[{"corr_author":"1","author":[{"full_name":"Riabov, Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","last_name":"Riabov","first_name":"Volodymyr"}],"oa":1,"title":"Universality in random matrices with spatial structure","publication_identifier":{"isbn":["978-3-99078-064-0"],"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20575","page":"436","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"month":"11","license":"https://creativecommons.org/licenses/by/4.0/","article_processing_charge":"No","date_created":"2025-10-29T19:12:24Z","degree_awarded":"PhD","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"related_material":{"record":[{"id":"20322","relation":"part_of_dissertation","status":"public"},{"id":"13317","relation":"part_of_dissertation","status":"public"},{"status":"deleted","id":"19368","relation":"part_of_dissertation"},{"status":"public","id":"20576","relation":"part_of_dissertation"},{"status":"public","id":"17174","relation":"part_of_dissertation"},{"id":"19547","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"19598"},{"id":"18554","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18764","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T08:41:47Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2025-10-29T18:54:53Z","abstract":[{"lang":"eng","text":"This thesis deals with eigenvalue and eigenvector universality results for random matrix ensembles equipped with non-trivial spatial structure. We consider both mean-field models with a general variance profile (Wigner-type matrices) and correlation structure (correlated matrices) among the entries, as well as non-mean-field random band matrices with bandwidth W >> N^(1/2).\r\n\r\nTo extract the universal properties of random matrix spectra and eigenvectors, we obtain concentration estimates for their resolvent, the local laws, which generalize the celebrated Wigner semicircle law for a broad class of random matrices to much finer spectral scales. The local laws hold for both a single resolvent as well as for products of multiple resolvents, known as resolvent chains, and express the remarkable approximately-deterministic behavior of these objects down to the microscopic scale.\r\n\r\nOur primary tool for establishing the local laws is the dynamical Zigzag strategy, which we develop in the setting of spatially-inhomogeneous random matrices. Our proof method systematically addresses the challenges arising from non-trivial spatial structures and is robust to all types of singularities in the spectrum, as we demonstrate in the correlated setting. Furthermore, we incorporate the analysis of the deterministic resolvent chain approximations into the dynamical framework of the Zigzag strategy, synthesizing a unified toolkit for establishing multi-resolvent local laws.\r\n\r\nUsing these methods, we prove complete eigenvector delocalization, the Eigenstate Thermalization Hypothesis, and Wigner-Dyson universality in the bulk for random band matrices down to the optimal bandwidth W >> N^(1/2). For mean-field ensembles, we establish universality of local eigenvalue statistics at the cups for random matrices with correlated entries, and the Eigenstate Thermalization Hypothesis for Wigner-type matrices in the bulk of the spectrum.\r\n\r\nFinally, this thesis also contains other applications of the multi-resolvent local laws to spatially-inhomogeneous random matrices, obtained prior to the development of the Zigzag strategy. In particular, we provide a complete analysis of mesoscopic linear-eigenvalue statistics of Wigner-type matrices in all spectral regimes, including the novel cusps, and rigorously establish the prethermalization phenomenon for deformed Wigner matrices.\r\n\r\nThe main body of this thesis consists of seven research papers (listed on page xi), each presented in a separate chapter with its own introduction and all relevant context, suitable to be read independently. We ask the reader’s indulgence for the repetitions in the historical overviews and other minor redundancies that remain among the chapters as a result. The overall Introduction, preceding the chapters, provides a condensed, informal summary of the main ideas and concepts at the core of these works.\r\n"}],"ec_funded":1,"has_accepted_license":"1","date_published":"2025-11-03T00:00:00Z","ddc":["515","519"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20575","OA_place":"publisher","status":"public","_id":"20575","oa_version":"Published Version","supervisor":[{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László"}],"day":"3","publisher":"Institute of Science and Technology Austria","acknowledgement":"The work comprising this thesis was supported by the ERC Advanced Grant \"RMTBeyond\"\r\nNo.101020331 awarded to my advisor.","citation":{"short":"V. Riabov, Universality in Random Matrices with Spatial Structure, Institute of Science and Technology Austria, 2025.","mla":"Riabov, Volodymyr. <i>Universality in Random Matrices with Spatial Structure</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20575\">10.15479/AT-ISTA-20575</a>.","chicago":"Riabov, Volodymyr. “Universality in Random Matrices with Spatial Structure.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20575\">https://doi.org/10.15479/AT-ISTA-20575</a>.","apa":"Riabov, V. (2025). <i>Universality in random matrices with spatial structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20575\">https://doi.org/10.15479/AT-ISTA-20575</a>","ieee":"V. Riabov, “Universality in random matrices with spatial structure,” Institute of Science and Technology Austria, 2025.","ista":"Riabov V. 2025. Universality in random matrices with spatial structure. Institute of Science and Technology Austria.","ama":"Riabov V. Universality in random matrices with spatial structure. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20575\">10.15479/AT-ISTA-20575</a>"},"year":"2025","file":[{"file_size":7536583,"date_created":"2025-10-29T18:53:59Z","file_name":"riabov_thesis-pdfa.pdf","file_id":"20577","success":1,"creator":"vriabov","content_type":"application/pdf","date_updated":"2025-10-29T18:53:59Z","relation":"main_file","access_level":"open_access","checksum":"6a0487b2b66bb35d44b394756d44b8b4"},{"content_type":"application/x-zip-compressed","date_updated":"2025-10-29T18:54:53Z","creator":"vriabov","access_level":"closed","checksum":"224efda6bf9864d296a1e5e0124c1e8f","relation":"source_file","file_name":"manuscript.zip","file_size":17841612,"date_created":"2025-10-29T18:54:53Z","file_id":"20578"}]},{"file":[{"date_created":"2025-04-10T21:14:18Z","file_size":4107587,"file_name":"Henheik-Thesis_source_final.zip","file_id":"19542","creator":"shenheik","content_type":"application/zip","date_updated":"2025-04-10T21:14:18Z","access_level":"closed","checksum":"b8477ae5578436c72c3bb4193ad34ac5","relation":"source_file"},{"file_name":"Henheik-Thesis-pdfa_FINAL.pdf","file_size":9999492,"date_created":"2025-04-11T13:16:05Z","file_id":"19553","success":1,"date_updated":"2025-04-11T13:16:05Z","content_type":"application/pdf","creator":"shenheik","relation":"main_file","access_level":"open_access","checksum":"e9fc0ea12ec46c9f71110c33217c4140"},{"file_id":"19615","file_name":"Henheik-Thesis-Volume1_print.pdf","file_size":13276442,"date_created":"2025-04-23T14:10:27Z","relation":"other","checksum":"f94580f86c785e7108eb116cd189e225","access_level":"closed","content_type":"application/pdf","date_updated":"2025-04-23T14:10:27Z","creator":"cchlebak"},{"access_level":"closed","checksum":"b927ead3c78020ffb32918911deedb74","relation":"other","creator":"cchlebak","content_type":"application/pdf","date_updated":"2025-04-23T14:11:05Z","file_id":"19616","date_created":"2025-04-23T14:11:05Z","file_size":7628767,"file_name":"Henheik-Thesis-Volume2_print.pdf"}],"supervisor":[{"orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"}],"day":"10","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Henheik SJ. 2025. Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems. Institute of Science and Technology Austria.","ama":"Henheik SJ. Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19540\">10.15479/AT-ISTA-19540</a>","apa":"Henheik, S. J. (2025). <i>Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19540\">https://doi.org/10.15479/AT-ISTA-19540</a>","ieee":"S. J. Henheik, “Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems,” Institute of Science and Technology Austria, 2025.","chicago":"Henheik, Sven Joscha. “Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19540\">https://doi.org/10.15479/AT-ISTA-19540</a>.","short":"S.J. Henheik, Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems, Institute of Science and Technology Austria, 2025.","mla":"Henheik, Sven Joscha. <i>Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19540\">10.15479/AT-ISTA-19540</a>."},"year":"2025","_id":"19540","status":"public","oa_version":"Published Version","OA_place":"publisher","date_published":"2025-04-10T00:00:00Z","has_accepted_license":"1","ddc":["519"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19540","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2025-04-23T14:11:05Z","ec_funded":1,"abstract":[{"text":"This thesis deals with several different models for complex quantum mechanical systems and is structured in three main parts. \r\n\t\r\nIn Part I, we study mean field random matrices as models for quantum Hamiltonians. Our focus lies on proving concentration estimates for resolvents of random matrices, so-called local laws, mostly in the setting of multiple resolvents. These estimates have profound consequences for eigenvector overlaps and thermalization problems. More concretely, we obtain, e.g., the optimal eigenstate thermalization hypothesis (ETH) uniformly in the spectrum for Wigner matrices, an optimal lower bound on non-Hermitian eigenvector overlaps, and prethermalization for deformed Wigner matrices.\tIn order to prove our novel multi-resolvent local laws, we develop and devise two main methods, the static Psi-method and the dynamical Zigzag strategy. \r\n\t\r\nIn Part II, we study Bardeen-Cooper-Schrieffer (BCS) theory, the standard mean field microscopic theory of superconductivity. We focus on asymptotic formulas for the characteristic critical temperature and energy gap of a superconductor and prove universality of their ratio in various physical regimes. Additionally, we investigate multi-band superconductors and show that inter-band coupling effects can only enhance the critical temperature. \r\n\t\r\nIn Part III, we study quantum lattice systems. On the one hand, we show a strong version of the local-perturbations-perturb-locally (LPPL) principle for the ground state of weakly interacting quantum spin systems with a uniform on-site gap. On the other hand, we introduce a notion of a local gap and rigorously justify response theory and the Kubo formula under the weakened assumption of a local gap. \r\n\t\r\nAdditionally, we discuss two classes of problems which do not fit into the three main parts of the thesis. These are deformational rigidity of Liouville metrics on the torus and relativistic toy models of particle creation via interior-boundary-conditions (IBCs).  ","lang":"eng"}],"date_updated":"2026-10-16T08:41:47Z","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"14343","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13317"},{"id":"11732","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12184"},{"status":"public","relation":"part_of_dissertation","id":"14421"},{"id":"10623","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18112"},{"status":"public","relation":"part_of_dissertation","id":"19001"},{"status":"public","relation":"part_of_dissertation","id":"10642"},{"status":"public","relation":"part_of_dissertation","id":"19545"},{"status":"public","relation":"part_of_dissertation","id":"19546"},{"status":"public","id":"19550","relation":"part_of_dissertation"},{"status":"public","id":"19551","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"19552"},{"status":"public","id":"19547","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"19548","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14542"},{"status":"public","relation":"part_of_dissertation","id":"18656"},{"status":"public","relation":"part_of_dissertation","id":"17049"},{"relation":"part_of_dissertation","id":"18764","status":"public"}]},"article_processing_charge":"No","date_created":"2025-04-10T21:21:18Z","month":"04","page":"720","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"language":[{"iso":"eng"}],"doi_confirm":"1","oa":1,"title":"Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-057-2"]},"type":"dissertation","doi":"10.15479/AT-ISTA-19540","author":[{"orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"}],"corr_author":"1"},{"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"publication_status":"published","month":"12","date_created":"2025-12-09T13:08:11Z","article_processing_charge":"No","related_material":{"record":[{"relation":"part_of_dissertation","id":"15118","status":"public"}]},"degree_awarded":"PhD","corr_author":"1","author":[{"orcid":"0000-0001-7244-8128","first_name":"Marko","full_name":"Kojic, Marko","last_name":"Kojic","id":"73e7ecd4-dc85-11ea-9058-88a16394b160"}],"doi":"10.15479/AT-ISTA-20741","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-073-2"],"issn":["2663-337X"]},"title":"Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria","oa":1,"oa_version":"Published Version","status":"public","_id":"20741","citation":{"chicago":"Kojic, Marko. “Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>.","short":"M. Kojic, Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria, Institute of Science and Technology Austria, 2025.","mla":"Kojic, Marko. <i>Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>.","ama":"Kojic M. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>","ista":"Kojic M. 2025. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria.","ieee":"M. Kojic, “Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria,” Institute of Science and Technology Austria, 2025.","apa":"Kojic, M. (2025). <i>Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>"},"year":"2025","publisher":"Institute of Science and Technology Austria","day":"09","supervisor":[{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin"}],"acknowledged_ssus":[{"_id":"Bio"}],"file":[{"date_created":"2025-12-10T13:09:58Z","file_size":142876975,"file_name":"2025_marko_kojic_thesis.docx","file_id":"20774","creator":"mkojic","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-12-10T13:09:58Z","checksum":"a3643d07e93134b2490a566b02a4517d","access_level":"closed","relation":"source_file"},{"file_name":"2025_marko_kojic_thesis.pdf","file_size":8597045,"date_created":"2025-12-10T13:09:38Z","success":1,"file_id":"20775","content_type":"application/pdf","date_updated":"2025-12-10T13:09:38Z","creator":"mkojic","checksum":"0a096f0af6ccc3a8329d5bb8797ad533","access_level":"open_access","relation":"main_file"}],"date_updated":"2026-10-16T10:35:47Z","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. \r\n\r\nFirstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. \r\n\r\nNext, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. \r\n\r\nFinally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. "}],"file_date_updated":"2025-12-10T13:09:58Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.15479/AT-ISTA-20741","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["572"],"has_accepted_license":"1","date_published":"2025-12-09T00:00:00Z","OA_place":"publisher"},{"oa_version":"Published Version","_id":"19393","status":"public","publisher":"Institute of Science and Technology Austria","year":"2025","citation":{"apa":"Karle, V. (2025). <i>Non-equilibrium topological phases with periodically driven molecules and quantum rotors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025.","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>","ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025.","mla":"Karle, Volker. <i>Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>.","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>."},"supervisor":[{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"day":"13","file":[{"file_name":"thesis_final.pdf","file_size":10625143,"date_created":"2025-03-12T12:56:46Z","file_id":"19394","success":1,"date_updated":"2025-03-12T12:56:46Z","content_type":"application/pdf","creator":"vkarle","relation":"main_file","access_level":"open_access","checksum":"d3ab25782c7ea38ce9910e57d25f6733"},{"creator":"vkarle","date_updated":"2025-03-20T08:02:35Z","content_type":"application/zip","checksum":"3ccfb0aeba4d860d71e18347913034e4","access_level":"closed","relation":"source_file","date_created":"2025-03-13T13:15:10Z","file_size":23119202,"file_name":"thesis.zip","file_id":"19400"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T12:16:52Z","file_date_updated":"2025-03-20T08:02:35Z","abstract":[{"lang":"eng","text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19393","has_accepted_license":"1","OA_type":"gold","date_published":"2025-03-13T00:00:00Z","ddc":["530"],"OA_place":"publisher","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"language":[{"iso":"eng"}],"page":"192","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"03","article_processing_charge":"No","date_created":"2025-03-12T13:04:59Z","related_material":{"record":[{"status":"public","id":"12788","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9903","status":"public"},{"status":"public","id":"19425","relation":"part_of_dissertation"},{"status":"public","id":"14851","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"15004","status":"public"}]},"degree_awarded":"PhD","corr_author":"1","author":[{"last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","first_name":"Volker"}],"type":"dissertation","doi":"10.15479/AT-ISTA-19393","title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","oa":1,"publication_identifier":{"eissn":["2663-337X"]}},{"scopus_import":"1","corr_author":"1","author":[{"last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","first_name":"Jake"},{"first_name":"Victor M","last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"first_name":"Rebecca","full_name":"Morse, Rebecca","last_name":"Morse","id":"ceb89ae7-dc8d-11ea-abe3-da3301d0eab4"},{"first_name":"Andrea C","orcid":"0000-0002-9280-8597","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","last_name":"Navas Olivé","full_name":"Navas Olivé, Andrea C"},{"full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba","orcid":"0000-0002-7667-6854"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Tomschik","full_name":"Tomschik, Matthias","first_name":"Matthias"},{"first_name":"Karl","last_name":"Rössler","full_name":"Rössler, Karl"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"}],"publication":"Cell","type":"journal_article","doi":"10.1016/j.cell.2024.11.022","oa":1,"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"pmid":1,"publication_status":"published","department":[{"_id":"JoDa"},{"_id":"PeJo"},{"_id":"GradSch"}],"volume":188,"language":[{"iso":"eng"}],"page":"501-514.e18","month":"01","article_processing_charge":"Yes (via OA deal)","date_created":"2025-01-26T23:01:49Z","related_material":{"record":[{"id":"18688","relation":"earlier_version","status":"public"}]},"quality_controlled":"1","project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635"},{"grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic networks of human brain","_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e","grant_number":"PAT 4178023"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"date_updated":"2026-10-20T08:20:04Z","file_date_updated":"2025-01-27T08:46:33Z","abstract":[{"lang":"eng","text":"Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. "}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1016/j.cell.2024.11.022","date_published":"2025-01-23T00:00:00Z","has_accepted_license":"1","OA_type":"hybrid","ddc":["570"],"OA_place":"publisher","oa_version":"Published Version","status":"public","_id":"18879","publisher":"Cell Press","acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.).","year":"2025","citation":{"mla":"Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>, vol. 188, no. 2, Cell Press, 2025, p. 501–514.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>.","short":"J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18.","chicago":"Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>.","ieee":"J. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>Cell</i>, vol. 188, no. 2. Cell Press, p. 501–514.e18, 2025.","apa":"Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>","ama":"Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. 2025;188(2):501-514.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>","ista":"Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18."},"isi":1,"day":"23","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"intvolume":"       188","file":[{"date_created":"2025-01-27T08:46:33Z","file_size":14082343,"file_name":"2025_Cell_Watson.pdf","file_id":"18884","success":1,"creator":"dernst","content_type":"application/pdf","date_updated":"2025-01-27T08:46:33Z","relation":"main_file","checksum":"d5a818edc32d249cdf75e1bb5b70a4b7","access_level":"open_access"}],"issue":"2","external_id":{"pmid":["39667938"],"isi":["001408395600001"]}},{"type":"journal_article","doi":"10.1016/j.bpr.2025.100211","title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","oa":1,"publication_identifier":{"eissn":["2667-0747"]},"article_number":"100211","scopus_import":"1","corr_author":"1","author":[{"last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","first_name":"Jakob","orcid":"0009-0000-7590-3501"},{"id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","last_name":"Semenov","full_name":"Semenov, Nikolai","first_name":"Nikolai"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","orcid":"0000-0003-2311-2112","first_name":"Manjunath"},{"full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","orcid":"0000-0002-9561-1239","first_name":"Bettina"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"first_name":"Mojtaba","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"first_name":"Marek","full_name":"Suplata, Marek","id":"EE8452B8-C26A-11E9-B157-E80CE6697425","last_name":"Suplata"},{"first_name":"Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke"},{"first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wartak, Andreas","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","last_name":"Wartak","first_name":"Andreas"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian Km","first_name":"Florian Km","orcid":"0000-0003-4790-8078"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"publication":"Biophysical Reports","article_processing_charge":"Yes","date_created":"2025-06-08T22:01:22Z","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"20206","relation":"dissertation_contains"},{"id":"22744","relation":"dissertation_contains","status":"public"}]},"project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"},{"grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"volume":5,"month":"06","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1016/j.bpr.2025.100211","article_type":"original","date_published":"2025-06-11T00:00:00Z","has_accepted_license":"1","OA_type":"gold","ddc":["570"],"DOAJ_listed":"1","OA_place":"publisher","date_updated":"2026-10-20T08:55:34Z","ec_funded":1,"abstract":[{"text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.","lang":"eng"}],"file_date_updated":"2025-06-10T07:24:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"intvolume":"         5","file":[{"relation":"main_file","access_level":"open_access","checksum":"4018c833f25a3ad3b57e3577fed70334","creator":"dernst","content_type":"application/pdf","date_updated":"2025-06-10T07:24:46Z","file_id":"19802","success":1,"file_size":7238179,"date_created":"2025-06-10T07:24:46Z","file_name":"2025_BiophysicalReports_Vorlaufer.pdf"}],"issue":"2","oa_version":"Published Version","status":"public","_id":"19795","publisher":"Cell Press","year":"2025","acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","citation":{"chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Cell Press, 2025.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>"},"day":"11"},{"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publication_status":"published","page":"107","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"08","date_created":"2025-08-22T08:12:55Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"19795","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","project":[{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"}],"corr_author":"1","author":[{"full_name":"Vorlaufer, Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","first_name":"Jakob","orcid":"0009-0000-7590-3501"}],"doi":"10.15479/AT-ISTA-20206","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","oa":1,"oa_version":"Published Version","_id":"20206","status":"public","citation":{"ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria.","apa":"Vorlaufer, J. (2025). <i>Construction of a cryo-super-resolution microscope to guide in situ structure analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>.","mla":"Vorlaufer, Jakob. <i>Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>.","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025."},"acknowledgement":"The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. ","year":"2025","publisher":"Institute of Science and Technology Austria","day":"25","supervisor":[{"orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file":[{"creator":"jvorlauf","date_updated":"2025-08-25T13:49:55Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"191db3367c19c9b32b65f4bc3a7c19de","access_level":"closed","relation":"source_file","date_created":"2025-08-25T13:49:55Z","file_size":39735535,"file_name":"2025_Vorlaufer_Jakob_Thesis.docx","file_id":"20228"},{"success":1,"file_id":"20229","file_size":10947446,"date_created":"2025-08-25T13:49:56Z","file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","checksum":"104400e6036921569610230c1d4899dc","access_level":"open_access","relation":"main_file","creator":"jvorlauf","date_updated":"2025-08-25T13:49:56Z","content_type":"application/pdf"}],"date_updated":"2026-10-20T08:55:33Z","alternative_title":["ISTA Thesis"],"file_date_updated":"2025-08-25T13:49:56Z","abstract":[{"lang":"eng","text":"The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.15479/AT-ISTA-20206","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"ddc":["621","535"],"date_published":"2025-08-25T00:00:00Z","has_accepted_license":"1","OA_place":"publisher"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process.","lang":"eng"}],"file_date_updated":"2025-05-19T07:45:31Z","date_updated":"2026-10-20T09:45:59Z","OA_place":"publisher","DOAJ_listed":"1","ddc":["000"],"date_published":"2025-05-01T00:00:00Z","has_accepted_license":"1","OA_type":"gold","article_type":"original","fulldoi":"https://doi.org/10.1371/journal.pcbi.1012868","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","arxiv":1,"isi":1,"citation":{"mla":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>, vol. 21, no. 5, Public Library of Science, 2025, p. e1012868, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>.","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.","chicago":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>. Public Library of Science, 2025. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>.","ieee":"L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,” <i>PLoS Computational Biology</i>, vol. 21, no. 5. Public Library of Science, p. e1012868, 2025.","apa":"Kopfová, L., &#38; Tkadlec, J. (2025). Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>","ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS Computational Biology. 21(5), e1012868.","ama":"Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. 2025;21(5):e1012868. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>"},"year":"2025","publisher":"Public Library of Science","_id":"19702","status":"public","oa_version":"Published Version","external_id":{"isi":["001481670600002"],"arxiv":["2410.09476"]},"issue":"5","file":[{"content_type":"application/pdf","date_updated":"2025-05-19T07:45:31Z","creator":"dernst","access_level":"open_access","checksum":"73e35151eebd5064972c5a07ffdf2b69","relation":"main_file","file_name":"2025_PloSCompBio_Kopfova.pdf","date_created":"2025-05-19T07:45:31Z","file_size":6805943,"success":1,"file_id":"19709"}],"intvolume":"        21","publication":"PLoS Computational Biology","author":[{"full_name":"Kopfová, Lenka","last_name":"Kopfová","id":"17691681-50b9-11ef-ad56-edf4cacb21b0","first_name":"Lenka"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","first_name":"Josef","orcid":"0000-0002-1097-9684"}],"scopus_import":"1","publication_identifier":{"eissn":["1553-7358"]},"oa":1,"title":"Colonization times in Moran process on graphs","doi":"10.1371/journal.pcbi.1012868","type":"journal_article","month":"05","page":"e1012868","volume":21,"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"}],"publication_status":"published","quality_controlled":"1","date_created":"2025-05-18T22:02:50Z","article_processing_charge":"Yes"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"file":[{"relation":"main_file","access_level":"open_access","checksum":"661b9d3786cfc985be811befc3262bf5","content_type":"application/pdf","date_updated":"2025-08-27T14:50:32Z","creator":"jsobarzo","file_id":"20237","success":1,"file_name":"2025_Sobarzo_JuanCarlos_Thesis.pdf","file_size":12667200,"date_created":"2025-08-27T14:50:32Z"},{"access_level":"closed","checksum":"ca2f24e6c3b55912982521707552a0f5","relation":"source_file","content_type":"application/x-zip-compressed","date_updated":"2025-08-28T08:19:07Z","creator":"jsobarzo","file_id":"20238","file_name":"2025_Sobarzo_JuanCarlos_Thesis.zip","date_created":"2025-08-27T14:50:32Z","file_size":18940521}],"oa_version":"Published Version","status":"public","_id":"20203","publisher":"Institute of Science and Technology Austria","citation":{"ieee":"J. C. A. Sobarzo Ponce, “Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges,” Institute of Science and Technology Austria, 2025.","apa":"Sobarzo Ponce, J. C. A. (2025). <i>Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20203\">https://doi.org/10.15479/AT-ISTA-20203</a>","ama":"Sobarzo Ponce JCA. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20203\">10.15479/AT-ISTA-20203</a>","ista":"Sobarzo Ponce JCA. 2025. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria.","short":"J.C.A. Sobarzo Ponce, Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges, Institute of Science and Technology Austria, 2025.","mla":"Sobarzo Ponce, Juan Carlos A. <i>Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20203\">10.15479/AT-ISTA-20203</a>.","chicago":"Sobarzo Ponce, Juan Carlos A. “Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20203\">https://doi.org/10.15479/AT-ISTA-20203</a>."},"year":"2025","acknowledgement":"The project in Chapter 2 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 3 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 4 has received financing from the European Research Council grant\r\nagreement No. 949120 under the European Union’s Horizon 2020 research and innovation\r\nprogramme. The Analytical Instrumentation Center of the TU Wien acknowledges support by\r\nthe FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state\r\nof Lower Austria and the European Regional Development Fund under grant no. WST3-F542638/004-2021.\r\n","supervisor":[{"first_name":"Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R"}],"day":"27","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20203","has_accepted_license":"1","date_published":"2025-08-27T00:00:00Z","ddc":["530"],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-21T08:38:30Z","file_date_updated":"2025-08-28T08:19:07Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","date_created":"2025-08-21T11:42:59Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"12109","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"19278"},{"status":"public","relation":"part_of_dissertation","id":"15322"}]},"project":[{"grant_number":"949120","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"degree_awarded":"PhD","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ScWa"}],"language":[{"iso":"eng"}],"page":"96","month":"08","type":"dissertation","doi":"10.15479/AT-ISTA-20203","title":"Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges","oa":1,"publication_identifier":{"isbn":["978-3-99078-062-6"],"issn":["2663-337X"]},"doi_confirm":"1","corr_author":"1","author":[{"first_name":"Juan Carlos A","last_name":"Sobarzo Ponce","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","full_name":"Sobarzo Ponce, Juan Carlos A"}]},{"file":[{"relation":"source_file","access_level":"closed","checksum":"b5eed6a3dccb83cd2a8a22e11fd7d867","creator":"smondal","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-11-13T16:47:47Z","file_id":"20644","date_created":"2025-11-13T16:47:47Z","file_size":32589295,"file_name":"2025_Mondal_Soumyadip_Thesis.docx"},{"file_id":"20645","embargo_to":"open_access","file_name":"2025_Mondal_Soumyadip_Thesis.pdf","date_created":"2025-11-13T16:47:46Z","embargo":"2026-11-13","file_size":5007370,"relation":"main_file","access_level":"closed","checksum":"89b1529e0a7b524f46624d73ecadf8cb","date_updated":"2025-11-13T16:47:46Z","content_type":"application/pdf","creator":"smondal"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"das_tickbox":"1","day":"19","supervisor":[{"orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"year":"2025","acknowledgement":"I gratefully acknowledge the support of the ISTA Graduate School and the Scientific Service Units of\r\nISTA, whose resources made this work possible—especially the Imaging & Optics Facility, the Lab\r\nSupport Facility, and the Miba Machine Shop. I would like to thank two staff scientists in particular:\r\nRobert Hauschild (Imaging & Optics Facility) and Daniel Balazs (Lab Support Facility), for their\r\nassistance and advice. My PhD was partially funded by the Austrian Science Fund (FWF)\r\n(10.55776/P37169 and 10.55776/COE5).","citation":{"short":"S. Mondal, Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria, Institute of Science and Technology Austria, 2025.","mla":"Mondal, Soumyadip. <i>Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20607\">10.15479/AT-ISTA-20607</a>.","chicago":"Mondal, Soumyadip. “Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20607\">https://doi.org/10.15479/AT-ISTA-20607</a>.","apa":"Mondal, S. (2025). <i>Oxygen and sulfur redox: Conversion kinetics and phase equilibria</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20607\">https://doi.org/10.15479/AT-ISTA-20607</a>","ieee":"S. Mondal, “Oxygen and sulfur redox: Conversion kinetics and phase equilibria,” Institute of Science and Technology Austria, 2025.","ista":"Mondal S. 2025. Oxygen and sulfur redox: Conversion kinetics and phase equilibria. Institute of Science and Technology Austria.","ama":"Mondal S. Oxygen and sulfur redox: Conversion kinetics and phase equilibria. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20607\">10.15479/AT-ISTA-20607</a>"},"publisher":"Institute of Science and Technology Austria","status":"public","_id":"20607","oa_version":"Published Version","OA_place":"publisher","ddc":["541","543","542"],"date_published":"2025-09-19T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-20607","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-11-13T16:47:47Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-21T10:25:04Z","project":[{"grant_number":"P37169","_id":"8df062be-16d5-11f0-9cad-f559b6612c7e","name":"Singlet oxygen in non-aqueous oxygen redox chemistry"},{"grant_number":"COE05","_id":"5eaf4378-b033-11f1-b276-f928018a46c1","name":"Materials for Energy Conversion and Storage (Freunberger)"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12065"},{"relation":"part_of_dissertation","id":"20437","status":"deleted"},{"id":"13044","relation":"part_of_dissertation","status":"public"},{"id":"14687","relation":"part_of_dissertation","status":"public"}]},"date_created":"2025-11-07T12:40:54Z","article_processing_charge":"No","month":"09","page":"71","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"StFr"}],"publication_status":"published","doi_confirm":"1","publication_identifier":{"isbn":["978-3-99078-071-8"],"issn":["2663-337X"]},"title":"Oxygen and sulfur redox: Conversion kinetics and phase equilibria","doi":"10.15479/AT-ISTA-20607","type":"dissertation","author":[{"first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","full_name":"Mondal, Soumyadip"}],"corr_author":"1"},{"supervisor":[{"orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"day":"10","publisher":"Institute of Science and Technology Austria","citation":{"short":"G. Tasinato, Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems, Institute of Science and Technology Austria, 2025.","mla":"Tasinato, Gianluca. <i>Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20339\">10.15479/AT-ISTA-20339</a>.","chicago":"Tasinato, Gianluca. “Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20339\">https://doi.org/10.15479/AT-ISTA-20339</a>.","apa":"Tasinato, G. (2025). <i>Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20339\">https://doi.org/10.15479/AT-ISTA-20339</a>","ieee":"G. Tasinato, “Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems,” Institute of Science and Technology Austria, 2025.","ista":"Tasinato G. 2025. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria.","ama":"Tasinato G. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20339\">10.15479/AT-ISTA-20339</a>"},"year":"2025","_id":"20339","status":"public","oa_version":"Published Version","file":[{"creator":"gtasinat","content_type":"application/x-zip-compressed","date_updated":"2025-09-11T12:24:12Z","checksum":"ae097a515b9bb4d4b025ca854ae2ed76","access_level":"closed","relation":"source_file","date_created":"2025-09-11T12:24:12Z","file_size":2218562,"file_name":"thesis-source.zip","file_id":"20344"},{"success":1,"file_id":"20345","date_created":"2025-09-11T12:26:14Z","file_size":10071982,"file_name":"2025_Tasinato_Gianluca_Thesis.pdf","checksum":"04b2e016409e52167ce42b0eef839fbf","access_level":"open_access","relation":"main_file","creator":"gtasinat","content_type":"application/pdf","date_updated":"2025-09-11T12:26:14Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2025-09-11T12:26:14Z","abstract":[{"text":"This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights.\r\n\r\nWe first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations.\r\n\r\nIn the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D.\r\n","lang":"eng"}],"date_updated":"2026-10-21T13:23:55Z","alternative_title":["ISTA Thesis"],"OA_place":"publisher","date_published":"2025-09-10T00:00:00Z","has_accepted_license":"1","ddc":["516"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20339","month":"09","page":"106","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"UlWa"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"20008","relation":"part_of_dissertation"},{"id":"19860","relation":"part_of_dissertation","status":"public"},{"id":"15168","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","date_created":"2025-09-10T12:17:55Z","author":[{"first_name":"Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","last_name":"Tasinato","full_name":"Tasinato, Gianluca"}],"corr_author":"1","doi_confirm":"1","oa":1,"title":"Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-20339"},{"fulldoi":"https://doi.org/10.15479/AT-ISTA-20485","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2025-10-23T00:00:00Z","has_accepted_license":"1","OA_place":"publisher","date_updated":"2026-10-23T22:30:03Z","alternative_title":["ISTA Thesis"],"ec_funded":1,"file_date_updated":"2026-10-23T22:30:02Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"relation":"source_file","checksum":"e042ea314e7e13fce76c6c95e126779a","access_level":"closed","date_updated":"2026-10-23T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mmisova","file_id":"20518","embargo_to":"open_access","file_name":"2025-Misova-Michaela-Thesis.docx","date_created":"2025-10-23T08:22:35Z","file_size":75070995},{"file_size":10974630,"embargo":"2026-10-23","date_created":"2025-10-23T08:21:21Z","file_name":"2025-Misova-Michaela-Thesis.pdf","file_id":"20519","creator":"mmisova","date_updated":"2026-10-23T22:30:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"fcd8973d6a025256eb0eb1a82c02172c"}],"oa_version":"Published Version","_id":"20485","status":"public","citation":{"mla":"Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>.","short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025.","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>.","apa":"Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans nervous system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>","ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria."},"year":"2025","acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","publisher":"Institute of Science and Technology Austria","day":"23","supervisor":[{"full_name":"de Bono, Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"doi":"10.15479/AT-ISTA-20485","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-068-8"],"issn":["2663-337X"]},"title":"Dissecting gap junction biology using the C. elegans nervous system","oa":1,"corr_author":"1","author":[{"first_name":"Michaela","orcid":"0000-0003-2427-6856","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","last_name":"Misova","full_name":"Misova, Michaela"}],"date_created":"2025-10-17T16:15:09Z","article_processing_charge":"No","degree_awarded":"PhD","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"155","month":"10"},{"OA_place":"publisher","ddc":["570"],"has_accepted_license":"1","date_published":"2025-04-14T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-19557","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2026-10-15T22:30:02Z","date_updated":"2026-10-15T22:30:03Z","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","access_level":"closed","checksum":"50290a8604edb0a720387f01e9d59fe4","creator":"lschwarz","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-10-15T22:30:02Z","file_id":"19561","embargo_to":"open_access","file_size":21783427,"date_created":"2025-04-15T08:43:36Z","file_name":"Schwarz_Thesis_2025_FINAL.docx"},{"file_id":"19562","file_name":"Schwarz_Thesis_2025_FINALpdfa.pdf","file_size":11432175,"embargo":"2026-10-15","date_created":"2025-04-15T08:43:42Z","access_level":"open_access","checksum":"ed028488180ac4901e018ef1c330cf01","relation":"main_file","content_type":"application/pdf","date_updated":"2026-10-15T22:30:02Z","creator":"lschwarz"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"day":"14","supervisor":[{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"citation":{"ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria.","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>","ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>.","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025."},"year":"2025","acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","publisher":"Institute of Science and Technology Austria","_id":"19557","status":"public","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution","oa":1,"doi":"10.15479/AT-ISTA-19557","type":"dissertation","author":[{"first_name":"Lena A","full_name":"Schwarz, Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","degree_awarded":"PhD","project":[{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964"},{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","grant_number":"101044865"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12802"},{"status":"public","id":"9429","relation":"part_of_dissertation"}]},"date_created":"2025-04-14T06:59:06Z","article_processing_charge":"No","month":"04","page":"124","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"related_material":{"record":[{"id":"14759","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","article_processing_charge":"No","date_created":"2025-12-11T11:48:11Z","month":"12","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"language":[{"iso":"eng"}],"page":"152","doi_confirm":"1","type":"dissertation","doi":"10.15479/AT-ISTA-20798","oa":1,"title":"Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry","publication_identifier":{"isbn":["978-3-99078-075-6"],"issn":["2663-337X"]},"author":[{"orcid":"0000-0002-5869-1604","first_name":"Sebastian","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","last_name":"Wald"}],"corr_author":"1","file":[{"creator":"swald","date_updated":"2026-06-15T22:30:03Z","content_type":"application/pdf","access_level":"open_access","checksum":"1be72faf529a5e8a2d03cb3d5f808b77","relation":"main_file","date_created":"2025-12-12T11:53:42Z","file_size":47536855,"embargo":"2026-06-15","file_name":"2025_Wald_Sebastian_Thesis.pdf","file_id":"20809"},{"file_id":"20810","embargo_to":"open_access","file_size":40127601,"date_created":"2025-12-12T11:54:55Z","file_name":"2025_Wald_Sebastian_Thesis.zip","relation":"source_file","checksum":"8c3a1904dceb4bcd04bc9f14b2594bab","access_level":"closed","creator":"swald","content_type":"application/x-zip-compressed","date_updated":"2026-06-15T22:30:03Z"}],"publisher":"Institute of Science and Technology Austria","year":"2025","citation":{"ama":"Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>","ista":"Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria.","ieee":"S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025.","apa":"Wald, S. (2025). <i>Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>","chicago":"Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>.","short":"S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025.","mla":"Wald, Sebastian. <i>Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>."},"supervisor":[{"first_name":"Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur"}],"day":"11","das_tickbox":"1","oa_version":"Published Version","_id":"20798","status":"public","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"keyword":["entanglement-enhanced atom interferometry","cavity QED","spin-squeezing","dipole trap","quantum optics"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20798","date_published":"2025-12-11T00:00:00Z","has_accepted_license":"1","ddc":["530"],"abstract":[{"lang":"eng","text":"Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry."}],"file_date_updated":"2026-06-15T22:30:03Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_embargo":"6","alternative_title":["ISTA Thesis"],"date_updated":"2026-07-24T08:07:28Z"},{"title":"Microwave-optic interconnects for superconducting circuits","oa":1,"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:18871","author":[{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876"}],"corr_author":"1","project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"6609","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8529","status":"public"},{"status":"public","id":"18953","relation":"part_of_dissertation"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"id":"9114","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"13200","status":"public"}]},"article_processing_charge":"No","date_created":"2025-01-24T10:28:39Z","month":"01","page":"135","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"},{"_id":"GradSch"}],"OA_place":"publisher","date_published":"2025-01-24T00:00:00Z","has_accepted_license":"1","ddc":["530"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"fulldoi":"https://doi.org/10.15479/at:ista:18871","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-01-29T23:30:03Z","abstract":[{"lang":"eng","text":"\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n"}],"ec_funded":1,"date_updated":"2026-04-16T12:20:43Z","alternative_title":["ISTA Thesis"],"file":[{"file_id":"18946","embargo_to":"open_access","file_name":"tex for upload.zip","file_size":18856130,"date_created":"2025-01-29T08:38:08Z","relation":"source_file","access_level":"closed","checksum":"71872702e8f46c275eaea44efc4d304f","date_updated":"2026-01-29T23:30:03Z","content_type":"application/x-zip-compressed","creator":"cchlebak"},{"relation":"main_file","access_level":"open_access","checksum":"dfaa06591970f4bff163705802fad56d","content_type":"application/pdf","date_updated":"2026-01-29T23:30:03Z","creator":"cchlebak","file_id":"18947","file_name":"ISTThesisGA2022_final.pdf","date_created":"2025-01-29T08:38:34Z","embargo":"2026-01-29","file_size":17344760}],"acknowledged_ssus":[{"_id":"SSU"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"supervisor":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"day":"24","publisher":"Institute of Science and Technology Austria","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n","year":"2025","citation":{"ista":"Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria.","ama":"Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>","apa":"Arnold, G. M. (2025). <i>Microwave-optic interconnects for superconducting circuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>","ieee":"G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025.","chicago":"Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>.","mla":"Arnold, Georg M. <i>Microwave-Optic Interconnects for Superconducting Circuits</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>.","short":"G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025."},"_id":"18871","status":"public","oa_version":"Published Version"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2025-11-27T23:30:02Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Cell migration is a crucial process in animal development and maintenance. It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment, where cells can switch between\r\nmigration modes as they encounter new environmental cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration strategy when encountering geometrically,\r\nmechanically and chemically distinct environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy, extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable. Instead, the cells use topography of the\r\nenvironment to propel their cell body forward. To migrate efficiently in the maze of different\r\npore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions into much denser environments with limited choice of large pores. In such invasive\r\ntransitions it is unclear if the cells can cross tight pores without the use of adhesions and\r\nextracellular proteolysis and whether they maintain the nucleus in the cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen gels, geometrically defined\r\nmicrochannels with constrictions and simplistic under agarose migration assay, we provide\r\na comprehensive characterization of invasive migration of dendritic cells. We show that\r\nduring invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody into the dense environment. In collagen gels, we show that dendritic cells can invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading\r\nto a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile force is simultaneously necessary for reverting the nucleus back to\r\nthe cell front after invasion and maintaining this positioning during permissive migration.\r\nA functional role of the reorientation was uncovered in the first collaboration project.\r\nA prominent central actin pool was identified around the MTOC, especially pronounced in\r\ndense and compressive environments. The actin pool was shown to generate pushing forces\r\nto dilate the space for cell translocation. These forces are only necessary in non-permissive\r\nenvironments, where the nucleus reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive environments where space generation is dispensable, the\r\nMTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second collaboration project, we investigated the effects of distinct chemical\r\nenvironments on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas explained by their ability to modulate and even self-generate chemokine gradients. This\r\nallows the cells to migrate faster and more persistent in uniform chemokine fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial\r\nplayer in this process, both sensing the signal and internalizing the chemokine to create a sink."}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-06-18T17:34:48Z","OA_embargo":"6","OA_place":"publisher","date_published":"2025-05-27T00:00:00Z","has_accepted_license":"1","ddc":["570"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19745","supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"day":"27","publisher":"Institute of Science and Technology Austria","acknowledgement":"This project has received funding from the Austrian Science Fund (FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","year":"2025","citation":{"ama":"Canigova N. Adaptive strategies of dendritic cell migration in response to environmental cues. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>","ista":"Canigova N. 2025. Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria.","apa":"Canigova, N. (2025). <i>Adaptive strategies of dendritic cell migration in response to environmental cues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>","ieee":"N. Canigova, “Adaptive strategies of dendritic cell migration in response to environmental cues,” Institute of Science and Technology Austria, 2025.","chicago":"Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19745\">https://doi.org/10.15479/AT-ISTA-19745</a>.","mla":"Canigova, Nikola. <i>Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19745\">10.15479/AT-ISTA-19745</a>.","short":"N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues, Institute of Science and Technology Austria, 2025."},"_id":"19745","status":"public","oa_version":"Published Version","file":[{"date_updated":"2025-11-27T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","relation":"source_file","access_level":"closed","checksum":"1a2d1525d19347fbb879ef57c02951bf","file_name":"NikolaCanigova_Thesis_final.docx","date_created":"2025-05-28T07:38:17Z","file_size":103879193,"file_id":"19748","embargo_to":"open_access"},{"relation":"main_file","access_level":"open_access","checksum":"c1d8f9a40a8e19fcf895373f4b773a46","date_updated":"2025-11-27T23:30:02Z","content_type":"application/pdf","creator":"cchlebak","file_id":"19749","file_name":"NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf","embargo":"2025-11-27","file_size":194530600,"date_created":"2025-05-28T07:39:53Z"}],"author":[{"full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","first_name":"Nikola","orcid":"0000-0002-8518-5926"}],"corr_author":"1","title":"Adaptive strategies of dendritic cell migration in response to environmental cues","oa":1,"publication_identifier":{"isbn":["978-3-99078-058-9"],"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-19745","month":"05","page":"133","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"GradSch"}],"degree_awarded":"PhD","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"W01250-B20","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"14274","status":"public"}]},"article_processing_charge":"No","date_created":"2025-05-26T08:49:00Z"},{"status":"public","_id":"19431","oa_version":"Published Version","day":"20","supervisor":[{"first_name":"Carrie A","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"year":"2025","citation":{"chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>.","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>","ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025."},"acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"file":[{"date_created":"2025-03-24T12:48:36Z","file_size":23506747,"file_name":"PhD_Thesis_Hlavata_final_submission.docx","embargo_to":"open_access","file_id":"19448","creator":"ahlavata","date_updated":"2026-03-20T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","access_level":"closed","relation":"source_file"},{"creator":"ahlavata","date_updated":"2026-03-20T23:30:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","date_created":"2025-03-24T12:51:10Z","embargo":"2026-03-20","file_size":9478591,"file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","file_id":"19449"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T11:46:32Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm.","lang":"eng"}],"file_date_updated":"2026-03-20T23:30:04Z","ddc":["572"],"has_accepted_license":"1","date_published":"2025-03-20T00:00:00Z","fulldoi":"https://doi.org/10.15479/10.15479/AT-ISTA-19431","OA_place":"publisher","page":"83","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"publication_status":"published","month":"03","date_created":"2025-03-20T12:52:47Z","article_processing_charge":"No","degree_awarded":"PhD","corr_author":"1","author":[{"first_name":"Annamaria","full_name":"Hlavata, Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-055-8"],"eissn":["2663-337X"]},"title":"Regulation of Cytoplasmic RNA Polymerase II","oa":1,"doi":"10.15479/10.15479/AT-ISTA-19431","type":"dissertation"},{"acknowledged_ssus":[{"_id":"LifeSc"}],"file":[{"date_updated":"2026-02-23T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lsartori","relation":"source_file","checksum":"7e9466dcf3681454211b74b5107e9f7b","access_level":"closed","file_name":"Thesis_Linda_Sartoris.docx","date_created":"2025-03-07T10:16:11Z","file_size":7129583,"file_id":"19310","embargo_to":"open_access"},{"creator":"lsartori","content_type":"application/pdf","date_updated":"2026-03-02T23:31:13Z","description":"for printing purposes only","access_level":"closed","checksum":"2ccfcf32f0590bb0ec1a488e606a73f5","relation":"other","date_created":"2025-03-11T10:42:20Z","file_size":3199703,"file_name":"thesis_Sartoris_for_print.pdf","embargo_to":"open_access","file_id":"19384"},{"file_size":3183186,"embargo":"2026-02-23","date_created":"2025-03-11T10:52:00Z","file_name":"Thesis_Linda_Sartoris.pdf","file_id":"19385","creator":"lsartori","date_updated":"2026-02-23T23:30:03Z","content_type":"application/pdf","checksum":"1d1f3c1279065b1a7f407ff6d1ee1503","access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","status":"public","_id":"19302","publisher":"Institute of Science and Technology Austria","acknowledgement":"Thank you to the Lab Support Facility at ISTA. Thank you to the European Research Council (ERC) for their funding under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402, to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt).","year":"2025","citation":{"mla":"Sartoris, Linda. <i>The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>.","short":"L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025.","chicago":"Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>.","ieee":"L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025.","apa":"Sartoris, L. (2025). <i>The effect of circadian rhythm on organisational immunity of ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>","ista":"Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria.","ama":"Sartoris L. The effect of circadian rhythm on organisational immunity of ant colonies. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>"},"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"day":"24","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19302","date_published":"2025-02-24T00:00:00Z","has_accepted_license":"1","OA_type":"closed access","ddc":["577"],"alternative_title":["ISTA Thesis"],"date_updated":"2026-03-02T23:31:14Z","ec_funded":1,"file_date_updated":"2026-03-02T23:31:13Z","abstract":[{"lang":"eng","text":"Social interaction networks of insect colonies facilitate efficient information exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission. While circadian rhythms\r\ninfluence individual behaviour, their role in shaping colony-level defences against pathogens\r\nremains unexplored. Here, we investigate whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies are exposed to a pathogen during the day or the night.\r\nWe first establish baseline daily variations in activity and network dynamics in pathogen-free\r\ncolonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting of nurses and the queen. These findings underscore the robustness and adaptability\r\nof ant colonies in balancing circadian rhythms with effective social immune responses."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","date_created":"2025-03-06T12:16:54Z","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"degree_awarded":"PhD","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"language":[{"iso":"eng"}],"page":"85","month":"02","type":"dissertation","doi":"10.15479/AT-ISTA-19302","title":"The effect of circadian rhythm on organisational immunity of ant colonies","oa":1,"publication_identifier":{"eissn":["2663-337X"]},"corr_author":"1","author":[{"last_name":"Sartoris","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda","first_name":"Linda"}]},{"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"file":[{"file_id":"19457","date_created":"2025-03-25T11:07:55Z","embargo":"2025-09-30","file_size":11869040,"file_name":"2025_Thesis_Cumpelik_corrections_PDFA.pdf","relation":"main_file","access_level":"open_access","checksum":"1c7573303d8e5f6da3eb03d59055390f","creator":"acumpeli","date_updated":"2025-09-30T22:30:02Z","content_type":"application/pdf"},{"file_name":"2025_Thesis_Cumpelik_corrections.docx","file_size":20436467,"date_created":"2025-03-25T11:08:05Z","file_id":"19458","embargo_to":"open_access","date_updated":"2025-09-30T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"acumpeli","relation":"source_file","access_level":"closed","checksum":"b93265ebd9a53f7a14100d0d48b4ff5b"}],"oa_version":"Published Version","_id":"19456","status":"public","publisher":"Institute of Science and Technology Austria","year":"2025","citation":{"short":"A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025.","mla":"Cumpelik, Andrea D. <i>The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>.","chicago":"Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>.","ieee":"A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025.","apa":"Cumpelik, A. D. (2025). <i>The role of prefrontal spatial coding in supporting a contextual association task</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>","ama":"Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>","ista":"Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria."},"supervisor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"day":"18","keyword":["neuroscience","decision making","learning","cognitive flexibility","medial prefrontal cortex","hippocampus","electrophysiology"],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19456","has_accepted_license":"1","date_published":"2025-02-18T00:00:00Z","ddc":["612"],"OA_place":"publisher","OA_embargo":"6 months","date_updated":"2026-04-07T12:37:58Z","alternative_title":["ISTA Thesis"],"file_date_updated":"2025-09-30T22:30:02Z","abstract":[{"text":"Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. ","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","date_created":"2025-03-25T11:22:38Z","degree_awarded":"PhD","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"language":[{"iso":"eng"}],"page":"96","month":"02","type":"dissertation","doi":"10.15479/AT-ISTA-19456","title":"The role of prefrontal spatial coding in supporting a contextual association task","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-056-5"]},"corr_author":"1","author":[{"id":"3F158B32-F248-11E8-B48F-1D18A9856A87","last_name":"Cumpelik","full_name":"Cumpelik, Andrea D","first_name":"Andrea D","orcid":"0000-0003-1727-6612"}]},{"oa":1,"title":"Social immunity in a tri-partite host-pathogen relationship","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/AT-ISTA-19993","author":[{"full_name":"Strahodinsky, Florian","id":"979E35EE-C996-11E9-8C7C-CF13E6697425","last_name":"Strahodinsky","first_name":"Florian"}],"corr_author":"1","degree_awarded":"PhD","article_processing_charge":"No","date_created":"2025-07-10T14:12:20Z","month":"07","page":"138","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"language":[{"iso":"eng"}],"OA_place":"publisher","date_published":"2025-07-11T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19993","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2026-01-15T23:30:03Z","abstract":[{"text":"Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T12:39:58Z","file":[{"file_size":9857392,"date_created":"2025-07-14T13:18:37Z","file_name":"Thesis_Florian_Strahodinsky_DOCX.docx","file_id":"20021","embargo_to":"open_access","creator":"fstrahod","date_updated":"2026-01-15T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"df3a02f0d937ea9a3d79d5fb94fff097"},{"checksum":"7164c21fe1946e839f7b8acd255ce803","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2026-01-15T23:30:03Z","creator":"fstrahod","file_id":"20022","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf","file_size":6439602,"embargo":"2026-01-15","date_created":"2025-07-14T13:18:38Z"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"day":"11","publisher":"Institute of Science and Technology Austria","year":"2025","citation":{"ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria.","ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025.","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>."},"_id":"19993","status":"public","oa_version":"Published Version"}]