[{"publication":"Representation Theory","publication_identifier":{"issn":["1088-4165"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2025-04-24T08:48:05Z","file_date_updated":"2025-05-05T06:57:49Z","status":"public","acknowledgement":"The authors were partially supported by the “Long-term program of support of the Ukrainian research teams at the Polish Academy of Sciences carried out in collaboration with the U.S. National Academy of Sciences with the financial support of external partners”. The second author was also supported by the Austrian Science Fund (FWF) grant “Geometry of the tip of the global nilpotent cone” no. 10.55776/P35847","oa_version":"Published Version","date_updated":"2025-05-05T06:59:07Z","intvolume":"        29","abstract":[{"text":"In this paper we obtain a complete description of all indecomposable characters (central positive-definite functions) of inductive limits of the symmetric groups under block diagonal embedding. As a corollary we obtain the full classification of the isomorphism classes of these inductive limits.","lang":"eng"}],"author":[{"last_name":"Nessonov","full_name":"Nessonov, Nikolay","first_name":"Nikolay"},{"full_name":"Ngo, Nhok T","last_name":"Ngo","first_name":"Nhok T","id":"28e53c8c-896a-11ed-bdf8-f809043ce2f0"}],"OA_type":"hybrid","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"project":[{"grant_number":"P35847","_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3","name":"Geometry of the tip of the global nilpotent cone"}],"title":"Indecomposable characters of inductive limits of symmetric groups","ddc":["510"],"day":"10","quality_controlled":"1","year":"2025","external_id":{"arxiv":["2206.01964"]},"page":"256-288","article_type":"original","file":[{"file_id":"19644","file_name":"2025_RepresentationTheory_Nessonov.pdf","access_level":"open_access","checksum":"f6541ea1736a7413c6d24f14d64a4dda","content_type":"application/pdf","date_updated":"2025-05-05T06:57:49Z","file_size":424364,"date_created":"2025-05-05T06:57:49Z","creator":"dernst","relation":"main_file","success":1}],"oa":1,"doi":"10.1090/ert/689","language":[{"iso":"eng"}],"date_published":"2025-04-10T00:00:00Z","publisher":"American Mathematical Society","issue":"8","publication_status":"published","citation":{"ieee":"N. Nessonov and N. T. Ngo, “Indecomposable characters of inductive limits of symmetric groups,” <i>Representation Theory</i>, vol. 29, no. 8. American Mathematical Society, pp. 256–288, 2025.","apa":"Nessonov, N., &#38; Ngo, N. T. (2025). Indecomposable characters of inductive limits of symmetric groups. <i>Representation Theory</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/ert/689\">https://doi.org/10.1090/ert/689</a>","ama":"Nessonov N, Ngo NT. Indecomposable characters of inductive limits of symmetric groups. <i>Representation Theory</i>. 2025;29(8):256-288. doi:<a href=\"https://doi.org/10.1090/ert/689\">10.1090/ert/689</a>","short":"N. Nessonov, N.T. Ngo, Representation Theory 29 (2025) 256–288.","chicago":"Nessonov, Nikolay, and Nhok T Ngo. “Indecomposable Characters of Inductive Limits of Symmetric Groups.” <i>Representation Theory</i>. American Mathematical Society, 2025. <a href=\"https://doi.org/10.1090/ert/689\">https://doi.org/10.1090/ert/689</a>.","mla":"Nessonov, Nikolay, and Nhok T. Ngo. “Indecomposable Characters of Inductive Limits of Symmetric Groups.” <i>Representation Theory</i>, vol. 29, no. 8, American Mathematical Society, 2025, pp. 256–88, doi:<a href=\"https://doi.org/10.1090/ert/689\">10.1090/ert/689</a>.","ista":"Nessonov N, Ngo NT. 2025. Indecomposable characters of inductive limits of symmetric groups. Representation Theory. 29(8), 256–288."},"corr_author":"1","volume":29,"type":"journal_article","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"_id":"19621","arxiv":1,"month":"04","scopus_import":"1"},{"doi":"10.15479/AT-ISTA-19630","language":[{"iso":"eng"}],"date_published":"2025-04-29T00:00:00Z","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"file_id":"19633","access_level":"closed","checksum":"f00b519c27529daa0c3b2d4102b4fa7b","file_name":"Thesis_source_Heiss_Synak.zip","date_updated":"2025-04-30T14:02:25Z","content_type":"application/x-zip-compressed","file_size":60670543,"date_created":"2025-04-30T14:02:25Z","relation":"source_file","creator":"cchlebak"},{"content_type":"application/pdf","date_updated":"2025-04-30T15:49:16Z","file_size":21319043,"file_id":"19634","file_name":"Thesis_PDFA_Heiss_Synak.pdf","access_level":"open_access","checksum":"6e40a2fd3b1b881af1385670854a682e","relation":"main_file","creator":"cchlebak","date_created":"2025-04-30T14:02:42Z"}],"page":"106","year":"2025","month":"04","_id":"19630","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","type":"dissertation","corr_author":"1","degree_awarded":"PhD","citation":{"short":"P. Synak, Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures, Institute of Science and Technology Austria, 2025.","ista":"Synak P. 2025. Methods for fluid simulation, surface tracking, and statistics of non-manifold structures. Institute of Science and Technology Austria.","chicago":"Synak, Peter. “Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19630\">https://doi.org/10.15479/AT-ISTA-19630</a>.","mla":"Synak, Peter. <i>Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19630\">10.15479/AT-ISTA-19630</a>.","ieee":"P. Synak, “Methods for fluid simulation, surface tracking, and statistics of non-manifold structures,” Institute of Science and Technology Austria, 2025.","apa":"Synak, P. (2025). <i>Methods for fluid simulation, surface tracking, and statistics of non-manifold structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19630\">https://doi.org/10.15479/AT-ISTA-19630</a>","ama":"Synak P. Methods for fluid simulation, surface tracking, and statistics of non-manifold structures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19630\">10.15479/AT-ISTA-19630</a>"},"supervisor":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publication_status":"published","acknowledgement":"The project in Chapter 2 has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176. The project in Chapter 3 was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). The project in Chapter 4 has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It was also partially supported by the DFG Collaborative Research Center TRR 109, 'Discretization in Geometry and Dynamics', through grant no. I02979-N35 of the Austrian Science Fund (FWF). Thank you for providing funds to support my work.","file_date_updated":"2025-04-30T15:49:16Z","status":"public","date_created":"2025-04-29T09:39:34Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","id":"8135","relation":"part_of_dissertation"},{"id":"17219","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8384","relation":"part_of_dissertation"}]},"day":"29","alternative_title":["ISTA Thesis"],"ddc":["519","006"],"title":"Methods for fluid simulation, surface tracking, and statistics of non-manifold structures","project":[{"grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"},{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF"}],"department":[{"_id":"ChWo"},{"_id":"GradSch"}],"has_accepted_license":"1","author":[{"last_name":"Synak","full_name":"Synak, Peter","first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"This thesis consists of three chapters, each corresponding to one publication. While each of these projects tackles a topic in a different area of research, they all share a common thread in the type of topological structure they handle - a partition of space into volumes separated by interfaces that meet in non-manifold junctions.\r\n\r\nIn Chapter 2, we study clusters of soap bubbles from a simulation perspective. In particular, we develop a surface-only algorithm that couples large scale motion and shape deformation of soap bubble clusters with the small scale evolution of the thin film's thickness, which is responsible for visual phenomena like surface vortices, Newton's interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. We model film thickness as a reduced degree of freedom in the Navier-Stokes equations and from them derive three sets of equations governing normal and tangential motion of the soap film surface, as well as the evolution of the thin film thickness. We discretize these equations on a non-manifold triangle mesh, extending and adapting operators to handle complex topology. We also present an incompressible fluid solver for 2.5D films and an advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.\r\n\r\nIn Chapter 3, we introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts mesh defects, such as overlaps, self-intersections, and inversions into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations, such as those presented in Chapter 2, but with an order of magnitude more interacting bubbles than what we could achieve before, and Boolean unions of non-manifold meshes consisting of millions of triangles.\r\n\r\nLastly, in Chapter 4, we utilize developments in the theory of random geometric complexes facilitated by observations from Discrete Morse theory. We survey the methods and results obtained with this new approach, and discuss some of its shortcomings. We use simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.","lang":"eng"}],"date_updated":"2026-04-16T08:29:34Z","oa_version":"Published Version"},{"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"id":"9558","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12105","status":"public"},{"id":"13274","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14466"},{"status":"public","id":"7563","relation":"part_of_dissertation"}]},"date_created":"2025-05-12T15:12:28Z","file_date_updated":"2025-05-12T15:43:28Z","status":"public","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","article_processing_charge":"No","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz","full_name":"Yalniz, Gökhan"}],"oa_version":"Published Version","date_updated":"2026-06-18T19:23:35Z","abstract":[{"lang":"eng","text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate."}],"title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","ddc":["514","519","532","004"],"day":"13","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"}],"page":"155","year":"2025","file":[{"success":1,"relation":"main_file","creator":"gyalniz","date_created":"2025-05-12T15:13:28Z","file_size":20058169,"date_updated":"2025-05-12T15:13:28Z","content_type":"application/pdf","access_level":"open_access","checksum":"0e452642b79f13633f1595bde71a67e3","file_name":"Gökhan Yalnız - PhD thesis.pdf","file_id":"19685"},{"date_created":"2025-05-12T15:15:59Z","title":"Chapter 2 - Movie 2A.1","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","relation":"supplementary_material","creator":"gyalniz","checksum":"921099d76adab2df784ce12ce41cfb22","access_level":"open_access","file_name":"Movie 2A.1.mp4","file_id":"19686","file_size":37763743,"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4"},{"creator":"gyalniz","relation":"supplementary_material","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.1","date_created":"2025-05-12T15:16:09Z","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_size":3902655,"file_id":"19687","file_name":"Movie 3A.1.mp4","checksum":"0ae5ac7d9896003c0c4207dd746808dc","access_level":"open_access"},{"file_size":7043169,"content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 3A.2.mp4","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","access_level":"open_access","file_id":"19688","description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","relation":"supplementary_material","creator":"gyalniz","title":"Chapter 3 - Movie 3A.2","date_created":"2025-05-12T15:16:21Z"},{"description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","relation":"supplementary_material","creator":"gyalniz","title":"Chapter 3 - Movie 3A.3","date_created":"2025-05-12T15:16:36Z","file_size":7748659,"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","access_level":"open_access","checksum":"7ed871f428100d6827ac9b0e8ca8e985","file_name":"Movie 3A.3.mp4","file_id":"19689"},{"date_created":"2025-05-12T15:16:50Z","title":"Chapter 3 - Movie 3A.4","creator":"gyalniz","relation":"supplementary_material","description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","file_id":"19690","file_name":"Movie 3A.4.mp4","access_level":"open_access","checksum":"dd5a252e1da00c8f303588e22e2baeef","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_size":5873052},{"title":"Chapter 4 - Movie 4A.1","date_created":"2025-05-12T15:17:11Z","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit.","creator":"gyalniz","relation":"supplementary_material","checksum":"5ac58b86810698db28cbfc28f351ff70","access_level":"open_access","file_name":"Movie 4A.1.mp4","file_id":"19691","file_size":9209327,"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4"},{"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_size":5893993,"file_id":"19692","checksum":"ac877f1e1ef39439911bf37cb1793b8e","access_level":"open_access","file_name":"Movie 5A.1.mp4","creator":"gyalniz","relation":"supplementary_material","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","title":"Chapter 5 - Movie 5A.1","date_created":"2025-05-12T15:17:43Z"},{"date_created":"2025-05-12T15:17:49Z","title":"Chapter 5 - Movie 5A.2","creator":"gyalniz","relation":"supplementary_material","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_id":"19693","access_level":"open_access","checksum":"fd17eabb70129ceaa414e40924d1d2fe","file_name":"Movie 5A.2.mp4","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_size":3990352},{"creator":"gyalniz","relation":"supplementary_material","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain.","title":"Chapter 5 - Movie 5A.3","date_created":"2025-05-12T15:17:58Z","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_size":5171009,"file_id":"19694","access_level":"open_access","checksum":"32f904497ab0bbee38f0788d96b91454","file_name":"Movie 5A.3.mp4"},{"checksum":"f313261b9bb12dfb943fead8318954c6","access_level":"closed","file_name":"Gökhan Yalnız - PhD thesis.zip","file_id":"19695","file_size":18991996,"date_updated":"2025-05-12T15:43:28Z","content_type":"application/x-zip-compressed","date_created":"2025-05-12T15:27:10Z","relation":"source_file","creator":"gyalniz"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT-ISTA-19684","date_published":"2025-05-13T00:00:00Z","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Yalniz G. Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>","apa":"Yalniz, G. (2025). <i>Transition to turbulence : Data-, solution-, and pattern-driven approaches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>","ieee":"G. Yalniz, “Transition to turbulence : Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","ista":"Yalniz G. 2025. Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","mla":"Yalniz, Gökhan. <i>Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>.","chicago":"Yalniz, Gökhan. “Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>.","short":"G. Yalniz, Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025."},"degree_awarded":"PhD","corr_author":"1","type":"dissertation","month":"05","_id":"19684"},{"date_created":"2025-05-18T22:02:50Z","status":"public","file_date_updated":"2025-05-19T07:45:31Z","article_processing_charge":"Yes","publication_identifier":{"eissn":["1553-7358"]},"DOAJ_listed":"1","publication":"PLoS computational biology","ddc":["000"],"day":"01","title":"Colonization times in Moran process on graphs","department":[{"_id":"GradSch"}],"OA_type":"gold","isi":1,"has_accepted_license":"1","author":[{"last_name":"Kopfová","full_name":"Kopfová, Lenka","first_name":"Lenka","id":"17691681-50b9-11ef-ad56-edf4cacb21b0"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-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"}],"oa_version":"Published Version","date_updated":"2025-09-30T12:34:03Z","intvolume":"        21","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1012868","date_published":"2025-05-01T00:00:00Z","publisher":"Public Library of Science","issue":"5","file":[{"file_size":6805943,"date_updated":"2025-05-19T07:45:31Z","content_type":"application/pdf","checksum":"73e35151eebd5064972c5a07ffdf2b69","access_level":"open_access","file_name":"2025_PloSCompBio_Kopfova.pdf","file_id":"19709","success":1,"relation":"main_file","creator":"dernst","date_created":"2025-05-19T07:45:31Z"}],"oa":1,"article_type":"original","page":"e1012868","external_id":{"isi":["001481670600002"],"arxiv":["2410.09476"]},"quality_controlled":"1","year":"2025","month":"05","scopus_import":"1","arxiv":1,"_id":"19702","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","volume":21,"type":"journal_article","publication_status":"published","citation":{"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>","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>","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.","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>.","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>.","ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS computational biology. 21(5), e1012868.","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868."}},{"_id":"19704","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"06","scopus_import":"1","pmid":1,"volume":642,"corr_author":"1","type":"journal_article","citation":{"ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>."},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_type":"original","date_published":"2025-06-12T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1038/s41586-025-08985-1","oa":1,"file":[{"file_id":"19959","file_name":"2025_Nature_Tavakoli.pdf","checksum":"ebc99d7108e728f46db0a009292675ef","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-07-03T06:55:20Z","file_size":133201290,"date_created":"2025-07-03T06:55:20Z","creator":"dernst","relation":"main_file","success":1}],"year":"2025","quality_controlled":"1","page":"398-410","external_id":{"isi":["001483477000001"],"pmid":["40335689"]},"project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"101044865","_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"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"OA_type":"hybrid","has_accepted_license":"1","isi":1,"day":"12","ddc":["570"],"title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner.","lang":"eng"}],"date_updated":"2026-04-28T13:33:34Z","intvolume":"       642","oa_version":"Published Version","author":[{"orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Januszewski, Michał","last_name":"Januszewski","first_name":"Michał"},{"last_name":"Vistunou","full_name":"Vistunou, Vitali","first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas"},{"orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","full_name":"Oliveira, Bárbara"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jain, Viren","last_name":"Jain","first_name":"Viren"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G"}],"article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","status":"public","file_date_updated":"2025-07-03T06:55:20Z","date_created":"2025-05-18T22:02:51Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"related_material":{"record":[{"relation":"earlier_version","id":"18677","status":"public"},{"relation":"research_data","id":"18697","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/"}]},"publication":"Nature","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"ec_funded":1},{"_id":"19738","scopus_import":"1","month":"05","citation":{"mla":"Acharya, Anasuya, et al. “Securely Instantiating ‘Half Gates’ Garbling in the Standard Model.” <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, vol. 15677, Springer Nature, 2025, pp. 37–75, doi:<a href=\"https://doi.org/10.1007/978-3-031-91829-2_2\">10.1007/978-3-031-91829-2_2</a>.","chicago":"Acharya, Anasuya, Karen Azari, Mirza Ahad Baig, Dennis Hofheinz, and Chethan Kamath. “Securely Instantiating ‘Half Gates’ Garbling in the Standard Model.” In <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, 15677:37–75. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-91829-2_2\">https://doi.org/10.1007/978-3-031-91829-2_2</a>.","ista":"Acharya A, Azari K, Baig MA, Hofheinz D, Kamath C. 2025. Securely instantiating ‘Half Gates’ garbling in the standard model. 28th IACR International Conference on Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography, LNCS, vol. 15677, 37–75.","short":"A. Acharya, K. Azari, M.A. Baig, D. Hofheinz, C. Kamath, in:, 28th IACR International Conference on Practice and Theory of Public-Key Cryptography, Springer Nature, 2025, pp. 37–75.","apa":"Acharya, A., Azari, K., Baig, M. A., Hofheinz, D., &#38; Kamath, C. (2025). Securely instantiating ‘Half Gates’ garbling in the standard model. In <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i> (Vol. 15677, pp. 37–75). Roros, Norway: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-91829-2_2\">https://doi.org/10.1007/978-3-031-91829-2_2</a>","ama":"Acharya A, Azari K, Baig MA, Hofheinz D, Kamath C. Securely instantiating ‘Half Gates’ garbling in the standard model. In: <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>. Vol 15677. Springer Nature; 2025:37-75. doi:<a href=\"https://doi.org/10.1007/978-3-031-91829-2_2\">10.1007/978-3-031-91829-2_2</a>","ieee":"A. Acharya, K. Azari, M. A. Baig, D. Hofheinz, and C. Kamath, “Securely instantiating ‘Half Gates’ garbling in the standard model,” in <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, Roros, Norway, 2025, vol. 15677, pp. 37–75."},"type":"conference","volume":15677,"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-91829-2_2","date_published":"2025-05-05T00:00:00Z","quality_controlled":"1","year":"2025","page":"37-75","OA_type":"green","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"title":"Securely instantiating ‘Half Gates’ garbling in the standard model","alternative_title":["LNCS"],"day":"05","oa_version":"Preprint","intvolume":"     15677","date_updated":"2025-06-02T07:01:45Z","abstract":[{"text":"Garbling is a fundamental cryptographic primitive, with numerous theoretical and practical applications. Since the first construction by Yao (FOCS’82, ’86), a line of work has concerned itself with reducing the communication and computational complexity of that construction. One of the most efficient garbling schemes presently is the ‘Half Gates’ scheme by Zahur, Rosulek, and Evans (Eurocrypt’15). Despite its widespread adoption, the provable security of this scheme has been based on assumptions whose only instantiations are in idealized models. For example, in their original paper, Zahur, Rosulek, and Evans showed that hash functions satisfying a notion called circular correlation robustness (CCR) suffice for this task, and then proved that CCR secure hash functions can be instantiated in the random permutation model.\r\nIn this work, we show how to securely instantiate the Half Gates scheme in the standard model. To this end, we first show how this scheme can be securely instantiated given a (family of) weak CCR hash function, a notion that we introduce. Furthermore, we show how a weak CCR hash function can be used to securely instantiate other efficient garbling schemes, namely the ones by Rosulek and Roy (Crypto’21) and Heath (Eurocrypt’24). Thus we believe this notion to be of independent interest.\r\nFinally, we construct such weak CCR hash functions using indistinguishability obfuscation and one-way functions. The security proof of this construction constitutes our main technical contribution. While our construction is not practical, it serves as a proof of concept supporting the soundness of these garbling schemes, which we regard to be particularly important given the recent initiative by NIST to standardize garbling, and the optimizations in Half Gates being potentially adopted.","lang":"eng"}],"author":[{"last_name":"Acharya","full_name":"Acharya, Anasuya","first_name":"Anasuya"},{"full_name":"Azari, Karen","last_name":"Azari","first_name":"Karen"},{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"last_name":"Hofheinz","full_name":"Hofheinz, Dennis","first_name":"Dennis"},{"first_name":"Chethan","full_name":"Kamath, Chethan","last_name":"Kamath"}],"article_processing_charge":"No","date_created":"2025-05-25T22:17:02Z","main_file_link":[{"url":"https://eprint.iacr.org/2025/281","open_access":"1"}],"status":"public","publication":"28th IACR International Conference on Practice and Theory of Public-Key Cryptography","conference":{"name":"PKC: Public-Key Cryptography","end_date":"2025-05-15","location":"Roros, Norway","start_date":"2025-05-12"},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031918285"],"issn":["0302-9743"]}},{"date_published":"2025-05-30T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.15479/10.15479/at-ista-19759","publisher":"Institute of Science and Technology Austria","file":[{"creator":"bprach","relation":"main_file","date_created":"2025-06-10T18:11:05Z","date_updated":"2025-06-10T18:11:05Z","content_type":"application/pdf","file_size":3578077,"file_id":"19829","checksum":"e5108e759014e2a9020c973c778fafc9","access_level":"open_access","file_name":"ThesisFinal.pdf"},{"file_name":"ThesisFinal.zip","access_level":"closed","checksum":"51bf6c11fb6d8a9f8010b458c600a83f","file_id":"19830","file_size":74894357,"content_type":"application/x-zip-compressed","date_updated":"2025-06-10T18:14:03Z","date_created":"2025-06-10T18:14:03Z","relation":"source_file","creator":"bprach"}],"oa":1,"page":"84","year":"2025","month":"05","_id":"19759","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","degree_awarded":"PhD","corr_author":"1","type":"dissertation","publication_status":"published","citation":{"short":"B. Prach, Robust Image Classification with 1-Lipschitz Networks, Institute of Science and Technology Austria, 2025.","ista":"Prach B. 2025. Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria.","mla":"Prach, Bernd. <i>Robust Image Classification with 1-Lipschitz Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>.","chicago":"Prach, Bernd. “Robust Image Classification with 1-Lipschitz Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>.","ieee":"B. Prach, “Robust image classification with 1-Lipschitz networks,” Institute of Science and Technology Austria, 2025.","apa":"Prach, B. (2025). <i>Robust image classification with 1-Lipschitz networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>","ama":"Prach B. Robust image classification with 1-Lipschitz networks. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>"},"supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"date_created":"2025-05-28T16:20:48Z","status":"public","file_date_updated":"2025-06-10T18:14:03Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"15039","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18874","status":"public"},{"relation":"part_of_dissertation","id":"17426","status":"public"},{"relation":"part_of_dissertation","id":"11839","status":"public"}]},"ddc":["000"],"day":"30","alternative_title":["ISTA Thesis"],"title":"Robust image classification with 1-Lipschitz networks","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"has_accepted_license":"1","author":[{"first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","last_name":"Prach"}],"abstract":[{"lang":"eng","text":"Despite generating remarkable results in various computer vision tasks, deep learning comes\r\nwith some surprising shortcomings. For example, tiny perturbations, often imperceptible to\r\nthe human eye, can completely change the predictions of image classifiers. Despite a decade\r\nof research, the field has made limited progress in developing image classifiers that are both\r\naccurate and robust. This thesis aims to address this gap.\r\nAs our first contribution, we aim to simplify the process of training certifiably robust image\r\nclassifiers. We do this by designing a convolutional layer that does not require executing an\r\niterative procedure in every forward pass, but relies on an explicit bound instead. We also\r\npropose a loss function that allows optimizing for a particular margin more precisely.\r\nNext, we provide an overview and comparison of various methods that create robust image\r\nclassifiers by constraining the Lipschitz constant. This is important since generally longer\r\ntraining times and more parameters improve the performance of robust classifiers, making it\r\nchallenging to determine the most practical and effective methods from existing literature.\r\nIn 1-Lipschitz classification, the performance of current methods is still much worse than what\r\nwe expect on the simple tasks we consider. Therefore, we next investigate potential causes of\r\nthis shortcoming. We first consider the role of the activation function. We prove a theoretical\r\nshortcoming of the commonly used activation function, and provide an alternative without it.\r\nHowever this theoretical improvement does barely translate to the empirical performance of\r\nrobust classifiers, suggesting a different bottleneck.\r\nTherefore, in the final chapter, we study how the performance depends on the amount of\r\ntraining data. We prove that in the worst case, we might require far more data to train a\r\nrobust classifier compared to a normal one. We furthermore find that the amount of training\r\ndata is a key determinant of the performance current methods achieve on popular datasets.\r\nAdditionally, we show that linear subspaces exist with tiny data variance, and yet we can\r\nstill train very accurate classifiers after projecting into those subspaces. This shows that on\r\nthe datasets considered, enforcing robustness in classification makes the task strictly more\r\nchallenging.\r\n\r\n-----------------“In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of [name of university or educational entity]’s products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.”\r\n"}],"oa_version":"Published Version","date_updated":"2026-04-07T11:49:52Z"},{"OA_place":"repository","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","citation":{"short":"C. Hoffmann, K.Z. Pietrzak, in:, 28th IACR International Conference on Practice and Theory of Public-Key Cryptography, Springer Nature, 2025, pp. 36–66.","ista":"Hoffmann C, Pietrzak KZ. 2025. Watermarkable and zero-knowledge Verifiable Delay Functions from any proof of exponentiation. 28th IACR International Conference on Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography, LNCS, vol. 15674, 36–66.","mla":"Hoffmann, Charlotte, and Krzysztof Z. Pietrzak. “Watermarkable and Zero-Knowledge Verifiable Delay Functions from Any Proof of Exponentiation.” <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, vol. 15674, Springer Nature, 2025, pp. 36–66, doi:<a href=\"https://doi.org/10.1007/978-3-031-91820-9_2\">10.1007/978-3-031-91820-9_2</a>.","chicago":"Hoffmann, Charlotte, and Krzysztof Z Pietrzak. “Watermarkable and Zero-Knowledge Verifiable Delay Functions from Any Proof of Exponentiation.” In <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, 15674:36–66. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-91820-9_2\">https://doi.org/10.1007/978-3-031-91820-9_2</a>.","ieee":"C. Hoffmann and K. Z. Pietrzak, “Watermarkable and zero-knowledge Verifiable Delay Functions from any proof of exponentiation,” in <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>, Roros, Norway, 2025, vol. 15674, pp. 36–66.","ama":"Hoffmann C, Pietrzak KZ. Watermarkable and zero-knowledge Verifiable Delay Functions from any proof of exponentiation. In: <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i>. Vol 15674. Springer Nature; 2025:36-66. doi:<a href=\"https://doi.org/10.1007/978-3-031-91820-9_2\">10.1007/978-3-031-91820-9_2</a>","apa":"Hoffmann, C., &#38; Pietrzak, K. Z. (2025). Watermarkable and zero-knowledge Verifiable Delay Functions from any proof of exponentiation. In <i>28th IACR International Conference on Practice and Theory of Public-Key Cryptography</i> (Vol. 15674, pp. 36–66). Roros, Norway: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-91820-9_2\">https://doi.org/10.1007/978-3-031-91820-9_2</a>"},"type":"conference","volume":15674,"corr_author":"1","month":"01","scopus_import":"1","_id":"19778","page":"36-66","quality_controlled":"1","year":"2025","oa":1,"doi":"10.1007/978-3-031-91820-9_2","publisher":"Springer Nature","language":[{"iso":"eng"}],"date_published":"2025-01-01T00:00:00Z","author":[{"id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","first_name":"Charlotte","orcid":"0000-0003-2027-5549","last_name":"Hoffmann","full_name":"Hoffmann, Charlotte"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"oa_version":"Preprint","date_updated":"2026-04-16T09:11:09Z","intvolume":"     15674","abstract":[{"text":"A verifiable delay function VDF(x, T)->(y, π) maps an input x and time parameter T to an output y together with an efficiently verifiable proof π certifying that y was correctly computed. The function runs in T sequential steps, and it should not be possible to compute y much faster than that. The only known practical VDFs use sequential squaring in groups of unknown order as the sequential function, i.e., y = x^2^T. There are two constructions for the proof of exponentiation (PoE) certifying that y = x^2^T, with Wesolowski (Eurocrypt’19) having very short proofs, but they are more expensive to compute and the soundness relies on stronger assumptions than the PoE proposed by Pietrzak (ITCS’19).\r\nA recent application of VDFs by Arun, Bonneau and Clark (Asiacrypt’22) are short-lived proofs and signatures, which are proofs and signatures that are only sound for some time t, but after that can be forged by anyone. For this they rely on “watermarkable VDFs”, where the proof embeds a prover chosen watermark. To achieve stronger notions of proofs/signatures with reusable forgeability, they rely on “zero-knowledge VDFs”, where instead of the output y, one just proves knowledge of this output. The existing proposals for watermarkable and zero-knowledge VDFs all build on Wesolowski’s PoE, for the watermarkable VDFs there’s currently no security proof.\r\n\r\nIn this work we give the first constructions that transform any PoEs in hidden order groups into watermarkable VDFs and into zkVDFs, solving an open question by Arun et al. Unlike our watermarkable VDF, the zkVDF (required for reusable forgeability) is not very practical as the number of group elements in the proof is a security parameter. To address this, we introduce the notion of zero-knowledge proofs of sequential work (zkPoSW), a notion that relaxes zkVDFs by not requiring that the output is unique. We show that zkPoSW are sufficient to construct proofs or signatures with reusable forgeability, and construct efficient zkPoSW from any PoE, ultimately achieving short lived proofs and signatures that improve upon Arun et al.’s construction in several dimensions (faster forging times, arguably weaker assumptions).\r\nA key idea underlying our constructions is to not directly construct a (watermarked or zk) proof for y = x^2^T, but instead give a (watermarked or zk) proof for the more basic statement that \r\nx^l, y^l satisfy x^l = x ^r, y^l = y^r for some r, together with a normal PoE for y^l = (x^l)^2^T.","lang":"eng"}],"title":"Watermarkable and zero-knowledge Verifiable Delay Functions from any proof of exponentiation","alternative_title":["LNCS"],"day":"01","OA_type":"green","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"conference":{"end_date":"2025-05-15","name":"PKC: Public-Key Cryptography","location":"Roros, Norway","start_date":"2025-05-12"},"publication_identifier":{"isbn":["9783031918193"],"eissn":["1611-3349"],"eisbn":["9783031918209"],"issn":["0302-9743"]},"related_material":{"record":[{"id":"20920","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"20556"}]},"publication":"28th IACR International Conference on Practice and Theory of Public-Key Cryptography","main_file_link":[{"url":"https://ia.cr/2024/481","open_access":"1"}],"date_created":"2025-06-03T07:30:21Z","status":"public","article_processing_charge":"No"},{"year":"2025","quality_controlled":"1","issue":"2","date_published":"2025-06-11T00:00:00Z","publisher":"Elsevier","doi":"10.1016/j.bpr.2025.100211","language":[{"iso":"eng"}],"oa":1,"file":[{"content_type":"application/pdf","date_updated":"2025-06-10T07:24:46Z","file_size":7238179,"file_id":"19802","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","access_level":"open_access","checksum":"4018c833f25a3ad3b57e3577fed70334","relation":"main_file","creator":"dernst","success":1,"date_created":"2025-06-10T07:24:46Z"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","corr_author":"1","volume":5,"type":"journal_article","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>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/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.","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, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">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).","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>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/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>","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. Elsevier, 2025."},"publication_status":"published","month":"06","scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"19795","publication_identifier":{"eissn":["2667-0747"]},"DOAJ_listed":"1","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publication":"Biophysical Reports","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20206"}]},"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.).","file_date_updated":"2025-06-10T07:24:46Z","status":"public","date_created":"2025-06-08T22:01:22Z","article_processing_charge":"Yes","author":[{"orcid":"0009-0000-7590-3501","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer"},{"first_name":"Nikolai","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","full_name":"Semenov, Nikolai","last_name":"Semenov"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"orcid":"0000-0003-2311-2112","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath","last_name":"Javoor"},{"last_name":"Zens","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas"},{"full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marek","id":"EE8452B8-C26A-11E9-B157-E80CE6697425","full_name":"Suplata, Marek","last_name":"Suplata"},{"orcid":"0000-0003-0201-2315","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wartak, Andreas","last_name":"Wartak","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","first_name":"Andreas"},{"full_name":"Schur, Florian Km","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G"}],"abstract":[{"lang":"eng","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."}],"date_updated":"2026-04-07T11:48:07Z","intvolume":"         5","oa_version":"Published Version","article_number":"100211","day":"11","ddc":["570"],"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"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","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24"},{"grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"OA_type":"gold","has_accepted_license":"1"},{"publication":"Physical Review B","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We acknowledge useful discussions with Georgios Katsaros, Andrew Higginbotham, and Oliver Schwarze. This research was funded in part by the Austrian Science Fund (FWF) F 86, the European Research Council (Grant Agreement No. 856526), and by the DFG Collaborative Research Center (CRC) 183 Project No. 277101999.","file_date_updated":"2025-06-23T10:31:11Z","status":"public","date_created":"2025-06-19T16:54:54Z","abstract":[{"lang":"eng","text":"Technology involving hybrid superconductor–semiconductor materials is a promising avenue for engineering quantum devices for information storage, manipulation, and transmission. Proximity-induced superconducting correlations are an essential part of such devices. While the proximity effect in the conduction band of common semiconductors is well understood, its manifestation in confined hole gases, realized for instance in germanium, is an active area of research. Lower-dimensional hole-based systems, particularly in germanium, are emerging as an attractive platform for a variety of solid-state quantum devices, due to their combination of efficient spin and charge control and long coherence times. The recent experimental realization of the proximity effect in germanium thus calls for a theoretical description that is tailored to hole gases. In this work, we propose a simple model to describe proximity-induced superconductivity in two-dimensional hole gases, incorporating both the heavy-hole (HH) and light-hole (LH) bands. We start from the Luttinger–Kohn model, introduce three parameters that characterize hopping across the superconductor–semiconductor interface, and derive explicit intraband and interband effective pairing terms for the HH and LH bands. Unlike previous approaches, our theory provides a quantitative relationship between induced pairings and interface properties. Restricting our general model to an experimentally relevant case where only the HH band crosses the chemical potential, we predict the coexistence of 𝑠-wave and 𝑑-wave singlet pairings, along with triplet-type pairings, and modified Zeeman and Rashba spin–orbit couplings. Our results thus present a starting point for theoretical modeling of quantum devices based on proximitized hole gases, fueling further progress in quantum technology."}],"intvolume":"       111","date_updated":"2025-09-30T12:53:47Z","article_number":"214518","oa_version":"Published Version","author":[{"last_name":"Babkin","full_name":"Babkin, Serafim","id":"e63d75c3-72ef-11ef-b75a-e303e149911f","first_name":"Serafim"},{"first_name":"Benjamin","full_name":"Joecker, Benjamin","last_name":"Joecker"},{"first_name":"Karsten","full_name":"Flensberg, Karsten","last_name":"Flensberg"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"}],"project":[{"_id":"34a7f947-11ca-11ed-8bc3-c5dc2bbaae25","grant_number":"F8609","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems:  Probing topology in circuits and quantum materials"}],"department":[{"_id":"MaSe"},{"_id":"GradSch"}],"isi":1,"OA_type":"hybrid","has_accepted_license":"1","day":"18","ddc":["530"],"title":"Superconducting proximity effect in two-dimensional hole gases","year":"2025","quality_controlled":"1","external_id":{"isi":["001514328000004"],"arxiv":["2412.04084"]},"article_type":"original","issue":"21","date_published":"2025-06-18T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1103/k4jh-pnxy","publisher":"American Physical Society","oa":1,"file":[{"file_id":"19869","file_name":"2025_PhysReviewB_Babkin.pdf","access_level":"open_access","checksum":"fa8757f4780cfaeb51579c626284a8c1","content_type":"application/pdf","date_updated":"2025-06-23T10:31:11Z","file_size":1719489,"date_created":"2025-06-23T10:31:11Z","relation":"main_file","creator":"dernst","success":1}],"volume":111,"type":"journal_article","corr_author":"1","citation":{"ama":"Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. Superconducting proximity effect in two-dimensional hole gases. <i>Physical Review B</i>. 2025;111(21). doi:<a href=\"https://doi.org/10.1103/k4jh-pnxy\">10.1103/k4jh-pnxy</a>","apa":"Babkin, S., Joecker, B., Flensberg, K., Serbyn, M., &#38; Danon, J. (2025). Superconducting proximity effect in two-dimensional hole gases. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/k4jh-pnxy\">https://doi.org/10.1103/k4jh-pnxy</a>","ieee":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, and J. Danon, “Superconducting proximity effect in two-dimensional hole gases,” <i>Physical Review B</i>, vol. 111, no. 21. American Physical Society, 2025.","short":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, J. Danon, Physical Review B 111 (2025).","ista":"Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. 2025. Superconducting proximity effect in two-dimensional hole gases. Physical Review B. 111(21), 214518.","chicago":"Babkin, Serafim, Benjamin Joecker, Karsten Flensberg, Maksym Serbyn, and Jeroen Danon. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” <i>Physical Review B</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/k4jh-pnxy\">https://doi.org/10.1103/k4jh-pnxy</a>.","mla":"Babkin, Serafim, et al. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” <i>Physical Review B</i>, vol. 111, no. 21, 214518, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/k4jh-pnxy\">10.1103/k4jh-pnxy</a>."},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"19852","scopus_import":"1","month":"06","arxiv":1},{"year":"2025","page":"38","keyword":["asteroseismology","stellar physics","red giant","magnetism","suppressed"],"publisher":"Institute of Science and Technology Austria","date_published":"2025-10-08T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.15479/AT-ISTA-19853","file":[{"date_created":"2025-10-08T08:01:42Z","creator":"ksmith","relation":"source_file","file_name":"2025_Smith_Kanah_Thesis.zip","access_level":"closed","checksum":"80d241d11b69af771c1fab0998be4f19","file_id":"20434","file_size":8263624,"content_type":"application/zip","date_updated":"2025-10-08T09:45:33Z"},{"checksum":"13cb48cc98e00fdfe32f3ff66f17aa26","access_level":"open_access","file_name":"2025_Smith_Kanah_Thesis.pdf","file_id":"20439","file_size":9748339,"date_updated":"2025-10-09T14:38:57Z","content_type":"application/pdf","date_created":"2025-10-09T14:38:57Z","success":1,"relation":"main_file","creator":"ksmith"}],"oa":1,"degree_awarded":"MS","corr_author":"1","type":"dissertation","publication_status":"published","supervisor":[{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"}],"citation":{"short":"K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant Stars, Institute of Science and Technology Austria, 2025.","ista":"Smith K. 2025. Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria.","mla":"Smith, Kanah. <i>Exploring Internal Magnetism in Partially Suppressed Red Giant Stars</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>.","chicago":"Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red Giant Stars.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>.","ama":"Smith K. Exploring internal magnetism in partially suppressed red giant stars. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>","apa":"Smith, K. (2025). <i>Exploring internal magnetism in partially suppressed red giant stars</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>","ieee":"K. Smith, “Exploring internal magnetism in partially suppressed red giant stars,” Institute of Science and Technology Austria, 2025."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","_id":"19853","month":"10","publication_identifier":{"issn":["2791-4585"]},"article_processing_charge":"No","acknowledgement":"I would like to give thanks to myself for my hard work on this document. This paper includes data collected by the Kepler mission and obtained from the MAST data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is operated by the Association of\r\nUniversities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.\r\n","date_created":"2025-06-20T13:27:08Z","status":"public","file_date_updated":"2025-10-09T14:38:57Z","abstract":[{"lang":"eng","text":"The internal dynamical properties of red giant stars have been explored extensively in recent\r\nyears as a result of the increase in high precision data availability from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been\r\ndiscovered that some of these stars are not behaving as expected. Red giants are stars that have\r\nevolved off of the main sequence after having completed fusing hydrogen into helium in their\r\ncore. Observational data shows that the cores are rotating significantly slower than models can\r\nrecreate consistently across evolutionary stages. This discrepancy has prompted investigation\r\ninto the efficiency of angular momentum transport mechanisms and mixing processes including\r\nmeridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc., to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only\r\nway in which the deep stellar interior can be probed and subsequently characterized; this is\r\npossible as global oscillations modulating the stellar surface are effected by internal processes.\r\nFor red giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes; resonating in the radiative interior) couple to create mixed modes. These\r\nmixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two\r\ndifferent power laws, respectively. And the other being a reduced visibility of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted; one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of\r\ntheir power spectra rather than across the entire spectra, will be the subject of this study as\r\nthe respective mode amplitudes are still visible at high frequencies.\r\nAs such, this study will search for asymmetric frequency shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the aim here is to investigate if both\r\nmode suppression and magnetic shifting of dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038,\r\na target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its\r\nmagnetic parameters. I present a novel method to model the stellar power spectra of\r\npartially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With the results of this study I aim at constraining\r\nthe cause of this partial dipole mode amplitude suppression, allowing for more detailed\r\nstudies regarding their astrophysical nature. Furthermore, the long term hope for the method\r\nused in this study will be to expand the sample of partially suppressed red giants and fit their\r\nasteroseismic parameters accordingly."}],"oa_version":"Published Version","date_updated":"2026-04-07T12:01:37Z","author":[{"last_name":"Smith","full_name":"Smith, Kanah","first_name":"Kanah","id":"7703505d-3211-11ee-a6a9-a2ab9d936c15"}],"department":[{"_id":"GradSch"},{"_id":"LiBu"}],"has_accepted_license":"1","ddc":["520"],"day":"08","alternative_title":["ISTA Master's Thesis"],"title":"Exploring internal magnetism in partially suppressed red giant stars"},{"year":"2025","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"date_created":"2025-06-24T06:56:03Z","file":[{"file_name":"DatasetsPaper.zip","checksum":"eff1ae9e46599fdfab8da00a2ca3c289","access_level":"open_access","file_id":"19893","file_size":3404814792,"content_type":"application/x-zip-compressed","date_updated":"2025-06-24T15:14:13Z","date_created":"2025-06-24T15:14:13Z","success":1,"creator":"jsaezmol","relation":"main_file"},{"relation":"main_file","creator":"jsaezmol","success":1,"date_created":"2025-06-25T07:11:52Z","date_updated":"2025-06-25T07:11:52Z","content_type":"text/plain","file_size":622,"file_id":"19899","access_level":"open_access","checksum":"21840ceac04d677a799b8e5bd919804f","file_name":"README.txt"}],"status":"public","oa":1,"file_date_updated":"2025-06-25T07:11:52Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:19885","date_published":"2025-06-01T00:00:00Z","acknowledgement":"The authors would like to thank Barnaby van Straaten, Jonas Schuff, Daniel Jirovec and Hanifa Tidjani for fruitful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. G.K. acknowledges support from the NOMIS Foundation, the HORIZON-RIA (project no. 101069515) and the FWF Projects (DOIs: 10.55776/F86 and 10.55776/I5060). N.A. acknowledges support from the European Research Council (grant agreement 948932), and the Royal Society (grant no. URF/R1/191150). This project received support from the US Army Research Office (ARO) under Award No. W911NF-24-2-0043. C.C. acknowledges support from the UKRI Doctoral Training Partnership related to EP/W524311/1 (project ref. 2887634).","contributor":[{"first_name":"Cornelius","last_name":"Carlsson","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Fedele","first_name":"Federico "},{"first_name":"Stefano","contributor_type":"researcher","last_name":"Calcaterra"},{"last_name":"Chrastina","contributor_type":"researcher","first_name":" Daniel "},{"contributor_type":"researcher","last_name":"Isella","first_name":"Giovanni "},{"last_name":"Katsaros","contributor_type":"researcher","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ares","contributor_type":"researcher","first_name":"Natalia"}],"article_processing_charge":"No","author":[{"id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2025-07-01T07:19:26Z","citation":{"short":"J. Saez Mollejo, (2025).","mla":"Saez Mollejo, Jaime. <i>Automated All-RF Tuning for Spin Qubit Readout and Control</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>.","chicago":"Saez Mollejo, Jaime. “Automated All-RF Tuning for Spin Qubit Readout and Control.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">https://doi.org/10.15479/AT:ISTA:19885</a>.","ista":"Saez Mollejo J. 2025. Automated All-RF Tuning for Spin Qubit Readout and Control, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>.","ieee":"J. Saez Mollejo, “Automated All-RF Tuning for Spin Qubit Readout and Control.” Institute of Science and Technology Austria, 2025.","apa":"Saez Mollejo, J. (2025). Automated All-RF Tuning for Spin Qubit Readout and Control. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">https://doi.org/10.15479/AT:ISTA:19885</a>","ama":"Saez Mollejo J. Automated All-RF Tuning for Spin Qubit Readout and Control. 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>"},"type":"research_data","corr_author":"1","abstract":[{"lang":"eng","text":"This .zip file contains the data to reproduce the figures and supplementary figures of \"Automated All-RF Tuning for Spin Qubit Readout and Control\" by Cornelius Carlsson and Jaime Saez-Mollejo et al."}],"title":"Automated All-RF Tuning for Spin Qubit Readout and Control","ddc":["530"],"day":"01","month":"06","has_accepted_license":"1","_id":"19885","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"project":[{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}]},{"degree_awarded":"PhD","corr_author":"1","type":"dissertation","publication_status":"published","citation":{"ieee":"V. Hübner, “Reciprocity and inequality in social dilemmas,” Institute of Science and Technology Austria, 2025.","ama":"Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>","apa":"Hübner, V. (2025). <i>Reciprocity and inequality in social dilemmas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>","short":"V. Hübner, Reciprocity and Inequality in Social Dilemmas, Institute of Science and Technology Austria, 2025.","ista":"Hübner V. 2025. Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria.","mla":"Hübner, Valentin. <i>Reciprocity and Inequality in Social Dilemmas</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>.","chicago":"Hübner, Valentin. “Reciprocity and Inequality in Social Dilemmas.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>."},"supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","_id":"19903","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"month":"06","year":"2025","page":"157","language":[{"iso":"eng"}],"date_published":"2025-06-25T00:00:00Z","doi":"10.15479/AT-ISTA-19903","publisher":"Institute of Science and Technology Austria","file":[{"creator":"vhuebner","relation":"source_file","date_created":"2025-06-25T13:38:07Z","file_size":6192760,"date_updated":"2025-06-25T13:38:07Z","content_type":"application/x-xz","checksum":"794c02f8c82ca59ba6dda3bd7eed871a","access_level":"closed","file_name":"Thesis Valentin Hübner source.tar.xz","file_id":"19905"},{"date_created":"2025-07-09T13:37:00Z","relation":"main_file","creator":"vhuebner","access_level":"open_access","checksum":"ac56063d81c81e40322b6ff5a8c4912e","file_name":"Thesis Valentin Hübner.pdf","file_id":"19976","file_size":4837864,"date_updated":"2025-07-09T13:37:00Z","content_type":"application/pdf"}],"oa":1,"abstract":[{"text":"Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.\r\nWith game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.\r\nIndividuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.\r\nCooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions.","lang":"eng"}],"oa_version":"Published Version","date_updated":"2026-04-07T12:30:57Z","author":[{"orcid":"0009-0001-5009-4987","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","full_name":"Hübner, Valentin","last_name":"Hübner"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"has_accepted_license":"1","ddc":["519"],"day":"25","alternative_title":["ISTA Thesis"],"title":"Reciprocity and inequality in social dilemmas","related_material":{"record":[{"status":"public","id":"19843","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15083"},{"id":"19074","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"article_processing_charge":"No","acknowledgement":"The research for this thesis was supported by the European Research Council\r\n(grant agreements No. 863818 and No. 850529), the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie grant agreement No. 754411),\r\nthe Austrian Science Fund (grant DOI 10.55776/COE12), the French Agence Nationale\r\nde la Recherche under the Programme d’investissements d’avenir (project reference 17-\r\nEURE-0010) and the Australian Government through the Australian Research Council\r\n(grant No. SR200100005, “Securing Antarctica’s Environmental Future”).","date_created":"2025-06-25T13:50:10Z","status":"public","file_date_updated":"2025-07-09T13:37:00Z"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11478"},{"status":"public","relation":"part_of_dissertation","id":"19593"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-060-2"]},"article_processing_charge":"No","date_created":"2025-07-24T12:37:22Z","file_date_updated":"2025-07-30T09:29:09Z","status":"public","oa_version":"Published Version","date_updated":"2026-05-06T12:49:36Z","abstract":[{"lang":"eng","text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development."}],"author":[{"first_name":"Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","full_name":"Hübschmann, Verena","last_name":"Hübschmann"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"project":[{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"}],"title":" Human microglia impact neuronal development in retinal organoids","ddc":["570"],"alternative_title":["ISTA Thesis"],"day":"24","year":"2025","page":"151","file":[{"content_type":"application/x-zip-compressed","date_updated":"2025-07-30T08:47:53Z","file_size":43566093,"file_id":"20086","file_name":"PhD_Thesis_Schmied.zip","access_level":"closed","checksum":"d09f9984002353ad7442358394919bf3","creator":"vhuebsch","relation":"source_file","date_created":"2025-07-30T08:47:53Z"},{"relation":"main_file","creator":"vhuebsch","date_created":"2025-07-30T08:47:46Z","file_size":13120922,"date_updated":"2025-07-30T09:29:09Z","content_type":"application/pdf","access_level":"open_access","checksum":"4833690d7283c587f518ba98eeb2c946","file_name":"PhD_Thesis_Schmied.pdf","file_id":"20087"}],"oa":1,"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT-ISTA-20074","date_published":"2025-07-24T00:00:00Z","publication_status":"published","citation":{"mla":"Schmied, Verena. <i> Human Microglia Impact Neuronal Development in Retinal Organoids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>.","ista":"Schmied V. 2025.  Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria.","chicago":"Schmied, Verena. “ Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>.","short":"V. Schmied,  Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025.","ieee":"V. Schmied, “ Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025.","apa":"Schmied, V. (2025). <i> Human microglia impact neuronal development in retinal organoids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>","ama":"Schmied V.  Human microglia impact neuronal development in retinal organoids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>"},"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra"}],"degree_awarded":"PhD","corr_author":"1","type":"dissertation","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"20074","month":"07"},{"article_type":"original","publisher":"Springer Nature","date_published":"2025-07-23T00:00:00Z","doi":"10.1038/s41586-025-09241-2","language":[{"iso":"eng"}],"oa":1,"file":[{"creator":"dernst","relation":"main_file","success":1,"date_created":"2025-12-30T07:39:45Z","date_updated":"2025-12-30T07:39:45Z","content_type":"application/pdf","file_size":53301589,"file_id":"20884","checksum":"7ea846a7a49b3b2a248f6a27ab13d591","access_level":"open_access","file_name":"2025_Nature_Baier.pdf"}],"year":"2025","quality_controlled":"1","page":"439-447","external_id":{"pmid":["40702175"]},"_id":"20101","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","month":"07","pmid":1,"volume":645,"type":"journal_article","citation":{"ama":"Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. 2025;645:439-447. doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>","apa":"Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>","ieee":"F. Baier <i>et al.</i>, “The neural basis of species-specific defensive behaviour in Peromyscus mice,” <i>Nature</i>, vol. 645. Springer Nature, pp. 439–447, 2025.","short":"F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447.","mla":"Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>, vol. 645, Springer Nature, 2025, pp. 439–47, doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>.","ista":"Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. 645, 439–447.","chicago":"Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E. Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J. Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice on optogenetic experiments; A. Calzoni for help aligning histological sections to a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with the electrophysiology analysis; I. Vlaemick for help with whole cell experiments; R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan Brockman Williamson Fellowship. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute, of which H.E.H. was an Investigator.","file_date_updated":"2025-12-30T07:39:45Z","status":"public","date_created":"2025-08-03T22:01:31Z","related_material":{"record":[{"status":"public","id":"20883","relation":"research_data"}]},"publication":"Nature","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"department":[{"_id":"GradSch"}],"OA_type":"hybrid","has_accepted_license":"1","day":"23","ddc":["570"],"title":"The neural basis of species-specific defensive behaviour in Peromyscus mice","abstract":[{"lang":"eng","text":"Evading imminent threat from predators is critical for animal survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours remains poorly understood1,2,3,4. Here we find that two sister species of deer mice (genus Peromyscus)5 show different responses to the same looming stimulus: Peromyscus maniculatus, which occupies densely vegetated habitats, predominantly escapes, whereas the open field specialist, Peromyscus polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal grey (dPAG) in driving behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus, and their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain."}],"intvolume":"       645","date_updated":"2026-01-05T11:38:40Z","oa_version":"Published Version","author":[{"full_name":"Baier, Felix","last_name":"Baier","first_name":"Felix"},{"first_name":"Katja","last_name":"Reinhard","full_name":"Reinhard, Katja"},{"first_name":"Bram","last_name":"Nuttin","full_name":"Nuttin, Bram"},{"first_name":"Arnau","last_name":"Sans-Dublanc","full_name":"Sans-Dublanc, Arnau"},{"last_name":"Liu","full_name":"Liu, Chen","first_name":"Chen"},{"last_name":"Tong","full_name":"Tong, Victoria","first_name":"Victoria"},{"first_name":"Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","full_name":"Murmann, Julie Stefanie","last_name":"Murmann"},{"last_name":"Wierda","full_name":"Wierda, Keimpe","first_name":"Keimpe"},{"first_name":"Karl","last_name":"Farrow","full_name":"Farrow, Karl"},{"first_name":"Hopi E.","full_name":"Hoekstra, Hopi E.","last_name":"Hoekstra"}]},{"_id":"20117","month":"08","corr_author":"1","type":"dissertation","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"}],"citation":{"chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>"},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","doi":"10.15479/AT-ISTA-20117","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"date_published":"2025-08-04T00:00:00Z","file":[{"date_created":"2025-08-22T08:22:10Z","relation":"source_file","creator":"yiqwang","file_id":"20209","file_name":"2025_Wang_Yiqun_Thesis.docx","checksum":"36b87c17d12c7bf5955d6d812acb8d77","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-08-22T08:53:46Z","file_size":25798848},{"file_id":"20211","checksum":"8d7a2383f66377da675d379ec30ea0fe","embargo":"2026-09-03","access_level":"closed","embargo_to":"open_access","file_name":"2025_Wang_Yiqun_Thesis.pdf","date_updated":"2025-09-03T09:36:52Z","content_type":"application/pdf","file_size":12628313,"date_created":"2025-08-22T10:32:30Z","creator":"yiqwang","relation":"main_file"}],"year":"2025","page":"108","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"has_accepted_license":"1","day":"04","alternative_title":["ISTA Thesis"],"ddc":["580"],"title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","date_updated":"2026-04-07T11:49:34Z","oa_version":"Published Version","author":[{"first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun","last_name":"Wang"}],"article_processing_charge":"No","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","status":"public","file_date_updated":"2025-09-03T09:36:52Z","date_created":"2025-08-04T15:24:21Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18063","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]}},{"date_updated":"2026-04-07T11:49:12Z","oa_version":"Published Version","abstract":[{"text":"The evolution shapes the world around us.\r\nNot only in biology, where the fittest individuals spread their genes but also in physics and social dynamics, the evolutionary forces determine the development of a state of matter or public opinions.\r\nMany models describe these dynamics.\r\nThis thesis examines the role of the structure in the models of selection.\r\nThe population structure is represented as a graph or a network, and each vertex is occupied by one individual.\r\nEvery individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors.\r\nThe evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness.\r\n\r\n\r\n\r\nThe role of the networks is widely examined in the literature.\r\nThe structures that promote the spread of the desired type compared to the structureless case are called amplifiers.\r\nThe existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified.\r\nMoreover, there are other important questions about the number of steps until one type spreads over the whole network (fixation time), the computational complexity, and the questions about the robustness of these processes.\r\n\r\n\r\nThis thesis explores the role of structure in evolution from many perspectives.\r\nFirst, it introduces different models and various choices that can be made in the models of evolution.\r\nIt highlights the role of the structure in the real world and how this is reflected in these models.\r\nThen, it describes the previous results and open problems.\r\nSecond, the thesis describes an amplifier for two variants of the Moran process: one with a constant birth rate and the other with a constant death rate.\r\nThis is an important contribution to the robustness of the amplification.\r\nThird, the thesis determines the complexity of spatial games.\r\nThese are processes where the fitness comes from a game, and the strength of selection is high.\r\nIt shows that determining the fate of cooperation in these games is a PSPACE-complete problem.\r\nFourth, the thesis describes the amplifier of cooperation for spatial games.\r\nThis is the first amplifier in this setting.\r\nFifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity.\r\nIn this setting, the fitness depends not only on the type of the individual but also on the occupied vertex.\r\nThe chapter determines the relationship between the interactions of vertices of different types and the coexistence time.\r\nSixth, the thesis examines the social balance on networks and proposes a stochastic dynamic partially aware of the state of the graph, which reaches a balanced position quickly.\r\nFinally, the thesis presents conclusions and outlines the directions for future work.\r\n\r\n\r\n","lang":"eng"}],"author":[{"last_name":"Svoboda","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","orcid":"0000-0002-1419-3267"}],"has_accepted_license":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"title":"Structural properties of games on graphs","alternative_title":["ISTA Thesis"],"day":"05","ddc":["000","519"],"related_material":{"record":[{"id":"12787","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12101","status":"public"},{"id":"12257","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"15297","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18703","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","status":"public","file_date_updated":"2025-08-21T11:48:39Z","date_created":"2025-08-05T14:33:59Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n","supervisor":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria.","mla":"Svoboda, Jakub. <i>Structural Properties of Games on Graphs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20138\">10.15479/AT-ISTA-20138</a>.","chicago":"Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20138\">https://doi.org/10.15479/AT-ISTA-20138</a>.","short":"J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025.","ieee":"J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025.","ama":"Svoboda J. Structural properties of games on graphs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20138\">10.15479/AT-ISTA-20138</a>","apa":"Svoboda, J. (2025). <i>Structural properties of games on graphs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20138\">https://doi.org/10.15479/AT-ISTA-20138</a>"},"publication_status":"published","corr_author":"1","type":"dissertation","degree_awarded":"PhD","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"_id":"20138","month":"08","year":"2025","page":"167","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2025-08-14T09:54:43Z","file_size":5927291,"file_id":"20177","file_name":"2025_Svoboda_Jakub_Thesis.pdf","access_level":"open_access","checksum":"c6c4df9777f4537940de7ab392ad57e2","creator":"jsvoboda","relation":"main_file","success":1,"date_created":"2025-08-14T09:54:43Z"},{"relation":"source_file","creator":"jsvoboda","date_created":"2025-08-14T09:55:20Z","file_size":6731815,"date_updated":"2025-08-21T11:48:39Z","content_type":"application/zip","access_level":"closed","checksum":"485e9f9822821bc03666d245d80aaa08","file_name":"2025_Svoboda_Jakub_Thesis.zip","file_id":"20178"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT-ISTA-20138","language":[{"iso":"eng"}],"date_published":"2025-08-05T00:00:00Z"},{"related_material":{"record":[{"status":"public","id":"11775","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13140","status":"deleted"},{"id":"19741","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9356"},{"status":"deleted","relation":"part_of_dissertation","id":"19643"},{"id":"17634","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"20342","relation":"part_of_dissertation"},{"status":"public","id":"13221","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","date_created":"2025-08-07T15:57:57Z","status":"public","file_date_updated":"2025-09-10T08:19:51Z","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n","oa_version":"Published Version","date_updated":"2026-04-07T12:02:57Z","abstract":[{"lang":"eng","text":"Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n-------------------------------------------------------------------------------------------------------------------------------------------------------------- In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink.\r\n"}],"author":[{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"title":"A monitoring-oriented theory and classification of quantitative specifications","ddc":["000"],"day":"07","alternative_title":["ISTA Thesis"],"year":"2025","page":"149","file":[{"file_id":"20200","checksum":"0f3015f1db36576a23d8d669afb60b41","access_level":"closed","file_name":"2025_Sarac_NaciEge_Thesis.zip","date_updated":"2025-09-10T08:19:51Z","content_type":"application/x-zip-compressed","file_size":8884801,"date_created":"2025-08-21T09:40:28Z","creator":"esarac","relation":"source_file"},{"date_created":"2025-08-21T09:40:34Z","success":1,"relation":"main_file","creator":"esarac","file_name":"2025_Sarac_NaciEge_Thesis.pdf","checksum":"332ed2fe61f580641664ec3f05d30f14","access_level":"open_access","file_id":"20201","file_size":2955584,"content_type":"application/pdf","date_updated":"2025-08-21T09:40:34Z"}],"oa":1,"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"date_published":"2025-08-07T00:00:00Z","doi":"10.15479/AT-ISTA-20147","publication_status":"published","citation":{"ieee":"N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025.","apa":"Sarac, N. E. (2025). <i>A monitoring-oriented theory and classification of quantitative specifications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>","ama":"Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>","mla":"Sarac, Naci E. <i>A Monitoring-Oriented Theory and Classification of Quantitative Specifications</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>.","chicago":"Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>.","ista":"Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria.","short":"N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025."},"supervisor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","corr_author":"1","type":"dissertation","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"20147","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"08"},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"20149","month":"08","type":"dissertation","corr_author":"1","degree_awarded":"PhD","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"citation":{"ama":"Dos Reis Rodrigues P. Coordination of protrusive forces in immune cell migration . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>","apa":"Dos Reis Rodrigues, P. (2025). <i>Coordination of protrusive forces in immune cell migration </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>","ieee":"P. Dos Reis Rodrigues, “Coordination of protrusive forces in immune cell migration ,” Institute of Science and Technology Austria, 2025.","short":"P. Dos Reis Rodrigues, Coordination of Protrusive Forces in Immune Cell Migration , Institute of Science and Technology Austria, 2025.","ista":"Dos Reis Rodrigues P. 2025. Coordination of protrusive forces in immune cell migration . Institute of Science and Technology Austria.","chicago":"Dos Reis Rodrigues, Patricia. “Coordination of Protrusive Forces in Immune Cell Migration .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>.","mla":"Dos Reis Rodrigues, Patricia. <i>Coordination of Protrusive Forces in Immune Cell Migration </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>."},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","doi":"10.15479/AT-ISTA-20149","date_published":"2025-08-08T00:00:00Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"oa":1,"file":[{"content_type":"application/pdf","date_updated":"2025-08-27T12:59:10Z","file_size":63885565,"file_id":"20232","file_name":"2025_ReisRodrigues_Patricia_Thesis.pdf","access_level":"open_access","checksum":"fda8a1070667c3562263f4867609b41b","relation":"main_file","creator":"prodrigu","success":1,"date_created":"2025-08-27T12:59:10Z"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-08-27T13:02:28Z","file_size":50483434,"file_id":"20233","file_name":"2025_ReisRodrigues_Patricia_Thesis.docx","access_level":"closed","checksum":"e8b65affcbce846a926454df4b2867b9","relation":"source_file","creator":"prodrigu","date_created":"2025-08-27T13:00:30Z"}],"year":"2025","page":"114","project":[{"grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces"}],"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"has_accepted_license":"1","day":"08","alternative_title":["ISTA Thesis"],"ddc":["570"],"title":"Coordination of protrusive forces in immune cell migration ","abstract":[{"lang":"eng","text":"Immune responses depend on the coordinated and efficient migration of leukocytes. These\r\ncells, which are embedded and tightly confined within tissues, must navigate and traverse\r\ndiverse and complex three-dimensional environments. Leukocytes adapt their locomotory\r\nbehavior to the mechanical, geometrical, and biochemical characteristics of their\r\nsurroundings. In low-density environments, where the pore size of the interstitial matrix\r\nallows free passage, these cells position the nucleus directly behind the lamellipodium, the\r\nprotrusive actin structure that forms the leading front of the cell. In this configuration, they\r\nuse the nucleus as a gauge to identify the path of least resistance.\r\nHere, we show that in high-density environments, where the pore size precludes free passage\r\nof the cell body, leukocytes reposition the microtubule-organizing center (MTOC) and\r\nassociated organelles in front of the nucleus. In this configuration, they use actin structures\r\nprotruding orthogonally to the direction of migration in order to open a path for the cell body.\r\nWe identify two distinct actin populations that serve this purpose at different subcellular\r\nlocalizations. At the leading edge, local indentation of the plasma membrane leads to\r\nrecruitment of the Wiskott-Aldrich syndrome protein (WASp), which, via Arp2/3, results in\r\nthe formation of individual actin foci. At the cell body, actin polymerization is triggered by\r\nDOCK8, a Cdc42 exchange factor, resulting in the formation of a central actin pool.\r\nWe demonstrate that the central and peripheral actin pools are functionally communicating\r\nand that depletion of the central actin pool leads to increased actin accumulation at the cell\r\nfront, resulting in excessive extension of the leading edge."}],"date_updated":"2026-04-28T13:26:50Z","oa_version":"Published Version","author":[{"full_name":"Dos Reis Rodrigues, Patricia","last_name":"Dos Reis Rodrigues","orcid":"0000-0003-1681-508X","first_name":"Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F"}],"article_processing_charge":"No","acknowledgement":"I would like to acknowledge the\r\nfinancial support of the European Research Council through the ERC-SyG grant “Pushing from\r\nwithin: Control of cell shape, integrity and motility by cytoskeletal pushing forces”\r\n(01071793), which made this research possible. ","status":"public","file_date_updated":"2025-08-27T13:02:28Z","date_created":"2025-08-08T09:18:02Z","related_material":{"record":[{"id":"10703","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"20082","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["2663-337X"]}},{"publisher":"Institute of Science and Technology Austria","date_published":"2025-08-13T00:00:00Z","doi":"10.15479/AT-ISTA-20167","language":[{"iso":"eng"}],"file":[{"date_created":"2025-09-08T14:33:50Z","creator":"hschoen","relation":"source_file","file_name":"2025_Schoen_Hanna_Thesis.docx","access_level":"closed","checksum":"b40c74404b8d9593802dabf57bfdf10f","file_id":"20311","file_size":78812587,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-09T08:57:04Z"},{"relation":"main_file","creator":"hschoen","date_created":"2025-09-11T14:20:59Z","file_size":9667057,"content_type":"application/pdf","date_updated":"2025-09-18T14:12:29Z","file_name":"2025_Schoen_Hanna_Thesis.pdf","embargo_to":"open_access","checksum":"16abc3ff66396ce2457fe07ffa8bed90","access_level":"closed","embargo":"2026-09-15","file_id":"20347"}],"year":"2025","page":"171","_id":"20167","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"08","degree_awarded":"PhD","corr_author":"1","type":"dissertation","publication_status":"published","supervisor":[{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono","full_name":"de Bono, Mario"}],"citation":{"ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria.","mla":"Schön, Hanna. <i>The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>.","chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>.","short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","apa":"Schön, H. (2025). <i>The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>","ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_processing_charge":"No","acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","date_created":"2025-08-13T11:13:13Z","file_date_updated":"2025-09-18T14:12:29Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-061-9"]},"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"},{"grant_number":"ALTF 302-2019","_id":"23813290-32DE-11EA-91FC-C7463DDC885E","name":"Control of gene expression at the endoplasmic reticulum"}],"has_accepted_license":"1","ddc":["570"],"alternative_title":["ISTA Thesis"],"day":"13","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","oa_version":"Published Version","date_updated":"2026-04-07T11:50:26Z","author":[{"full_name":"Schön, Hanna","last_name":"Schön","first_name":"Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425"}]}]