_size":34101468,"checksum":"520bdb61e95e66070e02824947d2c5fa","date_created":"2023-12-13T15:37:55Z","success":1,"date_updated":"2023-12-13T15:37:55Z","file_id":"14684","creator":"larathoo","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"Phd_Thesis_LA.pdf"},{"file_size":31052872,"checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-13T15:42:23Z","file_id":"14685","creator":"larathoo","file_name":"Phd_Thesis_LA.zip","relation":"source_file","access_level":"closed","content_type":"application/zip"},{"file_size":10713896,"checksum":"9a778c949932286f4519e1f1fca2820d","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-11T19:24:59Z","file_id":"14681","creator":"larathoo","file_name":"Supplementary_Materials.zip","relation":"supplementary_material","access_level":"closed","content_type":"application/zip"}],"status":"public","date_updated":"2026-04-07T13:28:30Z","publication_status":"published","ddc":["570"],"month":"12","author":[{"orcid":"0000-0003-1771-714X","first_name":"Louise S","full_name":"Arathoon, Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"page":"96","abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"year":"2023","date_created":"2023-12-11T19:30:37Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11411"}]},"oa_version":"Published Version"},{"related_material":{"record":[{"id":"461","relation":"part_of_dissertation","status":"public"},{"id":"10791","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7932","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"14530","relation":"new_edition","status":"public"}]},"date_created":"2023-03-15T13:22:13Z","oa_version":"None","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"page":"260","year":"2023","ddc":["530"],"date_updated":"2026-04-07T13:29:13Z","publication_status":"published","author":[{"full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl"}],"month":"03","_id":"12726","language":[{"iso":"eng"}],"title":"Synchronization in collectively moving active matter","status":"public","file":[{"date_updated":"2023-11-24T11:57:46Z","date_created":"2023-03-23T12:49:23Z","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_size":63734746,"description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","relation":"main_file","content_type":"application/pdf","access_level":"closed","file_id":"12745","creator":"cchlebak"},{"date_updated":"2023-09-24T22:30:03Z","embargo_to":"open_access","date_created":"2023-03-23T12:54:34Z","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_size":339473651,"file_name":"Thesis_Riedl_2023_source.rar","access_level":"closed","content_type":"application/octet-stream","relation":"source_file","creator":"cchlebak","file_id":"12746"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"corr_author":"1","file_date_updated":"2023-11-24T11:57:46Z","type":"dissertation","doi":"10.15479/at:ista:12726","day":"23","date_published":"2023-03-23T00:00:00Z","OA_place":"publisher","citation":{"ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>"},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"article_processing_charge":"No"},{"day":"16","date_published":"2023-11-16T00:00:00Z","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"citation":{"mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"has_accepted_license":"1","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"corr_author":"1","file_date_updated":"2023-11-15T09:52:54Z","type":"dissertation","oa":1,"doi":"10.15479/14530","ddc":["530","570"],"date_updated":"2026-04-07T13:29:13Z","publication_status":"published","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311"}],"month":"11","_id":"14530","language":[{"iso":"eng"}],"title":"Synchronization in collectively moving active matter","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Thesis_Riedl_2023_corr.pdf","creator":"mriedl","file_id":"14536","date_created":"2023-11-15T09:52:54Z","success":1,"date_updated":"2023-11-15T09:52:54Z","file_size":36743942,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a"}],"status":"public","related_material":{"record":[{"status":"public","id":"461","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10791"},{"status":"public","relation":"part_of_dissertation","id":"7932"},{"relation":"part_of_dissertation","id":"10703","status":"public"},{"relation":"old_edition","id":"12726","status":"public"}]},"date_created":"2023-11-15T09:59:03Z","oa_version":"Updated Version","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  ","lang":"eng"}],"page":"260","year":"2023"},{"oa_version":"Published Version","related_material":{"record":[{"id":"13053","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"11458","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12299","status":"public"}]},"date_created":"2023-05-23T17:07:53Z","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"year":"2023","abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"ec_funded":1,"page":"147","author":[{"first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87"}],"month":"05","ddc":["000"],"date_updated":"2026-04-07T13:30:20Z","publication_status":"published","title":"Efficiency and generalization of sparse neural networks","status":"public","file":[{"checksum":"6b3354968403cb9d48cc5a83611fb571","file_size":2152072,"date_updated":"2023-05-24T16:11:16Z","date_created":"2023-05-24T16:11:16Z","success":1,"creator":"epeste","file_id":"13087","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file"},{"checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_size":1658293,"date_created":"2023-05-24T16:12:59Z","date_updated":"2023-05-24T16:12:59Z","creator":"epeste","file_id":"13088","content_type":"application/zip","access_level":"closed","relation":"source_file","file_name":"PhD_Thesis_APeste.zip"}],"_id":"13074","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:13074","file_date_updated":"2023-05-24T16:12:59Z","type":"dissertation","date_published":"2023-05-23T00:00:00Z","OA_place":"publisher","day":"23","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"citation":{"ista":"Krumes A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","apa":"Krumes, A. (2023). <i>Efficiency and generalization of sparse neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>","chicago":"Krumes, Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>.","ieee":"A. Krumes, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","mla":"Krumes, Alexandra. <i>Efficiency and Generalization of Sparse Neural Networks</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>.","short":"A. Krumes, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ama":"Krumes A. Efficiency and generalization of sparse neural networks. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD"},{"ddc":["570"],"publication_status":"published","date_updated":"2026-04-07T13:29:59Z","author":[{"last_name":"Hennessey-Wesen","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","first_name":"Mike","full_name":"Hennessey-Wesen, Mike"}],"month":"11","_id":"14641","language":[{"iso":"eng"}],"status":"public","file":[{"checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_size":46405919,"date_created":"2023-12-06T13:13:26Z","embargo_to":"open_access","date_updated":"2024-11-30T23:30:05Z","file_id":"14648","creator":"mhenness","relation":"source_file","access_level":"closed","content_type":"application/vnd.oasis.opendocument.text","file_name":"mike_thesis_v06-12-2023.odt"},{"creator":"mhenness","file_id":"14649","file_name":"mike_thesis_v06-12-2023.pdf","content_type":"application/pdf","embargo":"2026-07-18","access_level":"closed","relation":"main_file","checksum":"f5203a61eddaf35235bbc51904d73982","file_size":21282155,"date_updated":"2025-07-17T11:20:25Z","embargo_to":"open_access","date_created":"2023-12-06T13:14:15Z"},{"file_id":"19720","title":"Print version","creator":"cchlebak","relation":"other","content_type":"application/pdf","access_level":"closed","file_name":"2023_Hennessey_Michael_Thesis_print.pdf","checksum":"902102d26d30e74dbd6cdd70a65820c3","description":"for printing purposes only","file_size":45847968,"date_created":"2025-05-20T12:59:12Z","embargo_to":"open_access","date_updated":"2025-05-20T22:31:34Z"}],"title":"Adaptive mutation in E. coli modulated by luxS","date_created":"2023-12-04T13:17:37Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments."}],"ec_funded":1,"page":"104","year":"2023","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"day":"30","date_published":"2023-11-30T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"citation":{"short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"has_accepted_license":"1","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"corr_author":"1","type":"dissertation","file_date_updated":"2025-07-17T11:20:25Z","doi":"10.15479/at:ista:14641"},{"has_accepted_license":"1","corr_author":"1","type":"dissertation","file_date_updated":"2023-11-23T10:30:08Z","doi":"10.15479/14506","oa":1,"day":"10","OA_place":"publisher","date_published":"2023-11-10T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"citation":{"short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>.","apa":"Yeo, M. X. (2023). <i>Advances in efficiency and privacy in payment channel network analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","mla":"Yeo, Michelle X. <i>Advances in Efficiency and Privacy in Payment Channel Network Analysis</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>."},"article_processing_charge":"No","supervisor":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"publication_identifier":{"issn":["2663-337X"]},"date_created":"2023-11-10T08:10:43Z","related_material":{"record":[{"status":"deleted","id":"13238","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9969","status":"public"},{"status":"public","id":"14490","relation":"part_of_dissertation"}]},"oa_version":"Published Version","page":"162","ec_funded":1,"abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"year":"2023","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_updated":"2026-04-07T13:29:45Z","ddc":["000"],"month":"11","author":[{"last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809","first_name":"Michelle X"}],"language":[{"iso":"eng"}],"_id":"14506","status":"public","file":[{"file_id":"14598","creator":"cchlebak","file_name":"thesis_yeo.zip","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"521c72818d720a52b377207b2ee87b6a","file_size":3037720,"date_updated":"2023-11-23T10:29:55Z","date_created":"2023-11-23T10:29:55Z"},{"date_updated":"2023-11-23T10:30:08Z","success":1,"date_created":"2023-11-23T10:30:08Z","file_size":2717256,"checksum":"0ed5d16899687aecf13d843c9878c9f2","file_name":"thesis_yeo.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"14599"}],"title":"Advances in efficiency and privacy in payment channel network analysis"},{"project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"year":"2023","ec_funded":1,"abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"page":"147","oa_version":"Published Version","related_material":{"record":[{"id":"12802","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-06-01T09:05:24Z","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","file":[{"date_created":"2023-06-01T13:48:41Z","date_updated":"2023-06-01T13:48:41Z","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_size":12991551,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Thesis_Lisa Knaus_approved_final.docx","file_id":"13112","creator":"lknaus"},{"file_size":9309015,"checksum":"6903d152aa01181d87a696085af31c83","date_created":"2023-06-02T09:47:29Z","date_updated":"2023-06-07T08:41:49Z","creator":"lknaus","file_id":"13114","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf"}],"status":"public","_id":"13107","language":[{"iso":"eng"}],"month":"05","author":[{"first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"}],"ddc":["570"],"date_updated":"2026-04-14T08:34:36Z","publication_status":"published","oa":1,"doi":"10.15479/at:ista:13107","file_date_updated":"2023-06-07T08:41:49Z","type":"dissertation","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"corr_author":"1","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2023-05-31T00:00:00Z","OA_place":"publisher","day":"31"},{"year":"2023","project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"page":"202","ec_funded":1,"abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"oa_version":"Published Version","related_material":{"record":[{"relation":"old_edition","id":"12900","status":"public"},{"relation":"part_of_dissertation","id":"10924","status":"public"},{"id":"9114","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-06-30T08:07:43Z","file":[{"file_name":"thesis_pdfa.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"13176","creator":"cchlebak","date_updated":"2023-06-30T08:17:25Z","success":1,"date_created":"2023-06-30T08:17:25Z","file_size":18688376,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f"},{"checksum":"c3b45317ae58e0527533f98c202d81b7","file_size":37847025,"date_updated":"2023-07-06T11:35:15Z","date_created":"2023-07-06T11:35:15Z","creator":"cchlebak","file_id":"13196","file_name":"thesis.zip","access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file"}],"status":"public","title":"Cavity quantum electrooptics","language":[{"iso":"eng"}],"_id":"13175","month":"05","author":[{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_updated":"2026-04-15T06:43:26Z","ddc":["537","535","539"],"doi":"10.15479/at:ista:13175","oa":1,"type":"dissertation","file_date_updated":"2023-07-06T11:35:15Z","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"has_accepted_license":"1","supervisor":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-030-5"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"citation":{"ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria."},"OA_place":"publisher","date_published":"2023-05-05T00:00:00Z","day":"05"},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"new_edition","id":"13175"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"id":"9114","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-05-05T11:08:50Z","project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"year":"2023","page":"190","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"ec_funded":1,"author":[{"last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","first_name":"Rishabh"}],"month":"05","date_updated":"2026-04-15T06:43:26Z","publication_status":"published","ddc":["537","535","539"],"title":"Cavity quantum electrooptics","file":[{"file_size":36767177,"checksum":"8cbdab9c37ee55e591092a6f66b272c4","date_created":"2023-05-09T08:45:14Z","embargo_to":"open_access","date_updated":"2023-06-06T22:30:03Z","creator":"rsahu","file_id":"12928","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_name":"thesis.zip"},{"creator":"rsahu","file_id":"12929","content_type":"application/pdf","access_level":"closed","relation":"main_file","file_name":"thesis_pdfa_final.pdf","file_size":17501990,"checksum":"439659ead46618147309be39d9dd5a8c","date_created":"2023-05-09T08:51:17Z","date_updated":"2023-07-06T11:37:40Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"12900","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"corr_author":"1","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","doi":"10.15479/at:ista:12900","file_date_updated":"2023-07-06T11:37:40Z","type":"dissertation","OA_place":"publisher","date_published":"2023-05-05T00:00:00Z","day":"05","article_processing_charge":"No","supervisor":[{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-030-5"]},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"citation":{"ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria"},{"month":"05","author":[{"first_name":"Christian","full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T07:16:15Z","publication_status":"published","ddc":["516","004","518","531"],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","file":[{"file_size":50714445,"checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","date_updated":"2023-12-08T23:30:04Z","date_created":"2023-05-11T10:43:20Z","creator":"chafner","file_id":"12942","file_name":"thesis-hafner-2023may11-a2b.pdf","embargo":"2023-12-07","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"creator":"chafner","file_id":"12943","access_level":"closed","content_type":"application/pdf","relation":"source_file","file_name":"thesis-release-form.pdf","checksum":"a6b51334be2b81672357b1549afab40c","file_size":265319,"date_created":"2023-05-11T10:43:44Z","embargo_to":"open_access","date_updated":"2023-12-08T23:30:04Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"12897","oa_version":"Published Version","date_created":"2023-05-05T10:40:14Z","related_material":{"record":[{"status":"public","id":"9817","relation":"part_of_dissertation"},{"relation":"dissertation_contains","id":"13188","status":"public"},{"status":"public","id":"7117","relation":"part_of_dissertation"}]},"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"year":"2023","page":"180","ec_funded":1,"abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"date_published":"2023-05-05T00:00:00Z","day":"05","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"degree_awarded":"PhD","citation":{"ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>"},"alternative_title":["ISTA Thesis"],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","doi":"10.15479/at:ista:12897","oa":1,"file_date_updated":"2023-12-08T23:30:04Z","type":"dissertation"},{"page":"187","abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"year":"2023","date_created":"2023-02-02T14:50:20Z","related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"12491","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","status":"public","file":[{"file_id":"12527","creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.pdf","relation":"main_file","content_type":"application/pdf","embargo":"2024-02-07","access_level":"open_access","file_size":23082464,"checksum":"069d87f025e0799bf9e3c375664264f2","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z"},{"creator":"bzens","file_id":"12528","file_name":"PhDThesis_BettinaZens_2023_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_size":106169509,"checksum":"8c66ed203495d6e078ed1002a866520c","date_updated":"2024-02-08T23:30:04Z","embargo_to":"open_access","date_created":"2023-02-07T13:09:05Z"}],"date_updated":"2026-04-07T13:49:23Z","publication_status":"published","ddc":["570"],"author":[{"last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","first_name":"Bettina","full_name":"Zens, Bettina"}],"month":"02","file_date_updated":"2024-02-08T23:30:04Z","type":"dissertation","doi":"10.15479/at:ista:12491","oa":1,"keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"day":"02","OA_place":"publisher","date_published":"2023-02-02T00:00:00Z"},{"page":"89","abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"year":"2023","date_created":"2023-08-08T15:33:29Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"13984","title":"Individual and social immunity against viral infections in ants","status":"public","file":[{"embargo_to":"open_access","date_created":"2024-03-01T08:56:06Z","date_updated":"2024-10-29T23:31:04Z","checksum":"55c876b73d49db15228a7f571592ec77","file_size":10416761,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","creator":"cchlebak","title":"Combined Version of original Thesis and Addendum","file_id":"15044"},{"date_updated":"2024-08-09T22:30:03Z","date_created":"2023-08-08T18:01:28Z","file_size":10797612,"checksum":"27220243d5d51c3b0d7d61c0879d7a0c","file_name":"Thesis_AnnaFranschitz_202308.pdf","relation":"main_file","embargo":"2024-08-08","content_type":"application/pdf","access_level":"open_access","file_id":"13986","creator":"afransch"},{"creator":"afransch","file_id":"13987","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"Thesis_AnnaFranschitz_202308.docx","checksum":"40abf7ccca14a3893f72dc7fb88585d6","file_size":2619085,"date_created":"2023-08-08T18:02:25Z","embargo_to":"open_access","date_updated":"2024-08-09T22:30:03Z"},{"file_name":"Addendum_AnnaFranschitz202402.pdf","relation":"main_file","content_type":"application/pdf","embargo":"2024-08-08","access_level":"open_access","file_id":"15042","creator":"cchlebak","title":"Addendum","date_updated":"2024-10-29T23:31:04Z","date_created":"2024-03-01T08:37:15Z","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_size":85956,"description":"Minor modifications and clarifications - Feb 2024"},{"checksum":"66745aa01f960f17472c024875c049ed","file_size":11818,"date_updated":"2024-08-09T22:30:03Z","date_created":"2024-03-01T08:39:20Z","embargo_to":"open_access","title":"Addendum - source file","creator":"cchlebak","file_id":"15043","file_name":"Addendum_AnnaFranschitz202402.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"}],"date_updated":"2026-04-07T13:51:29Z","publication_status":"published","ddc":["570","577"],"month":"08","author":[{"full_name":"Franschitz, Anna","first_name":"Anna","last_name":"Franschitz","id":"480826C8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2024-10-29T23:31:04Z","type":"dissertation","doi":"10.15479/at:ista:13984","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","mla":"Franschitz, Anna. <i>Individual and Social Immunity against Viral Infections in Ants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>.","apa":"Franschitz, A. (2023). <i>Individual and social immunity against viral infections in ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-034-3"]},"day":"08","OA_place":"publisher","date_published":"2023-08-08T00:00:00Z"},{"date_published":"2023-05-17T00:00:00Z","OA_place":"publisher","day":"17","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"supervisor":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>."},"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"oa":1,"doi":"10.15479/at:ista:12964","file_date_updated":"2024-05-18T22:30:03Z","type":"dissertation","month":"05","author":[{"id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","full_name":"Boocock, Daniel R","first_name":"Daniel R","orcid":"0000-0002-1585-2631"}],"ddc":["530"],"date_updated":"2026-04-07T13:52:57Z","publication_status":"published","title":"Mechanochemical pattern formation across biological scales","status":"public","file":[{"embargo":"2024-05-17","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"thesis_boocock.pdf","creator":"dboocock","file_id":"12988","date_created":"2023-05-17T13:39:54Z","date_updated":"2024-05-18T22:30:03Z","file_size":40414730,"checksum":"d51240675fc6dc0e3f5dc0c902695d3a"},{"date_updated":"2024-05-18T22:30:03Z","embargo_to":"open_access","date_created":"2023-05-17T13:39:53Z","checksum":"581a2313ffeb40fe77e8a122a25a7795","file_size":34338567,"file_name":"thesis_boocock.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","creator":"dboocock","file_id":"12989"}],"_id":"12964","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-05-15T14:52:36Z","related_material":{"record":[{"id":"8602","relation":"part_of_dissertation","status":"public"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2023","abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"ec_funded":1,"page":"146"},{"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:12891","type":"dissertation","file_date_updated":"2024-05-06T22:30:03Z","date_published":"2023-05-05T00:00:00Z","day":"05","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7888","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8966"}]},"date_created":"2023-05-05T08:48:20Z","year":"2023","project":[{"grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"ec_funded":1,"abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"page":"190","month":"05","author":[{"last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra","full_name":"Schauer, Alexandra"}],"ddc":["570"],"publication_status":"published","date_updated":"2025-06-12T06:56:58Z","file":[{"date_updated":"2024-05-06T22:30:03Z","date_created":"2023-05-05T13:01:14Z","file_size":31434230,"checksum":"59b0303dc483f40a96a610a90aab7ee9","file_name":"Thesis_Schauer_final.pdf","content_type":"application/pdf","access_level":"open_access","embargo":"2024-05-05","relation":"main_file","creator":"aschauer","file_id":"12907"},{"embargo_to":"open_access","date_created":"2023-05-05T13:04:15Z","date_updated":"2024-05-06T22:30:03Z","checksum":"25f54e12479b6adaabd129a20568e6c1","file_size":43809109,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Schauer_final.docx","creator":"aschauer","file_id":"12908"}],"status":"public","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","_id":"12891","language":[{"iso":"eng"}]},{"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","corr_author":"1","file_date_updated":"2024-10-13T22:30:04Z","type":"dissertation","doi":"10.15479/at:ista:14422","oa":1,"day":"12","OA_place":"publisher","date_published":"2023-10-12T00:00:00Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"9633","relation":"part_of_dissertation"}]},"date_created":"2023-10-12T14:13:25Z","oa_version":"Published Version","page":"148","ec_funded":1,"abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"year":"2023","date_updated":"2026-04-07T13:53:13Z","publication_status":"published","ddc":["610"],"author":[{"first_name":"Basile J","full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux"}],"month":"10","language":[{"iso":"eng"}],"_id":"14422","title":"Synapseek: Meta-learning synaptic plasticity rules","file":[{"file_size":30599717,"checksum":"7f636555eae7803323df287672fd13ed","date_updated":"2024-10-13T22:30:04Z","date_created":"2023-10-12T14:53:50Z","file_id":"14424","creator":"cchlebak","file_name":"Confavreux_Thesis_2A.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2024-10-12"},{"file_name":"Confavreux Thesis.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"14440","creator":"cchlebak","date_updated":"2024-10-13T22:30:04Z","embargo_to":"open_access","date_created":"2023-10-18T07:38:34Z","file_size":68406739,"checksum":"725e85946db92290a4583a0de9779e1b"}],"status":"public"},{"day":"06","OA_place":"publisher","date_published":"2023-04-06T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"RySh"}],"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"corr_author":"1","type":"dissertation","file_date_updated":"2024-04-08T22:30:03Z","doi":"10.15479/at:ista:12809","oa":1,"publication_status":"published","date_updated":"2026-04-07T13:53:28Z","ddc":["570"],"month":"04","author":[{"last_name":"Alcarva","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","first_name":"Catarina","full_name":"Alcarva, Catarina"}],"language":[{"iso":"eng"}],"_id":"12809","status":"public","file":[{"date_created":"2023-04-07T06:16:06Z","date_updated":"2024-04-08T22:30:03Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","file_size":9881969,"access_level":"open_access","content_type":"application/pdf","embargo":"2024-04-07","relation":"main_file","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","creator":"cchlebak","file_id":"12814"},{"date_updated":"2024-04-08T22:30:03Z","embargo_to":"open_access","date_created":"2023-04-07T06:17:11Z","file_size":44201583,"checksum":"81198f63c294890f6d58e8b29782efdc","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","access_level":"closed","content_type":"application/pdf","relation":"source_file","creator":"cchlebak","file_id":"12815"},{"file_size":84731244,"checksum":"0317bf7f457bb585f99d453ffa69eb53","date_updated":"2024-04-08T22:30:03Z","embargo_to":"open_access","date_created":"2023-04-07T06:18:05Z","creator":"cchlebak","file_id":"12816","file_name":"Thesis_CatarinaAlcarva_final.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","date_created":"2023-04-06T07:54:09Z","oa_version":"Published Version","page":"115","abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"year":"2023","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}]},{"has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"corr_author":"1","type":"dissertation","file_date_updated":"2024-11-30T23:30:03Z","oa":1,"doi":"10.15479/at:ista:14622","day":"30","date_published":"2023-11-30T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Sack S. 2023. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","ieee":"S. Sack, “Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","apa":"Sack, S. (2023). <i>Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","short":"S. Sack, Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>"},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"article_processing_charge":"No","date_created":"2023-11-28T10:58:13Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13125"},{"status":"public","relation":"part_of_dissertation","id":"11471"},{"status":"public","id":"9760","relation":"part_of_dissertation"}]},"oa_version":"Published Version","ec_funded":1,"abstract":[{"lang":"eng","text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation."}],"page":"142","year":"2023","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IMB PhD Nomination Fellowship - Stefan Sack"},{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"ddc":["530"],"publication_status":"published","date_updated":"2026-04-07T13:53:47Z","month":"11","author":[{"last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","full_name":"Sack, Stefan"}],"_id":"14622","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-11-30T23:30:03Z","date_created":"2023-11-30T15:53:10Z","checksum":"068fd3570506ec42b2faa390de784bc4","file_size":11947523,"file_name":"PhD_Thesis.pdf","relation":"main_file","embargo":"2024-11-30","access_level":"open_access","content_type":"application/pdf","file_id":"14635","creator":"ssack"},{"file_name":"PhD Thesis (1).zip","content_type":"application/zip","access_level":"closed","relation":"source_file","creator":"ssack","file_id":"14636","date_updated":"2024-11-30T23:30:03Z","date_created":"2023-11-30T15:54:11Z","embargo_to":"open_access","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_size":18422964}],"status":"public","title":"Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems"},{"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2024-12-20T23:30:04Z","type":"dissertation","doi":"10.15479/at:ista:14697","oa":1,"day":"20","OA_place":"publisher","date_published":"2023-12-20T00:00:00Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"citation":{"mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"date_created":"2023-12-18T19:14:28Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14360"},{"id":"12272","relation":"part_of_dissertation","status":"public"},{"id":"14274","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"6328","relation":"part_of_dissertation"},{"id":"7885","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","page":"226","abstract":[{"lang":"eng","text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies."}],"ec_funded":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"year":"2023","date_updated":"2026-04-07T13:57:40Z","publication_status":"published","ddc":["570"],"author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"}],"month":"12","language":[{"iso":"eng"}],"_id":"14697","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","file":[{"file_name":"Thesis.pdf","relation":"main_file","embargo":"2024-12-20","content_type":"application/pdf","access_level":"open_access","file_id":"14699","creator":"jstopp","date_updated":"2024-12-20T23:30:04Z","date_created":"2023-12-20T09:35:34Z","file_size":51585778,"checksum":"457927165d5d556305d3086f6b83e5c7"},{"checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"embargo_to":"open_access","date_created":"2023-12-20T09:35:35Z","date_updated":"2024-12-20T23:30:04Z","file_id":"14700","creator":"jstopp","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Thesis.docx"}],"status":"public"},{"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin"}],"citation":{"mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2023-09-25T00:00:00Z","OA_place":"publisher","day":"25","oa":1,"doi":"10.15479/at:ista:14280","file_date_updated":"2024-10-05T22:30:03Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","title":"Spatiotemporal signaling during assembly of the bacterial divisome","file":[{"creator":"pradler","file_id":"14390","file_name":"PhD Thesis_Philipp Radler_20231004.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":114932847,"checksum":"87eef11fbc5c7df0826f12a3a629b444","date_updated":"2024-10-05T22:30:03Z","embargo_to":"open_access","date_created":"2023-10-04T10:11:53Z"},{"checksum":"3253e099b7126469d941fd9419d68b4f","file_size":37838778,"date_created":"2023-10-04T10:11:21Z","date_updated":"2024-10-05T22:30:03Z","creator":"pradler","file_id":"14391","access_level":"open_access","content_type":"application/pdf","embargo":"2024-10-04","relation":"main_file","file_name":"PhD Thesis_Philipp Radler_20231004.pdf"}],"status":"public","_id":"14280","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"month":"09","ddc":["572"],"date_updated":"2026-04-07T14:06:05Z","publication_status":"published","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"year":"2023","ec_funded":1,"abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"page":"156","oa_version":"Published Version","date_created":"2023-09-06T10:58:25Z","related_material":{"record":[{"id":"10934","relation":"research_data","status":"public"},{"status":"public","id":"11373","relation":"part_of_dissertation"},{"id":"7387","relation":"part_of_dissertation","status":"public"}]}},{"day":"23","OA_place":"publisher","date_published":"2023-03-23T00:00:00Z","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"alternative_title":["ISTA Thesis"],"citation":{"mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"corr_author":"1","file_date_updated":"2024-04-22T22:30:06Z","type":"dissertation","doi":"10.15479/at:ista:12781","oa":1,"date_updated":"2026-04-07T14:10:40Z","publication_status":"published","ddc":["570","572"],"author":[{"last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","first_name":"Vladyslav"}],"month":"03","language":[{"iso":"eng"}],"_id":"12781","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","status":"public","file":[{"creator":"vkravchu","file_id":"12852","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo":"2024-04-20","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":6071553,"checksum":"5ebb6345cb4119f93460c81310265a6d","date_updated":"2024-04-22T22:30:06Z","date_created":"2023-04-19T14:33:41Z"},{"checksum":"c12055c48411d030d2afa51de2166221","file_size":19468766,"date_created":"2023-04-19T14:33:52Z","date_updated":"2024-04-22T22:30:06Z","file_id":"12853","creator":"vkravchu","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo":"2024-04-20","access_level":"open_access","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx"}],"date_created":"2023-03-31T12:24:42Z","related_material":{"record":[{"status":"public","id":"12138","relation":"part_of_dissertation"}]},"oa_version":"Published Version","page":"127","ec_funded":1,"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697"}],"year":"2023"}]