[{"supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"type":"dissertation","article_processing_charge":"No","oa_version":"Published Version","_id":"20964","doi":"10.15479/AT-ISTA-20964","citation":{"ieee":"D. Vladimirtsev, “Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels,” Institute of Science and Technology Austria, 2026.","short":"D. Vladimirtsev, Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels, Institute of Science and Technology Austria, 2026.","ista":"Vladimirtsev D. 2026. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria.","apa":"Vladimirtsev, D. (2026). <i>Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20964\">https://doi.org/10.15479/AT-ISTA-20964</a>","mla":"Vladimirtsev, Dmitrii. <i>Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20964\">10.15479/AT-ISTA-20964</a>.","chicago":"Vladimirtsev, Dmitrii. “Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20964\">https://doi.org/10.15479/AT-ISTA-20964</a>.","ama":"Vladimirtsev D. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20964\">10.15479/AT-ISTA-20964</a>"},"page":"22","date_updated":"2026-04-07T11:41:44Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2026-01-28T12:38:19Z","language":[{"iso":"eng"}],"month":"01","degree_awarded":"MS","day":"14","alternative_title":["ISTA Master’s Thesis"],"status":"public","file":[{"date_created":"2026-01-21T14:12:13Z","file_name":"2026_Vladimirtsev_Dmitrii_Thesis.pdf","content_type":"application/pdf","date_updated":"2026-01-21T14:12:13Z","access_level":"closed","file_id":"21033","embargo_to":"open_access","embargo":"2027-01-01","file_size":2867531,"creator":"dvladimi","checksum":"812857b2fbe3f6113bef22fd04bccd3e","relation":"main_file"},{"access_level":"closed","date_updated":"2026-01-28T12:38:19Z","file_id":"21034","date_created":"2026-01-21T14:41:58Z","content_type":"application/x-zip-compressed","file_name":"Source Files.zip","relation":"source_file","creator":"dvladimi","checksum":"2b969f97f8d7461bea3d255f48c2219c","file_size":25023066}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","corr_author":"1","title":"Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"id":"20982","relation":"part_of_dissertation","status":"public"}]},"date_published":"2026-01-14T00:00:00Z","date_created":"2026-01-09T09:22:48Z","ddc":["570"],"publication_identifier":{"issn":["2791-4585"]},"year":"2026","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii"}],"OA_place":"publisher"},{"date_updated":"2026-03-13T13:37:20Z","oa":1,"acknowledgement":"This work is part of the project VAMOS, which has received funding from the European\r\nResearch Council (ERC) under grant agreement No. 101020093, and the Austrian Science\r\nFund (FWF) SFB project SpyCoDe F8502.\r\n","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"60","citation":{"ieee":"M. Karimi, “Privacy-preserving runtime verification,” Institute of Science and Technology Austria, 2026.","short":"M. Karimi, Privacy-Preserving Runtime Verification, Institute of Science and Technology Austria, 2026.","ista":"Karimi M. 2026. Privacy-preserving runtime verification. Institute of Science and Technology Austria.","apa":"Karimi, M. (2026). <i>Privacy-preserving runtime verification</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21401\">https://doi.org/10.15479/AT-ISTA-21401</a>","mla":"Karimi, Mahyar. <i>Privacy-Preserving Runtime Verification</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21401\">10.15479/AT-ISTA-21401</a>.","chicago":"Karimi, Mahyar. “Privacy-Preserving Runtime Verification.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21401\">https://doi.org/10.15479/AT-ISTA-21401</a>.","ama":"Karimi M. Privacy-preserving runtime verification. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21401\">10.15479/AT-ISTA-21401</a>"},"type":"dissertation","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"},{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512","name":"Security and Privacy by Design for Complex Systems"}],"_id":"21401","abstract":[{"text":"Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification.\r\n\r\nIn this thesis, we propose a protocol for privacy-preserving runtime verification of systems against formal sequential specifications. We develop the protocol in two steps. In the first step, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. In the second step, we extend the protocol to ensure that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocol adapts and improves existing techniques used in cryptography, and more specifically, multi-party computation.\r\n\r\nThe sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocol exchanges a single message per observation step, after an initialization phase. This design minimizes communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally.\r\n","lang":"eng"}],"doi":"10.15479/AT-ISTA-21401","oa_version":"Published Version","article_processing_charge":"No","supervisor":[{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"day":"05","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"03","file_date_updated":"2026-03-10T15:20:09Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"has_accepted_license":"1","corr_author":"1","publication_status":"published","file":[{"relation":"main_file","checksum":"3f49f05c9d123e14d7adb73d3bc50fe2","creator":"mkarimi","file_size":766048,"file_id":"21404","date_updated":"2026-03-10T15:20:09Z","access_level":"open_access","content_type":"application/pdf","file_name":"2026_Karimi_Mahyar_Thesis.pdf","date_created":"2026-03-06T14:06:25Z"},{"content_type":"application/zip","file_name":"2026_Karimi_Mahyar_Thesis_src.zip","date_created":"2026-03-06T14:06:25Z","file_id":"21405","access_level":"closed","date_updated":"2026-03-06T14:06:25Z","checksum":"8fb9db4b4187e26443369a993427a5ff","creator":"mkarimi","file_size":1243394,"relation":"source_file"}],"alternative_title":["ISTA Master’s Thesis"],"status":"public","keyword":["Privacy-preserving verification","Runtime verification","Monitoring","Reactive functionalities","Cryptographic protocols"],"year":"2026","author":[{"first_name":"Mahyar","id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","full_name":"Karimi, Mahyar","orcid":"0009-0005-0820-1696","last_name":"Karimi"}],"OA_place":"repository","publisher":"Institute of Science and Technology Austria","ddc":["000"],"date_created":"2026-03-05T15:20:47Z","publication_identifier":{"issn":["2791-4585"]},"ec_funded":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21020"}]},"date_published":"2026-03-05T00:00:00Z","title":"Privacy-preserving runtime verification"},{"oa_version":"Published Version","article_processing_charge":"No","_id":"22399","abstract":[{"lang":"eng","text":"Gaining an understanding of how biological regulation evolves is a fundamental research \r\nquestion in both evolutionary biology and molecular genetics. In order to gain more insight \r\ninto this topic, we focus on studying the simple gene regulatory system of the lac operon in \r\nE. coli. We show that simple population genetic models can shed light on evolution \r\nexperiments and that this combined approach of modelling the experimental system gives \r\ninsight to better understand the causes of evolutionary change in the experiment. We also \r\nstudy the natural diversity in the lac operon from 308 publicly available E. coli genomes that \r\ncome from various host species and different regions of the world. Evidence that selection is \r\ngenerally maintaining the function of the lac operon across the sample regardless of host \r\nspecies is provided and we show that different protein coding genes in the operon are under \r\ndifferent selective constraints on protein sequence preservation. A similar frameshift \r\nmutation found in experimental evolution studies is shown to be present in the sample we \r\nanalyzed, indicating that selectively relevant variants in evolution experiments are also \r\npresent in natural populations. We show that there is no simple phylogenetic relationship \r\nbetween host species, geographical location and the lac operon sequence. Finally, we argue \r\nthat a combined approach of comparative genomics, experimental evolution and theoretical \r\nmodelling contributes to a more complete understanding of molecular evolution. "}],"doi":"10.15479/AT-ISTA-22399","type":"dissertation","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-31T10:52:08Z","citation":{"mla":"Spasić, Aleksa. <i>Studying the Evolutionary Systems Biology of the Lac Operon</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>.","chicago":"Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>.","ama":"Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>","ieee":"A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026.","short":"A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026.","ista":"Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria.","apa":"Spasić, A. (2026). <i>Studying the evolutionary systems biology of the lac operon</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>"},"page":"32","doi_confirm":"1","file_date_updated":"2026-07-27T13:07:23Z","day":"27","language":[{"iso":"eng"}],"month":"07","degree_awarded":"MS","file":[{"date_created":"2026-07-27T13:00:07Z","file_name":"Aleksa_Spasic_Thesis_final.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2026-07-27T13:00:07Z","file_id":"22588","file_size":1986078,"creator":"aspasic","checksum":"c29880dd71fcc37f23ac6e2843066ede","relation":"main_file"},{"relation":"source_file","creator":"aspasic","checksum":"4ebe3bd2d833d913c0756343cca5e5f0","file_size":1868853,"file_id":"22589","date_updated":"2026-07-27T13:07:23Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_final.docx","date_created":"2026-07-27T13:00:22Z"}],"status":"public","alternative_title":["ISTA Master’s Thesis"],"corr_author":"1","publication_status":"published","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"CaGu"}],"date_published":"2026-07-27T00:00:00Z","title":"Studying the evolutionary systems biology of the lac operon","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Spasić, Aleksa","last_name":"Spasić","first_name":"Aleksa","id":"ecee9d38-4040-11ef-8843-b941efb445d6"}],"OA_place":"publisher","year":"2026","das_tickbox":"0","publication_identifier":{"issn":["2791-4585"]},"date_created":"2026-07-25T13:08:32Z","ddc":["576"]},{"OA_place":"publisher","author":[{"first_name":"Kanah","id":"7703505d-3211-11ee-a6a9-a2ab9d936c15","last_name":"Smith","full_name":"Smith, Kanah"}],"publisher":"Institute of Science and Technology Austria","keyword":["asteroseismology","stellar physics","red giant","magnetism","suppressed"],"year":"2025","publication_identifier":{"issn":["2791-4585"]},"ddc":["520"],"date_created":"2025-06-20T13:27:08Z","date_published":"2025-10-08T00:00:00Z","title":"Exploring internal magnetism in partially suppressed red giant stars","corr_author":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LiBu"}],"has_accepted_license":"1","file":[{"checksum":"80d241d11b69af771c1fab0998be4f19","creator":"ksmith","file_size":8263624,"relation":"source_file","content_type":"application/zip","file_name":"2025_Smith_Kanah_Thesis.zip","date_created":"2025-10-08T08:01:42Z","file_id":"20434","access_level":"closed","date_updated":"2025-10-08T09:45:33Z"},{"content_type":"application/pdf","success":1,"file_name":"2025_Smith_Kanah_Thesis.pdf","date_created":"2025-10-09T14:38:57Z","file_id":"20439","date_updated":"2025-10-09T14:38:57Z","access_level":"open_access","checksum":"13cb48cc98e00fdfe32f3ff66f17aa26","creator":"ksmith","file_size":9748339,"relation":"main_file"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"day":"08","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"10","file_date_updated":"2025-10-09T14:38:57Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"I would like to give thanks to myself for my hard work on this document. This paper includes data collected by the Kepler mission and obtained from the MAST data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is operated by the Association of\r\nUniversities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.\r\n","date_updated":"2026-04-07T12:01:37Z","page":"38","citation":{"ama":"Smith K. Exploring internal magnetism in partially suppressed red giant stars. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>","mla":"Smith, Kanah. <i>Exploring Internal Magnetism in Partially Suppressed Red Giant Stars</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>.","chicago":"Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red Giant Stars.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>.","short":"K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant Stars, Institute of Science and Technology Austria, 2025.","ista":"Smith K. 2025. Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria.","apa":"Smith, K. (2025). <i>Exploring internal magnetism in partially suppressed red giant stars</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>","ieee":"K. Smith, “Exploring internal magnetism in partially suppressed red giant stars,” Institute of Science and Technology Austria, 2025."},"doi":"10.15479/AT-ISTA-19853","_id":"19853","abstract":[{"lang":"eng","text":"The internal dynamical properties of red giant stars have been explored extensively in recent\r\nyears as a result of the increase in high precision data availability from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been\r\ndiscovered that some of these stars are not behaving as expected. Red giants are stars that have\r\nevolved off of the main sequence after having completed fusing hydrogen into helium in their\r\ncore. Observational data shows that the cores are rotating significantly slower than models can\r\nrecreate consistently across evolutionary stages. This discrepancy has prompted investigation\r\ninto the efficiency of angular momentum transport mechanisms and mixing processes including\r\nmeridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc., to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only\r\nway in which the deep stellar interior can be probed and subsequently characterized; this is\r\npossible as global oscillations modulating the stellar surface are effected by internal processes.\r\nFor red giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes; resonating in the radiative interior) couple to create mixed modes. These\r\nmixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two\r\ndifferent power laws, respectively. And the other being a reduced visibility of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted; one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of\r\ntheir power spectra rather than across the entire spectra, will be the subject of this study as\r\nthe respective mode amplitudes are still visible at high frequencies.\r\nAs such, this study will search for asymmetric frequency shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the aim here is to investigate if both\r\nmode suppression and magnetic shifting of dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038,\r\na target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its\r\nmagnetic parameters. I present a novel method to model the stellar power spectra of\r\npartially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With the results of this study I aim at constraining\r\nthe cause of this partial dipole mode amplitude suppression, allowing for more detailed\r\nstudies regarding their astrophysical nature. Furthermore, the long term hope for the method\r\nused in this study will be to expand the sample of partially suppressed red giants and fit their\r\nasteroseismic parameters accordingly."}],"article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","supervisor":[{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"}]},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13097"}]},"date_published":"2025-12-09T00:00:00Z","title":"Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog","year":"2025","author":[{"last_name":"Wilson","full_name":"Wilson, Alexia C","orcid":"0000-0001-6191-1367","id":"5230e794-15b2-11ec-abd3-e2d5335ebd1d","first_name":"Alexia C"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","ddc":["570","596","005"],"date_created":"2025-12-08T09:49:41Z","publication_identifier":{"issn":["2791-4585"]},"file":[{"relation":"source_file","file_size":566072368,"checksum":"9e3b6b73f8cbec2c3687d17fe8e30410","creator":"awilson","file_id":"20919","date_updated":"2026-01-02T13:05:07Z","access_level":"closed","file_name":"tadpoleAdEx.zip","content_type":"application/zip","date_created":"2026-01-01T17:26:30Z"},{"date_created":"2026-01-04T12:58:49Z","content_type":"application/pdf","success":1,"file_name":"Masters_Thesis_Alexia_Wilson_FINAL_pdfA.pdf","access_level":"open_access","date_updated":"2026-01-04T12:58:49Z","file_id":"20923","checksum":"13f4c0d33923e9d5c9d56731345cf21d","creator":"awilson","file_size":7170097,"relation":"main_file"}],"alternative_title":["ISTA Master's Thesis"],"status":"public","department":[{"_id":"GradSch"},{"_id":"TiVo"},{"_id":"LoSw"}],"has_accepted_license":"1","corr_author":"1","publication_status":"published","file_date_updated":"2026-01-04T12:58:49Z","doi_confirm":"1","day":"09","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"12","type":"dissertation","doi":"10.15479/AT-ISTA-20735","_id":"20735","abstract":[{"lang":"eng","text":"Left–right alternation is a defining feature of spinal locomotor circuits, yet the level of neuronal\r\ndetail required to generate and maintain this pattern remains unclear. This thesis investigates how\r\nmodels spanning multiple levels of abstraction—from biophysically detailed Hodgkin–Huxley (HH)\r\nneurons to adaptive integrate–and–fire (I&F) formulations and synfire-chain modules—can account\r\nfor the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole. The guiding\r\nhypothesis is that a small set of neuronal mechanisms is sufficient to reproduce the essential features\r\nof rhythmic alternation, and that moving between modeling scales helps distinguish core principles\r\nfrom biological detail.\r\nA minimal bilateral HH network comprising only four canonical neuron classes—excitatory\r\ndescending interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory\r\ninterneurons (aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce\r\nexperimentally observed firing modes, the model demonstrated that rebound-prone dIN excitability,\r\ncontralateral inhibition and modest electrical coupling are sufficient to generate stable alternating\r\nactivity, even in very small networks. These results motivated the transition to simpler models\r\ncapable of efficient analysis and scaling.\r\nAdaptive exponential I&F (AdEx) neurons were calibrated to physiological recordings using\r\nsimulation-based inference, yielding tonic and phasic/rebound templates that preserved the key\r\ndynamical signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying\r\nsingle-spike responses and rebound firing in dINs. At network level, the I&F models robustly\r\nreproduced left–right alternation, while highlighting constraints on synaptic kinetics and adaptation\r\nneeded to avoid multi-spike responses.\r\nFinally, a synfire-chain framework provided a complementary, timing-centric perspective, demonstrating how precise spike synchrony, synaptic delays and minimal inhibitory coupling can generate\r\nalternating left–right sequences in a feedforward setting. Together, these approaches converge on a\r\ncommon conclusion: rebound-prone ipsilateral excitation combined with precisely timed contralateral inhibition constitutes a sufficient substrate for alternating spinal rhythms.\r\nBy integrating bottom-up and top-down modeling strategies, this thesis provides a unified, extensible framework for studying spinal pattern generation. The results show that essential locomotor\r\ndynamics can be captured across multiple abstraction levels, offering both mechanistic insight and\r\npractical tools for future data-driven investigations of spinal circuit development, robustness and\r\nmodulation."}],"oa_version":"Published Version","article_processing_charge":"No","supervisor":[{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger"}],"date_updated":"2026-07-29T12:55:12Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"page":"110","citation":{"ama":"Wilson AC. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20735\">10.15479/AT-ISTA-20735</a>","chicago":"Wilson, Alexia C. “Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20735\">https://doi.org/10.15479/AT-ISTA-20735</a>.","mla":"Wilson, Alexia C. <i>Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20735\">10.15479/AT-ISTA-20735</a>.","apa":"Wilson, A. C. (2025). <i>Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20735\">https://doi.org/10.15479/AT-ISTA-20735</a>","ista":"Wilson AC. 2025. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology Austria.","short":"A.C. Wilson, Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog, Institute of Science and Technology Austria, 2025.","ieee":"A. C. Wilson, “Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog,” Institute of Science and Technology Austria, 2025."}},{"publication_identifier":{"issn":["2791-4585"]},"date_created":"2024-11-27T09:12:02Z","ddc":["530"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"first_name":"Cecelia N","id":"2a69ab4b-896a-11ed-bdf8-cb8641cf2b21","last_name":"Mweka","full_name":"Mweka, Cecelia N"}],"year":"2024","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"title":"Non equilibrium dynamics of driven individual particles and 3D printing across scales","date_published":"2024-11-29T00:00:00Z","corr_author":"1","publication_status":"published","has_accepted_license":"1","department":[{"_id":"GradSch"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"file":[{"relation":"main_file","file_size":3836671,"creator":"cmweka","checksum":"054ed7a5e5ae6e7220e6bb37ea57a3c3","file_id":"18597","date_updated":"2024-11-28T12:50:32Z","access_level":"open_access","file_name":"Cecelia Mweka Master Thesis.pdf","content_type":"application/pdf","success":1,"date_created":"2024-11-28T12:50:32Z"},{"date_updated":"2024-12-13T11:30:53Z","access_level":"closed","file_id":"18598","date_created":"2024-11-28T12:51:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Cecelia Mweka Master Thesis.docx","relation":"source_file","checksum":"7d7d9299f090d83e628d65d93116e8c2","creator":"cmweka","file_size":7068210}],"language":[{"iso":"eng"}],"month":"11","degree_awarded":"MS","day":"29","file_date_updated":"2024-12-13T11:30:53Z","citation":{"mla":"Mweka, Cecelia N. <i>Non Equilibrium Dynamics of Driven Individual Particles and 3D Printing across Scales</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18588\">10.15479/at:ista:18588</a>.","chicago":"Mweka, Cecelia N. “Non Equilibrium Dynamics of Driven Individual Particles and 3D Printing across Scales.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18588\">https://doi.org/10.15479/at:ista:18588</a>.","ama":"Mweka CN. Non equilibrium dynamics of driven individual particles and 3D printing across scales. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18588\">10.15479/at:ista:18588</a>","ieee":"C. N. Mweka, “Non equilibrium dynamics of driven individual particles and 3D printing across scales,” Institute of Science and Technology Austria, 2024.","short":"C.N. Mweka, Non Equilibrium Dynamics of Driven Individual Particles and 3D Printing across Scales, Institute of Science and Technology Austria, 2024.","apa":"Mweka, C. N. (2024). <i>Non equilibrium dynamics of driven individual particles and 3D printing across scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18588\">https://doi.org/10.15479/at:ista:18588</a>","ista":"Mweka CN. 2024. Non equilibrium dynamics of driven individual particles and 3D printing across scales. Institute of Science and Technology Austria."},"page":"61","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"I would like to acknowledge Scott Waitukaitis and Jérémie Palacci, for their supervision, and their extensive support of my learning. \r\n\r\nFor the beautiful characterization images used in this work, I would like to thank Dr. Daniel Grober, Samuel Hajek and Felix Pertl.\r\n\r\nThe Palacci group, particularly Malina Strugaru and Dan Grober, for their continuous guidance in decoding and following my streams of thought.\r\n\r\nTo the Waitukaitis group, for helping me find my footing in science, and making me feel at\r\nhome.\r\n\r\nTo the Nanofabrication Facility (NFF) at ISTA, for training me in significant aspects of my research. The MIBA Facility, and particularly Todor Asenov for consistently picking up the phone for my machining and designing needs.\r\n\r\nTo my friends, Mariana, Lenka, Aaron, Rebecca, Eavan who provided an ear, wine, and a lot more when I needed to vent, talk through my crises as well as experiment. For the walks, for the coffees, for reading through my work and providing edits, for dinners to take me out of blocks and binds and for cheering me on when it felt insurmountable. \r\n\r\nFinally, I am grateful to Griff and Fletcher, whose music helped me through several blocks, especially with my writing.\r\n\r\nMy science would not have been possible without the guidance, support and contributions of\r\nall these people, and more.","date_updated":"2026-04-07T12:42:13Z","supervisor":[{"last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"article_processing_charge":"No","oa_version":"Published Version","_id":"18588","doi":"10.15479/at:ista:18588","abstract":[{"lang":"eng","text":"This thesis is an experimental work about two distinct research projects that evolved from a single project: non-equilibrium dynamics of an acoustically vibrated particle and microfabrication of particles with nano-scale 3D printing. The first project explores non equilibrium dynamics of a particle driven by ultrasonic vibrations. We design an experimental system consisting of an electromechanical vibration scheme to drive the particle’s vibrations and an imaging scheme to track its trajectories. We study the trajectories to determine how the particle’s dynamics evolve under the driven conditions, considering out of equilibrium systems in the context of equilibrium statistical mechanics. Using a Langevin framework and the Boltzmann factor, we characterize the particle’s dynamics as complex; the particle motion\r\nis not purely diffusive. We extract physical parameters like spring constant, effective temperature, damping coefficient and resonance frequency.\r\n\r\nIn the second project, we explore and develop techniques in the design and microfabrication of particles across scales. Microfabrication involves building structures at the micron or submicron scale. These designed miniaturized patterns, objects, or devices are useful in biophysics, pharmacology, medical biology, and nanotechnology. We specifically apply two-photon polymerization, a form of 3D nano printing. We print millimetric particles, characterizing different designs to evaluate and showcase the resolution, aspect ratio integrity and print quality of the printing process. We also design and fabricate a microsensor to deflect under applicable force of order 0.1 pN. We present fundamental concepts needed to design the microsensor, showcasing 3D printing at considerably smaller scales down to the µm or below."}],"type":"dissertation"},{"article_processing_charge":"No","oa_version":"Published Version","_id":"18301","abstract":[{"text":"Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh.","lang":"eng"}],"doi":"10.15479/at:ista:18301","type":"dissertation","supervisor":[{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:02:36Z","citation":{"ama":"Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>","mla":"Etemadi, Arian. <i>Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>.","chicago":"Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>.","short":"A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024.","apa":"Etemadi, A. (2024). <i>Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>","ista":"Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria.","ieee":"A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024."},"page":"39","file_date_updated":"2024-10-24T14:34:54Z","day":"15","language":[{"iso":"eng"}],"month":"10","degree_awarded":"MS","file":[{"file_name":"thesis-arian-etemadi.pdf","success":1,"content_type":"application/pdf","date_created":"2024-10-24T14:34:42Z","file_id":"18469","access_level":"open_access","date_updated":"2024-10-24T14:34:42Z","file_size":8914218,"creator":"aetemadi","checksum":"80fb7923e229ad9d39253d7c8a8083d0","relation":"main_file"},{"relation":"source_file","file_size":9802650,"creator":"aetemadi","checksum":"1c02586ed7d441d5ec441867650568d1","date_updated":"2024-10-24T14:34:54Z","access_level":"closed","file_id":"18470","date_created":"2024-10-24T14:34:54Z","file_name":"thesis-arian-etemadi-latex-source.zip","content_type":"application/x-zip-compressed"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"corr_author":"1","publication_status":"published","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_published":"2024-10-15T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"17219","status":"public"}]},"title":"Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"last_name":"Etemadihaghighi","full_name":"Etemadihaghighi, Arian","first_name":"Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f"}],"year":"2024","keyword":["surface tracking","non-manifold","hole-filling","topology change","multi-material","solid-modeling"],"publication_identifier":{"issn":["2791-4585"]},"date_created":"2024-10-11T19:52:20Z","ddc":["000"]},{"file_date_updated":"2025-05-02T22:30:04Z","day":"02","degree_awarded":"MS","month":"05","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15352","_id":"15352","abstract":[{"text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. ","lang":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","supervisor":[{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-04-07T13:05:00Z","page":"54","citation":{"ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>"},"date_published":"2024-05-02T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","OA_place":"publisher","author":[{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie","full_name":"Murmann, Julie Stefanie","last_name":"Murmann"}],"publisher":"Institute of Science and Technology Austria","year":"2024","publication_identifier":{"issn":["2791-4585"]},"ddc":["570"],"date_created":"2024-05-02T08:31:38Z","file":[{"date_created":"2024-05-02T12:26:13Z","content_type":"application/pdf","file_name":"Murmann_Thesis_final_2024_2.pdf","access_level":"open_access","date_updated":"2025-05-02T22:30:04Z","file_id":"15354","creator":"cchlebak","checksum":"095817a6c944954ac3f277e547031a33","file_size":5936142,"embargo":"2025-05-02","relation":"main_file"},{"file_name":"Murmann_Thesis_final_2024.zip","content_type":"application/x-zip-compressed","date_created":"2024-05-02T12:37:56Z","file_id":"15355","embargo_to":"open_access","date_updated":"2025-05-02T22:30:04Z","access_level":"closed","file_size":20645510,"creator":"cchlebak","checksum":"43b632255372973a437ac87739cfd4db","relation":"source_file"}],"status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["ISTA Master's Thesis"],"corr_author":"1","publication_status":"published","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"has_accepted_license":"1"},{"day":"13","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"08","file_date_updated":"2025-02-14T23:30:03Z","date_updated":"2026-04-07T13:03:41Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"page":"60","citation":{"ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria.","apa":"Villanueva Marijuan, A. (2024). <i>Bayesian linear regression for analyzing general omics data with time-to-event phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>","short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>.","mla":"Villanueva Marijuan, Ariadna. <i>Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>"},"type":"dissertation","_id":"17368","doi":"10.15479/at:ista:17368","abstract":[{"lang":"eng","text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n"}],"oa_version":"Published Version","article_processing_charge":"No","supervisor":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"keyword":["Epigenetics","Multi-omics","Bayesian regression"],"year":"2024","OA_place":"publisher","author":[{"last_name":"Villanueva Marijuan","full_name":"Villanueva Marijuan, Ariadna","first_name":"Ariadna","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540"}],"publisher":"Institute of Science and Technology Austria","ddc":["610"],"date_created":"2024-08-02T10:52:40Z","publication_identifier":{"issn":["2791-4585"]},"date_published":"2024-08-13T00:00:00Z","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"has_accepted_license":"1","publication_status":"published","corr_author":"1","file":[{"file_size":13052436,"embargo":"2025-02-14","checksum":"0c2daa174609f0c00919dccc5701d375","creator":"avillanu","relation":"main_file","date_created":"2024-08-14T11:51:24Z","file_name":"Masters_thesis_AriadnaVillanueva.pdf","content_type":"application/pdf","date_updated":"2025-02-14T23:30:03Z","access_level":"open_access","file_id":"17433"},{"relation":"source_file","file_size":45642547,"creator":"avillanu","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","date_updated":"2025-02-14T23:30:03Z","access_level":"closed","file_id":"17434","embargo_to":"open_access","date_created":"2024-08-14T11:51:57Z","file_name":"Masters thesis-AriadnaVillanueva.zip","content_type":"application/zip"}],"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"alternative_title":["ISTA Master's Thesis"],"status":"public"},{"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:29:29Z","citation":{"ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>.","mla":"Köse, Seyda. <i>Exterior Algebra and Combinatorics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","apa":"Köse, S. (2023). <i>Exterior algebra and combinatorics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023."},"page":"26","oa_version":"Published Version","article_processing_charge":"No","doi":"10.15479/at:ista:13331","_id":"13331","abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"type":"dissertation","supervisor":[{"orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"day":"31","month":"07","language":[{"iso":"eng"}],"degree_awarded":"MS","file_date_updated":"2023-08-03T15:28:55Z","publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"file":[{"creator":"skoese","checksum":"96ee518d796d02af71395622c45de03c","file_size":28684,"relation":"source_file","date_created":"2023-07-31T10:16:32Z","content_type":"application/x-zip-compressed","file_name":"Exterior Algebra and Combinatorics.zip","access_level":"closed","date_updated":"2023-07-31T10:16:32Z","file_id":"13333"},{"relation":"main_file","creator":"skoese","checksum":"f610f4713f88bc477de576aaa46b114e","file_size":4953418,"date_updated":"2023-08-03T15:28:55Z","access_level":"open_access","file_id":"13480","date_created":"2023-08-03T15:28:55Z","success":1,"content_type":"application/pdf","file_name":"thesis-pdfa.pdf"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0009-0008-0457-9730","full_name":"Köse, Seyda","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda"}],"OA_place":"publisher","year":"2023","publication_identifier":{"issn":["2791-4585"]},"date_created":"2023-07-31T10:20:55Z","ddc":["510","516"],"date_published":"2023-07-31T00:00:00Z","related_material":{"record":[{"id":"12680","relation":"part_of_dissertation","status":"public"}]},"title":"Exterior algebra and combinatorics"},{"date_published":"2023-02-08T00:00:00Z","title":"Panoramic functional gradients across the mouse retina","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"last_name":"Kirillova","full_name":"Kirillova, Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia"}],"year":"2023","publication_identifier":{"issn":["2791-4585"]},"date_created":"2023-02-09T07:45:05Z","ddc":["570"],"file":[{"file_id":"12532","date_updated":"2024-02-09T23:30:03Z","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","date_created":"2023-02-09T08:03:32Z","relation":"main_file","creator":"cchlebak","checksum":"57d8da3a6c749eb1556b7435fe266a5f","embargo":"2024-02-08","file_size":8369317},{"relation":"source_file","creator":"cchlebak","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_size":11204408,"access_level":"closed","date_updated":"2024-02-09T23:30:03Z","embargo_to":"open_access","file_id":"12535","date_created":"2023-02-10T09:32:06Z","content_type":"application/x-zip-compressed","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file_date_updated":"2024-02-09T23:30:03Z","day":"08","month":"02","language":[{"iso":"eng"}],"degree_awarded":"MS","oa_version":"Published Version","article_processing_charge":"No","_id":"12531","doi":"10.15479/at:ista:12531","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"type":"dissertation","supervisor":[{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-04-07T14:06:26Z","citation":{"ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>"},"page":"46"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-04-07T14:01:51Z","page":"21","citation":{"apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>."},"abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"_id":"12800","doi":"10.15479/at:ista:12800","article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"day":"05","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"04","file_date_updated":"2023-06-02T22:30:04Z","publication_status":"published","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","file":[{"access_level":"closed","date_updated":"2023-06-02T22:30:04Z","embargo_to":"open_access","file_id":"12805","date_created":"2023-04-06T06:09:40Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"Dispersaldata.xlsx","relation":"supplementary_material","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","creator":"mjulseth","file_size":52795},{"access_level":"open_access","date_updated":"2023-06-02T22:30:04Z","file_id":"12806","date_created":"2023-04-06T06:11:27Z","content_type":"application/vnd.wolfram.nb","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","relation":"supplementary_material","creator":"mjulseth","checksum":"5a13b6d204371572e249f03795bc0d04","embargo":"2023-06-01","file_size":787239},{"embargo_to":"open_access","file_id":"12812","access_level":"closed","date_updated":"2023-06-02T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"ThesisMaraJulseth_04_23.docx","date_created":"2023-04-06T08:26:12Z","relation":"source_file","creator":"mjulseth","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_size":1061763},{"relation":"main_file","embargo":"2023-06-01","file_size":1741364,"creator":"mjulseth","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_id":"12813","access_level":"open_access","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf","content_type":"application/pdf","date_created":"2023-04-06T08:26:37Z"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"OA_place":"publisher","author":[{"last_name":"Julseth","full_name":"Julseth, Mara","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1"}],"publisher":"Institute of Science and Technology Austria","year":"2023","publication_identifier":{"issn":["2791-4585"]},"ddc":["576"],"date_created":"2023-04-04T18:57:11Z","date_published":"2023-04-05T00:00:00Z","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone"},{"file_date_updated":"2024-02-26T23:30:03Z","day":"24","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"08","doi":"10.15479/at:ista:14226","_id":"14226","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","supervisor":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-04-07T14:02:30Z","page":"43","citation":{"apa":"Stephenson, E. R. (2023). <i>Generalizing medial axes with homology switches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>.","mla":"Stephenson, Elizabeth R. <i>Generalizing Medial Axes with Homology Switches</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>."},"date_published":"2023-08-24T00:00:00Z","title":"Generalizing medial axes with homology switches","author":[{"orcid":"0000-0002-6862-208X","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","year":"2023","publication_identifier":{"issn":["2791-4585"]},"ddc":["500"],"date_created":"2023-08-24T13:01:18Z","file":[{"relation":"source_file","creator":"cchlebak","checksum":"453caf851d75c3478c10ed09bd242a91","file_size":15501411,"embargo_to":"open_access","file_id":"14227","date_updated":"2024-02-26T23:30:03Z","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"documents-export-2023-08-24.zip","date_created":"2023-08-24T13:02:49Z"},{"relation":"main_file","checksum":"7349d29963d6695e555e171748648d9a","creator":"cchlebak","embargo":"2024-02-25","file_size":6854783,"file_id":"14228","access_level":"open_access","date_updated":"2024-02-26T23:30:03Z","content_type":"application/pdf","file_name":"thesis_pdf_a.pdf","date_created":"2023-08-24T13:03:42Z"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"corr_author":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"has_accepted_license":"1"},{"publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"status":"public","alternative_title":["ISTA Master's Thesis"],"file":[{"content_type":"application/x-zip-compressed","file_name":"Thesis.zip","date_created":"2021-12-07T11:13:52Z","file_id":"10424","date_updated":"2022-03-10T12:10:25Z","access_level":"closed","creator":"cchlebak","checksum":"114e8f4b2c002c6c352416c12de2c695","file_size":394018,"relation":"source_file"},{"file_id":"10425","date_updated":"2022-03-10T12:10:25Z","access_level":"closed","file_name":"Preliminary_pages_Piankov.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-12-07T11:14:01Z","relation":"source_file","file_size":47638,"creator":"cchlebak","checksum":"cd15ae991ced352a9959815f794e657c"},{"date_created":"2021-12-07T11:20:35Z","file_name":"2021_Piankov_combined.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2021-12-07T11:20:35Z","file_id":"10426","file_size":484965,"creator":"cchlebak","checksum":"e6899c798b75ba42fab9822bce309050","relation":"main_file"}],"publication_identifier":{"issn":["2791-4585"]},"date_created":"2021-12-07T10:48:06Z","ddc":["530"],"publisher":"Institute of Science and Technology Austria","author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","first_name":"Anton","last_name":"Piankov","full_name":"Piankov, Anton"}],"OA_place":"publisher","year":"2021","title":"Towards designer materials using customizable particle shape","date_published":"2021-12-07T00:00:00Z","citation":{"mla":"Piankov, Anton. <i>Towards Designer Materials Using Customizable Particle Shape</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>.","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","apa":"Piankov, A. (2021). <i>Towards designer materials using customizable particle shape</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>"},"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T06:58:55Z","supervisor":[{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"}],"oa_version":"Published Version","article_processing_charge":"No","_id":"10422","doi":"10.15479/at:ista:10422","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"type":"dissertation","language":[{"iso":"eng"}],"month":"12","degree_awarded":"MS","day":"07","file_date_updated":"2022-03-10T12:10:25Z"}]