[{"doi":"10.15479/14530","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"file_date_updated":"2023-11-15T09:52:54Z","type":"dissertation","oa_version":"Updated Version","date_published":"2023-11-16T00:00:00Z","ddc":["530","570"],"author":[{"full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"page":"260","year":"2023","date_created":"2023-11-15T09:59:03Z","date_updated":"2023-11-30T10:55:13Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"file":[{"file_name":"Thesis_Riedl_2023_corr.pdf","date_created":"2023-11-15T09:52:54Z","file_id":"14536","content_type":"application/pdf","success":1,"date_updated":"2023-11-15T09:52:54Z","access_level":"open_access","relation":"main_file","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","file_size":36743942,"creator":"mriedl"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","_id":"14530","title":"Synchronization in collectively moving active matter","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10703"},{"status":"public","relation":"part_of_dissertation","id":"10791"},{"id":"7932","status":"public","relation":"part_of_dissertation"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"relation":"old_edition","status":"public","id":"12726"}]},"oa":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","status":"public","abstract":[{"lang":"eng","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.  "}],"day":"16","has_accepted_license":"1","supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"}],"keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"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>.","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>.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">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."}},{"file":[{"relation":"main_file","checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_size":2116426,"creator":"cchlebak","file_name":"main.pdf","date_created":"2023-11-15T13:43:28Z","file_id":"14540","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-11-15T13:43:28Z","success":1},{"file_name":"thesis_source.zip","date_created":"2023-11-15T13:44:24Z","content_type":"application/x-zip-compressed","file_id":"14541","date_updated":"2023-11-15T13:44:24Z","access_level":"closed","relation":"source_file","checksum":"80ca37618a3c7b59866875f8be9b15ed","file_size":35884057,"creator":"cchlebak"}],"date_updated":"2025-07-14T09:10:10Z","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"page":"256","date_created":"2023-11-15T13:39:10Z","year":"2023","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"article_processing_charge":"No","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"file_date_updated":"2023-11-15T13:44:24Z","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/14539","ddc":["000"],"author":[{"first_name":"Dorde","full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699"}],"date_published":"2023-11-15T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"status":"public","ec_funded":1,"degree_awarded":"PhD","citation":{"apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>.","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>"},"supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"day":"15","title":"Automated verification and control of infinite state stochastic systems","related_material":{"record":[{"id":"1194","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12000"},{"relation":"part_of_dissertation","status":"public","id":"12511"},{"id":"14600","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14601"},{"id":"9644","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10414"}]},"oa":1,"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14539","month":"11","alternative_title":["ISTA Thesis"],"department":[{"_id":"KrCh"},{"_id":"GradSch"}]},{"department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges  partial  financial  support  by  the  ERC  Advanced  Grant  “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14542","month":"10","title":"Universality in low-dimensional BCS theory","oa":1,"publication_status":"epub_ahead","article_type":"original","day":"31","has_accepted_license":"1","citation":{"ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023.","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>, 2360005, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","apa":"Henheik, S. J., Lauritsen, A. B., &#38; Roos, B. (2023). Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>.","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. 2023. doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023)."},"ec_funded":1,"article_number":"2360005 ","status":"public","abstract":[{"lang":"eng","text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."}],"external_id":{"arxiv":["2301.05621"]},"oa_version":"Published Version","date_published":"2023-10-31T00:00:00Z","publication":"Reviews in Mathematical Physics","author":[{"full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","last_name":"Henheik","orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"},{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara","first_name":"Barbara","last_name":"Roos"}],"doi":"10.1142/s0129055x2360005x","publisher":"World Scientific Publishing","arxiv":1,"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1142/S0129055X2360005X","open_access":"1"}],"quality_controlled":"1","year":"2023","date_created":"2023-11-15T23:48:14Z","date_updated":"2023-11-20T10:04:38Z","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427"}]},{"language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1093/brain/awad380","publisher":"Oxford University Press","publication":"Brain","author":[{"full_name":"Kaiyrzhanov, Rauan","first_name":"Rauan","last_name":"Kaiyrzhanov"},{"last_name":"Rad","first_name":"Aboulfazl","full_name":"Rad, Aboulfazl"},{"first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia","last_name":"Lin"},{"full_name":"Bertoli-Avella, Aida","first_name":"Aida","last_name":"Bertoli-Avella"},{"last_name":"Kallemeijn","full_name":"Kallemeijn, Wouter W","first_name":"Wouter W"},{"first_name":"Annie","full_name":"Godwin, Annie","last_name":"Godwin"},{"last_name":"Zaki","first_name":"Maha S","full_name":"Zaki, Maha S"},{"orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang","first_name":"Kevin","full_name":"Huang, Kevin"},{"last_name":"Lau","first_name":"Tracy","full_name":"Lau, Tracy"},{"last_name":"Petree","first_name":"Cassidy","full_name":"Petree, Cassidy"},{"first_name":"Stephanie","full_name":"Efthymiou, Stephanie","last_name":"Efthymiou"},{"first_name":"Ehsan","full_name":"Ghayoor Karimiani, Ehsan","last_name":"Ghayoor Karimiani"},{"last_name":"Hempel","full_name":"Hempel, Maja","first_name":"Maja"},{"last_name":"Normand","first_name":"Elizabeth A","full_name":"Normand, Elizabeth A"},{"first_name":"Sabine","full_name":"Rudnik-Schöneborn, Sabine","last_name":"Rudnik-Schöneborn"},{"first_name":"Ulrich A","full_name":"Schatz, Ulrich A","last_name":"Schatz"},{"last_name":"Baggelaar","first_name":"Marc P","full_name":"Baggelaar, Marc P"},{"last_name":"Ilyas","first_name":"Muhammad","full_name":"Ilyas, Muhammad"},{"first_name":"Tipu","full_name":"Sultan, Tipu","last_name":"Sultan"},{"last_name":"Alvi","first_name":"Javeria Raza","full_name":"Alvi, Javeria Raza"},{"last_name":"Ganieva","first_name":"Manizha","full_name":"Ganieva, Manizha"},{"full_name":"Fowler, Ben","first_name":"Ben","last_name":"Fowler"},{"first_name":"Ruxandra","full_name":"Aanicai, Ruxandra","last_name":"Aanicai"},{"full_name":"Akay Tayfun, Gulsen","first_name":"Gulsen","last_name":"Akay Tayfun"},{"last_name":"Al Saman","full_name":"Al Saman, Abdulaziz","first_name":"Abdulaziz"},{"last_name":"Alswaid","full_name":"Alswaid, Abdulrahman","first_name":"Abdulrahman"},{"first_name":"Nafise","full_name":"Amiri, Nafise","last_name":"Amiri"},{"last_name":"Asilova","first_name":"Nilufar","full_name":"Asilova, Nilufar"},{"last_name":"Shotelersuk","full_name":"Shotelersuk, Vorasuk","first_name":"Vorasuk"},{"last_name":"Yeetong","full_name":"Yeetong, Patra","first_name":"Patra"},{"last_name":"Azam","first_name":"Matloob","full_name":"Azam, Matloob"},{"last_name":"Babaei","full_name":"Babaei, Meisam","first_name":"Meisam"},{"last_name":"Bahrami Monajemi","full_name":"Bahrami Monajemi, Gholamreza","first_name":"Gholamreza"},{"first_name":"Pouria","full_name":"Mohammadi, Pouria","last_name":"Mohammadi"},{"last_name":"Samie","full_name":"Samie, Saeed","first_name":"Saeed"},{"first_name":"Selina Husna","full_name":"Banu, Selina Husna","last_name":"Banu"},{"first_name":"Jorge Pinto","full_name":"Basto, Jorge Pinto","last_name":"Basto"},{"full_name":"Kortüm, Fanny","first_name":"Fanny","last_name":"Kortüm"},{"first_name":"Mislen","full_name":"Bauer, Mislen","last_name":"Bauer"},{"full_name":"Bauer, Peter","first_name":"Peter","last_name":"Bauer"},{"last_name":"Beetz","first_name":"Christian","full_name":"Beetz, Christian"},{"first_name":"Masoud","full_name":"Garshasbi, Masoud","last_name":"Garshasbi"},{"first_name":"Awatif","full_name":"Hameed Issa, Awatif","last_name":"Hameed Issa"},{"last_name":"Eyaid","first_name":"Wafaa","full_name":"Eyaid, Wafaa"},{"last_name":"Ahmed","full_name":"Ahmed, Hind","first_name":"Hind"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"last_name":"Hassanpour","first_name":"Kazem","full_name":"Hassanpour, Kazem"},{"full_name":"Herman, Isabella","first_name":"Isabella","last_name":"Herman"},{"last_name":"Ibrohimov","full_name":"Ibrohimov, Sherozjon","first_name":"Sherozjon"},{"last_name":"Abdul-Majeed","full_name":"Abdul-Majeed, Ban A","first_name":"Ban A"},{"first_name":"Maria","full_name":"Imdad, Maria","last_name":"Imdad"},{"full_name":"Isrofilov, Maksudjon","first_name":"Maksudjon","last_name":"Isrofilov"},{"last_name":"Kaiyal","full_name":"Kaiyal, Qassem","first_name":"Qassem"},{"last_name":"Khan","full_name":"Khan, Suliman","first_name":"Suliman"},{"first_name":"Brian","full_name":"Kirmse, Brian","last_name":"Kirmse"},{"first_name":"Janet","full_name":"Koster, Janet","last_name":"Koster"},{"last_name":"Lourenço","first_name":"Charles Marques","full_name":"Lourenço, Charles Marques"},{"full_name":"Mitani, Tadahiro","first_name":"Tadahiro","last_name":"Mitani"},{"last_name":"Moldovan","full_name":"Moldovan, Oana","first_name":"Oana"},{"full_name":"Murphy, David","first_name":"David","last_name":"Murphy"},{"last_name":"Najafi","first_name":"Maryam","full_name":"Najafi, Maryam"},{"first_name":"Davut","full_name":"Pehlivan, Davut","last_name":"Pehlivan"},{"full_name":"Rocha, Maria Eugenia","first_name":"Maria Eugenia","last_name":"Rocha"},{"first_name":"Vincenzo","full_name":"Salpietro, Vincenzo","last_name":"Salpietro"},{"last_name":"Schmidts","full_name":"Schmidts, Miriam","first_name":"Miriam"},{"first_name":"Adel","full_name":"Shalata, Adel","last_name":"Shalata"},{"last_name":"Mahroum","full_name":"Mahroum, Mohammad","first_name":"Mohammad"},{"full_name":"Talbeya, Jawabreh Kassem","first_name":"Jawabreh Kassem","last_name":"Talbeya"},{"first_name":"Robert W","full_name":"Taylor, Robert W","last_name":"Taylor"},{"last_name":"Vazquez","full_name":"Vazquez, Dayana","first_name":"Dayana"},{"last_name":"Vetro","first_name":"Annalisa","full_name":"Vetro, Annalisa"},{"last_name":"Waterham","first_name":"Hans R","full_name":"Waterham, Hans R"},{"last_name":"Zaman","full_name":"Zaman, Mashaya","first_name":"Mashaya"},{"last_name":"Schrader","first_name":"Tina A","full_name":"Schrader, Tina A"},{"full_name":"Chung, Wendy K","first_name":"Wendy K","last_name":"Chung"},{"last_name":"Guerrini","full_name":"Guerrini, Renzo","first_name":"Renzo"},{"last_name":"Lupski","full_name":"Lupski, James R","first_name":"James R"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"},{"full_name":"Suri, Mohnish","first_name":"Mohnish","last_name":"Suri"},{"first_name":"Yalda","full_name":"Jamshidi, Yalda","last_name":"Jamshidi"},{"last_name":"Bhatia","full_name":"Bhatia, Kailash P","first_name":"Kailash P"},{"last_name":"Vona","first_name":"Barbara","full_name":"Vona, Barbara"},{"first_name":"Michael","full_name":"Schrader, Michael","last_name":"Schrader"},{"first_name":"Mariasavina","full_name":"Severino, Mariasavina","last_name":"Severino"},{"first_name":"Matthew","full_name":"Guille, Matthew","last_name":"Guille"},{"last_name":"Tate","first_name":"Edward W","full_name":"Tate, Edward W"},{"last_name":"Varshney","first_name":"Gaurav K","full_name":"Varshney, Gaurav K"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"last_name":"Maroofian","full_name":"Maroofian, Reza","first_name":"Reza"}],"oa_version":"Submitted Version","date_published":"2023-11-10T00:00:00Z","year":"2023","date_created":"2023-11-16T12:36:51Z","quality_controlled":"1","date_updated":"2023-11-20T10:17:32Z","publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awad380"}],"scopus_import":"1","article_processing_charge":"No","publication_status":"epub_ahead","oa":1,"title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","article_type":"original","month":"11","_id":"14543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"}],"status":"public","article_number":"awad380","extern":"1","abstract":[{"lang":"eng","text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders."}],"keyword":["Neurology (clinical)"],"citation":{"ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. 2023. doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>, awad380, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>.","ieee":"R. Kaiyrzhanov <i>et al.</i>, “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” <i>Brain</i>. Oxford University Press, 2023.","ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>.","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>"},"day":"10"},{"day":"16","has_accepted_license":"1","supervisor":[{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"citation":{"ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>.","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023."},"degree_awarded":"PhD","status":"public","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","_id":"14547","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10851"},{"relation":"part_of_dissertation","status":"public","id":"13264"}]},"title":"Resonant microwave spectroscopy of Al-InAs","oa":1,"publication_status":"published","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"page":"80","date_created":"2023-11-17T13:45:26Z","year":"2023","date_updated":"2023-11-30T10:56:04Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"file":[{"creator":"pduc","file_size":34828019,"checksum":"db0c37d213bc002125bd59690e9db246","relation":"main_file","date_updated":"2023-11-22T09:46:06Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-11-17T13:36:44Z","file_id":"14548","file_name":"Phan_Thesis_pdfa.pdf"},{"file_size":279319709,"creator":"pduc","relation":"source_file","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_id":"14549","content_type":"application/zip","date_created":"2023-11-17T13:44:53Z","date_updated":"2023-11-17T13:47:54Z","access_level":"closed","file_name":"dissertation_src.zip"}],"oa_version":"Published Version","date_published":"2023-11-16T00:00:00Z","ddc":["530"],"author":[{"full_name":"Phan, Duc T","first_name":"Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/14547","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"file_date_updated":"2023-11-22T09:46:06Z","type":"dissertation"},{"ec_funded":1,"degree_awarded":"PhD","abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"status":"public","has_accepted_license":"1","day":"21","citation":{"apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>.","mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>"},"supervisor":[{"last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","_id":"14587","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11842"},{"id":"14597","status":"public","relation":"part_of_dissertation"}]},"oa":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","alternative_title":["ISTA Thesis"],"date_updated":"2023-11-30T13:25:03Z","project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"page":"228","date_created":"2023-11-21T11:41:05Z","year":"2023","file":[{"file_name":"thesis_Marveggio.pdf","content_type":"application/pdf","file_id":"14626","date_created":"2023-11-29T09:09:31Z","access_level":"open_access","date_updated":"2023-11-29T09:09:31Z","success":1,"relation":"main_file","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","file_size":2881100,"creator":"amarvegg"},{"file_id":"14627","content_type":"application/zip","date_created":"2023-11-29T09:10:19Z","access_level":"open_access","date_updated":"2023-11-29T09:28:30Z","file_name":"Thesis_Marveggio.zip","file_size":10189696,"creator":"amarvegg","relation":"source_file","checksum":"52f28bdf95ec82cff39f3685f9c48e7d"}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14587","file_date_updated":"2023-11-29T09:28:30Z","type":"dissertation","language":[{"iso":"eng"}],"date_published":"2023-11-21T00:00:00Z","oa_version":"Published Version","ddc":["515"],"author":[{"first_name":"Alice","full_name":"Marveggio, Alice","last_name":"Marveggio","id":"25647992-AA84-11E9-9D75-8427E6697425"}]},{"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","_id":"14622","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11471"},{"id":"13125","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9760"}]},"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","publication_status":"published","day":"30","has_accepted_license":"1","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"citation":{"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>","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>.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","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>.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023."},"degree_awarded":"PhD","ec_funded":1,"status":"public","oa_version":"Published Version","date_published":"2023-11-30T00:00:00Z","ddc":["530"],"author":[{"last_name":"Sack","first_name":"Stefan","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"}],"doi":"10.15479/at:ista:14622","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"file_date_updated":"2023-12-01T11:10:46Z","type":"dissertation","article_processing_charge":"No","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_identifier":{"issn":["2663 - 337X"]},"page":"142","year":"2023","date_created":"2023-11-28T10:58:13Z","date_updated":"2023-12-13T14:47:25Z","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"file":[{"creator":"ssack","file_size":11947523,"checksum":"068fd3570506ec42b2faa390de784bc4","relation":"main_file","date_updated":"2023-12-01T11:10:46Z","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","file_id":"14635","date_created":"2023-11-30T15:53:10Z","embargo":"2024-11-30","file_name":"PhD_Thesis.pdf"},{"access_level":"closed","date_updated":"2023-12-01T11:10:46Z","content_type":"application/zip","date_created":"2023-11-30T15:54:11Z","file_id":"14636","file_name":"PhD Thesis (1).zip","creator":"ssack","file_size":18422964,"checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","relation":"source_file"}]},{"abstract":[{"text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.","lang":"eng"}],"article_number":"168","status":"public","has_accepted_license":"1","day":"01","citation":{"short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>","chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>.","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &#38; Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>","ieee":"L. Makatura <i>et al.</i>, “Procedural metamaterials: A unified procedural graph for metamaterial design,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>."},"intvolume":"        42","keyword":["Computer Graphics and Computer-Aided Design"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14628","month":"10","article_type":"original","oa":1,"title":"Procedural metamaterials: A unified procedural graph for metamaterial design","publication_status":"published","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program.","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"date_updated":"2023-12-04T08:09:05Z","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"quality_controlled":"1","year":"2023","date_created":"2023-11-29T15:02:03Z","volume":42,"file":[{"file_size":95467870,"creator":"yichen","relation":"main_file","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","content_type":"application/zip","date_created":"2023-11-29T15:16:01Z","file_id":"14630","access_level":"open_access","date_updated":"2023-11-29T15:16:01Z","success":1,"file_name":"tog-22-0089-File004.zip"},{"relation":"main_file","checksum":"7fb024963be81933494f38de191e4710","file_size":103731880,"creator":"yichen","file_name":"tog-22-0089-File005.zip","file_id":"14631","content_type":"application/zip","date_created":"2023-11-29T15:16:01Z","access_level":"open_access","date_updated":"2023-11-29T15:16:01Z","success":1},{"relation":"main_file","checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_size":57067476,"creator":"dernst","file_name":"2023_ACMToG_Makatura.pdf","file_id":"14638","content_type":"application/pdf","date_created":"2023-12-04T08:04:14Z","date_updated":"2023-12-04T08:04:14Z","success":1,"access_level":"open_access"}],"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0730-0301","1557-7368"]},"publisher":"Association for Computing Machinery","doi":"10.1145/3605389","file_date_updated":"2023-12-04T08:04:14Z","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2023-10-01T00:00:00Z","oa_version":"Published Version","ddc":["531","006"],"author":[{"last_name":"Makatura","full_name":"Makatura, Liane","first_name":"Liane"},{"first_name":"Bohan","full_name":"Wang, Bohan","last_name":"Wang"},{"id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu","full_name":"Chen, Yi-Lu","last_name":"Chen"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"}],"issue":"5","publication":"ACM Transactions on Graphics"},{"date_published":"2023-11-30T00:00:00Z","oa_version":"Published Version","author":[{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike","first_name":"Mike","last_name":"Hennessey-Wesen"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14641","type":"dissertation","file_date_updated":"2023-12-06T13:14:15Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"date_updated":"2023-12-07T14:12:25Z","year":"2023","date_created":"2023-12-04T13:17:37Z","page":"104","file":[{"checksum":"4127c285b34f4bf7fb31ef24f9d14c25","relation":"source_file","creator":"mhenness","file_size":46405919,"file_name":"mike_thesis_v06-12-2023.odt","access_level":"closed","date_updated":"2023-12-06T13:13:26Z","file_id":"14648","date_created":"2023-12-06T13:13:26Z","content_type":"application/vnd.oasis.opendocument.text"},{"checksum":"f5203a61eddaf35235bbc51904d73982","relation":"main_file","creator":"mhenness","file_size":21282155,"embargo":"2024-11-30","file_name":"mike_thesis_v06-12-2023.pdf","date_updated":"2023-12-06T13:14:15Z","access_level":"closed","date_created":"2023-12-06T13:14:15Z","embargo_to":"open_access","content_type":"application/pdf","file_id":"14649"}],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"alternative_title":["ISTA Thesis"],"month":"11","_id":"14641","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","title":"Adaptive mutation in E. coli modulated by luxS","has_accepted_license":"1","day":"30","citation":{"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>","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>.","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>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","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>"},"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"}],"ec_funded":1,"degree_awarded":"PhD","status":"public"},{"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-12-22T11:04:45Z","year":"2023","date_created":"2023-12-11T19:30:37Z","page":"96","file":[{"checksum":"520bdb61e95e66070e02824947d2c5fa","relation":"main_file","creator":"larathoo","file_size":34101468,"file_name":"Phd_Thesis_LA.pdf","date_updated":"2023-12-13T15:37:55Z","access_level":"open_access","success":1,"date_created":"2023-12-13T15:37:55Z","content_type":"application/pdf","file_id":"14684"},{"file_name":"Phd_Thesis_LA.zip","file_id":"14685","content_type":"application/zip","date_created":"2023-12-13T15:42:23Z","date_updated":"2023-12-14T08:58:18Z","access_level":"closed","relation":"source_file","checksum":"d8e59afd0817c98fba2564a264508e5c","file_size":31052872,"creator":"larathoo"},{"relation":"supplementary_material","checksum":"9a778c949932286f4519e1f1fca2820d","file_size":10713896,"creator":"larathoo","file_name":"Supplementary_Materials.zip","file_id":"14681","date_created":"2023-12-11T19:24:59Z","content_type":"application/zip","date_updated":"2023-12-14T08:58:18Z","access_level":"closed"}],"date_published":"2023-12-12T00:00:00Z","oa_version":"Published Version","author":[{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14651","type":"dissertation","file_date_updated":"2023-12-14T08:58:18Z","language":[{"iso":"eng"}],"has_accepted_license":"1","day":"12","citation":{"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>.","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>"},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"ec_funded":1,"degree_awarded":"PhD","abstract":[{"lang":"eng","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."}],"status":"public","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"month":"12","_id":"14651","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11411"}]},"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","oa":1},{"language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1016/j.ijms.2023.117168","publisher":"Elsevier","publication":"International Journal of Mass Spectrometry","author":[{"full_name":"Kluibenschedl, Florian","first_name":"Florian","last_name":"Kluibenschedl","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"first_name":"Anna","full_name":"Ploner, Anna","last_name":"Ploner"},{"first_name":"Christina","full_name":"Meisenbichler, Christina","last_name":"Meisenbichler"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"},{"last_name":"Müller","full_name":"Müller, Thomas","first_name":"Thomas"}],"oa_version":"Published Version","date_published":"2023-11-23T00:00:00Z","volume":495,"quality_controlled":"1","year":"2023","date_created":"2023-12-10T23:00:57Z","date_updated":"2026-03-02T09:38:59Z","publication_identifier":{"issn":["1387-3806"]},"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.ijms.2023.117168","open_access":"1"}],"dataavailabilitystatement":"Data will be made available on request.","article_processing_charge":"Yes (in subscription journal)","title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","oa":1,"publication_status":"epub_ahead","supplementarymaterial":"yes","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14653","month":"11","researchdata_availability":"upon request","department":[{"_id":"GradSch"}],"acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","article_number":"117168","status":"public","abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"intvolume":"       495","citation":{"mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>, vol. 495, 117168, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>.","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” <i>International Journal of Mass Spectrometry</i>, vol. 495. Elsevier, 2023.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., &#38; Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>","ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>.","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. 2023;495. doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023)."},"day":"23"},{"author":[{"orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B","last_name":"Jethwa"},{"full_name":"Mondal, Soumyadip","first_name":"Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"full_name":"Pant, Bhargavi","first_name":"Bhargavi","last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger"}],"publication":"Angewandte Chemie International Edition","date_published":"2023-12-14T00:00:00Z","department":[{"_id":"StFr"},{"_id":"GradSch"}],"oa_version":"Published Version","article_type":"review","type":"journal_article","oa":1,"title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","publication_status":"epub_ahead","language":[{"iso":"eng"}],"publisher":"Wiley","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14687","month":"12","doi":"10.1002/anie.202316476","scopus_import":"1","citation":{"mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, e202316476, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>.","ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte Chemie International Edition</i>. Wiley, 2023.","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2023). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>.","ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2023. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition., e202316476.","ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2023. doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition (2023)."},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1002/anie.202316476"}],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"keyword":["General Chemistry","Catalysis"],"article_processing_charge":"Yes (via OA deal)","day":"14","abstract":[{"lang":"eng","text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity."}],"article_number":"e202316476","status":"public","date_updated":"2024-02-15T14:43:05Z","quality_controlled":"1","date_created":"2023-12-15T16:10:13Z","year":"2023"},{"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"alternative_title":["ISTA Thesis"],"month":"12","_id":"14697","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","related_material":{"record":[{"id":"6328","status":"public","relation":"part_of_dissertation"},{"id":"7885","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12272"},{"id":"14274","relation":"part_of_dissertation","status":"public"},{"id":"14360","status":"public","relation":"part_of_dissertation"}]},"has_accepted_license":"1","day":"20","citation":{"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.","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.","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>.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","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>"},"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"ec_funded":1,"degree_awarded":"PhD","status":"public","date_published":"2023-12-20T00:00:00Z","oa_version":"Published Version","author":[{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14697","type":"dissertation","file_date_updated":"2023-12-20T10:41:42Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-038-1"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"date_updated":"2023-12-21T14:30:02Z","date_created":"2023-12-18T19:14:28Z","year":"2023","page":"226","file":[{"date_updated":"2023-12-20T09:35:34Z","access_level":"closed","content_type":"application/pdf","file_id":"14699","embargo_to":"open_access","date_created":"2023-12-20T09:35:34Z","embargo":"2024-12-20","file_name":"Thesis.pdf","creator":"jstopp","file_size":51585778,"checksum":"457927165d5d556305d3086f6b83e5c7","relation":"main_file"},{"file_name":"Thesis.docx","file_id":"14700","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-12-20T09:35:35Z","date_updated":"2023-12-20T10:41:42Z","access_level":"closed","relation":"source_file","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"creator":"jstopp"}]},{"date_published":"2023-12-19T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.","external_id":{"arxiv":["2312.12213"]},"oa_version":"Preprint","author":[{"first_name":"Sadashige","full_name":"Ishida, Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Lavenant","full_name":"Lavenant, Hugo","first_name":"Hugo"}],"publication":"arXiv","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14703","doi":"10.48550/arXiv.2312.12213","month":"12","type":"preprint","title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","oa":1,"language":[{"iso":"eng"}],"publication_status":"submitted","arxiv":1,"article_processing_charge":"No","day":"19","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.12213","open_access":"1"}],"citation":{"short":"S. Ishida, H. Lavenant, ArXiv (n.d.).","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2312.12213\">10.48550/arXiv.2312.12213</a>","apa":"Ishida, S., &#38; Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2312.12213\">https://doi.org/10.48550/arXiv.2312.12213</a>","ista":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213.","chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2312.12213\">https://doi.org/10.48550/arXiv.2312.12213</a>.","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” <i>arXiv</i>. .","mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” <i>ArXiv</i>, 2312.12213, doi:<a href=\"https://doi.org/10.48550/arXiv.2312.12213\">10.48550/arXiv.2312.12213</a>."},"keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"date_updated":"2023-12-27T13:44:33Z","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"year":"2023","date_created":"2023-12-21T10:14:37Z","abstract":[{"text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.","lang":"eng"}],"article_number":"2312.12213","status":"public"},{"language":[{"iso":"eng"}],"type":"conference","doi":"10.1007/978-3-031-47754-6_1","publisher":"Springer Nature","publication":"27th International Conference on Financial Cryptography and Data Security","author":[{"id":"a20e8902-32b0-11ee-9fa8-b23fa638b793","full_name":"Stefo, Christos","first_name":"Christos","last_name":"Stefo"},{"last_name":"Xiang","first_name":"Zhuolun","full_name":"Xiang, Zhuolun"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"}],"oa_version":"Preprint","conference":{"end_date":"2023-05-05","location":"Bol, Brac, Croatia","start_date":"2023-05-01","name":"FC: Financial Cryptography and Data Security"},"date_published":"2023-12-01T00:00:00Z","volume":13950,"date_created":"2024-01-08T09:17:38Z","year":"2023","page":"3-20","quality_controlled":"1","project":[{"grant_number":"F8512","name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"date_updated":"2024-01-08T09:28:14Z","publication_identifier":{"eisbn":["9783031477546"],"isbn":["9783031477539"],"issn":["1611-3349"],"eissn":["0302-9743"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1554"}],"scopus_import":"1","article_processing_charge":"No","publication_status":"published","title":"Executing and proving over dirty ledgers","oa":1,"_id":"14735","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.","department":[{"_id":"ElKo"},{"_id":"GradSch"}],"status":"public","abstract":[{"lang":"eng","text":"Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs."}],"intvolume":"     13950","citation":{"ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: <i>27th International Conference on Financial Cryptography and Data Security</i>. Vol 13950. Springer Nature; 2023:3-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">10.1007/978-3-031-47754-6_1</a>","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","mla":"Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” <i>27th International Conference on Financial Cryptography and Data Security</i>, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">10.1007/978-3-031-47754-6_1</a>.","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in <i>27th International Conference on Financial Cryptography and Data Security</i>, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","ista":"Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.","apa":"Stefo, C., Xiang, Z., &#38; Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In <i>27th International Conference on Financial Cryptography and Data Security</i> (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">https://doi.org/10.1007/978-3-031-47754-6_1</a>","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In <i>27th International Conference on Financial Cryptography and Data Security</i>, 13950:3–20. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">https://doi.org/10.1007/978-3-031-47754-6_1</a>."},"day":"01"},{"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"oa":1,"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12291","month":"09","intvolume":"       609","citation":{"short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"day":"15","has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"ec_funded":1,"issue":"7927","publication":"Nature","ddc":["580"],"author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"full_name":"Gelová, Zuzana","first_name":"Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","full_name":"Monzer, Aline","last_name":"Monzer"},{"full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"first_name":"Inge","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"first_name":"Branka D.","full_name":"Živanović, Branka D.","last_name":"Živanović"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","first_name":"Minxia","last_name":"Zou"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","first_name":"Lukas","last_name":"Fiedler"},{"last_name":"Giannini","full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","full_name":"Hrtyan, Mónika","last_name":"Hrtyan"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha"},{"last_name":"Randuch","full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"last_name":"Rýdza","first_name":"Nikola","full_name":"Rýdza, Nikola"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang"},{"last_name":"Teplova","full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"}],"oa_version":"Submitted Version","external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"date_published":"2022-09-15T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2023-11-02T17:12:37Z","type":"journal_article","doi":"10.1038/s41586-022-05187-x","publisher":"Springer Nature","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"scopus_import":"1","pmid":1,"article_processing_charge":"No","volume":609,"isi":1,"file":[{"relation":"main_file","checksum":"a6055c606aefb900bf62ae3e7d15f921","file_size":79774945,"creator":"amally","file_name":"Friml Nature 2022_merged.pdf","file_id":"14483","date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-11-02T17:12:37Z","success":1}],"quality_controlled":"1","page":"575-581","year":"2022","date_created":"2023-01-16T10:04:48Z","date_updated":"2023-11-07T08:16:09Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"scopus_import":"1","publication_identifier":{"issn":["1051-1970"],"eissn":["1935-4053"]},"article_processing_charge":"No","volume":32,"date_updated":"2023-01-30T13:02:30Z","year":"2022","date_created":"2023-01-16T10:07:21Z","quality_controlled":"1","page":"593-609","author":[{"first_name":"Barbara A.","full_name":"Shipman, Barbara A.","last_name":"Shipman"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson"}],"publication":"PRIMUS","issue":"5","date_published":"2022-05-28T00:00:00Z","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Taylor & Francis","doi":"10.1080/10511970.2021.1872750","citation":{"ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. <i>PRIMUS</i>. 2022;32(5):593-609. doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>","short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609.","mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>, vol. 32, no. 5, Taylor &#38; Francis, 2022, pp. 593–609, doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>.","ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” <i>PRIMUS</i>, vol. 32, no. 5. Taylor &#38; Francis, pp. 593–609, 2022.","apa":"Shipman, B. A., &#38; Stephenson, E. R. (2022). Tangible topology through the lens of limits. <i>PRIMUS</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609.","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>."},"intvolume":"        32","keyword":["Education","General Mathematics"],"day":"28","abstract":[{"text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.","lang":"eng"}],"status":"public","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"article_type":"original","publication_status":"published","title":"Tangible topology through the lens of limits","_id":"12307","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Sperl, Georg","last_name":"Sperl"}],"ddc":["000","620"],"date_published":"2022-09-22T00:00:00Z","oa_version":"Published Version","type":"dissertation","file_date_updated":"2023-02-02T09:39:25Z","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12103","publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"article_processing_charge":"No","file":[{"checksum":"083722acbb8115e52e3b0fdec6226769","relation":"main_file","creator":"cchlebak","file_size":104497530,"title":"Thesis","file_name":"thesis_gsperl.pdf","access_level":"open_access","date_updated":"2023-02-02T09:29:57Z","description":"This is the main PDF file of the thesis. File size: 105 MB","date_created":"2023-01-25T12:04:41Z","content_type":"application/pdf","file_id":"12371"},{"relation":"main_file","checksum":"511f82025e5fcb70bff4731d6896ca07","file_size":23183710,"creator":"cchlebak","file_name":"thesis_gsperl_compressed.pdf","title":"Thesis (compressed 23MB)","content_type":"application/pdf","date_created":"2023-02-02T09:33:37Z","file_id":"12483","date_updated":"2023-02-02T09:33:37Z","access_level":"open_access","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB."},{"file_name":"thesis-source.zip","date_created":"2023-02-02T09:39:25Z","content_type":"application/x-zip-compressed","file_id":"12484","date_updated":"2023-02-02T09:39:25Z","access_level":"open_access","relation":"source_file","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_size":98382247,"creator":"cchlebak"}],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"acknowledged_ssus":[{"_id":"SSU"}],"date_updated":"2024-02-28T12:57:46Z","date_created":"2023-01-24T10:49:46Z","year":"2022","page":"138","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"published","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11736"},{"id":"9818","relation":"part_of_dissertation","status":"public"},{"id":"8385","status":"public","relation":"part_of_dissertation"}]},"oa":1,"month":"09","_id":"12358","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022."},"supervisor":[{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","day":"22","abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}],"status":"public","ec_funded":1,"degree_awarded":"PhD"},{"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"alternative_title":["ISTA Thesis"],"month":"09","_id":"12364","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","related_material":{"record":[{"id":"3","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11160"}]},"oa":1,"has_accepted_license":"1","day":"19","citation":{"ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>"},"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"ec_funded":1,"degree_awarded":"PhD","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"status":"public","date_published":"2022-09-19T00:00:00Z","oa_version":"Published Version","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","last_name":"Dotter","full_name":"Dotter, Christoph","first_name":"Christoph"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12094","type":"dissertation","file_date_updated":"2023-09-20T22:30:03Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"},{"grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF"}],"date_updated":"2023-11-16T13:10:22Z","date_created":"2023-01-24T13:09:57Z","year":"2022","page":"152","file":[{"creator":"cchlebak","file_size":20457465,"checksum":"896f4cac9adb6d3f26a6605772f4e1a3","relation":"main_file","date_updated":"2023-09-20T22:30:03Z","access_level":"open_access","date_created":"2023-01-24T13:15:45Z","content_type":"application/pdf","file_id":"12365","embargo":"2023-09-19","file_name":"220923_Thesis_CDotter_Final.pdf"},{"checksum":"ad01bb20da163be6893b7af832e58419","relation":"source_file","creator":"cchlebak","file_size":22433512,"file_name":"latex_source_CDotter_Thesis_2022.zip","date_updated":"2023-09-20T22:30:03Z","access_level":"closed","date_created":"2023-02-02T09:15:35Z","embargo_to":"open_access","file_id":"12482","content_type":"application/x-zip-compressed"}]},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies"}],"date_updated":"2024-08-07T07:11:56Z","date_created":"2023-01-25T09:17:02Z","year":"2022","page":"168","file":[{"creator":"cchlebak","file_size":56076868,"checksum":"39eabb1e006b41335f17f3b29af09648","relation":"main_file","date_updated":"2023-01-26T23:30:44Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-25T09:41:49Z","file_id":"12367","embargo":"2022-12-28","file_name":"Final_Thesis_ES_Redchenko.pdf"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12132","type":"dissertation","file_date_updated":"2023-01-26T23:30:44Z","language":[{"iso":"eng"}],"date_published":"2022-09-26T00:00:00Z","oa_version":"Published Version","author":[{"first_name":"Elena","full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"ec_funded":1,"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"status":"public","has_accepted_license":"1","day":"26","citation":{"short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022."},"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"}],"_id":"12366","month":"09","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa":1,"title":"Controllable states of superconducting Qubit ensembles","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"alternative_title":["ISTA Thesis"]}]