@article{20864, abstract = {Studies of the distant Universe are providing key insights into our understanding of the formation of galaxies. The advent of the James Webb Space Telescope (JWST) has significantly enhanced our observational capabilities, leading to an expanded redshift frontier, providing unprecedented detail in the characterisation of early galaxies and enabling the discovery of new populations of accreting black holes. This review aims to provide an introduction to the basic processes and components that shape the observed spectra of galaxies, with a focus on their relevance to techniques with which high-redshift galaxies are selected. The review further introduces specific topics that have attracted significant attention in recent literature, including the discovery of highly efficient galaxy formation in the early Universe, the relation between galaxies and the process of reionization, new insights into the formation of the first stars and the enrichment of interstellar gas with heavy elements, and breakthroughs in our understanding of the origins of supermassive black holes.}, author = {Matthee, Jorryt J}, issn = {1366-5812}, journal = {Contemporary Physics}, number = {1-4}, pages = {116--151}, publisher = {Taylor & Francis}, title = {{JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies}}, doi = {10.1080/00107514.2025.2586370}, volume = {66}, year = {2025}, } @article{21322, abstract = {Habitat fragmentation poses a significant risk to population survival, causing both demographic stochasticity and genetic drift within local populations to increase, thereby increasing genetic load. Higher load causes population numbers to decline, which reduces the efficiency of selection and further increases load, resulting in a positive feedback that may drive entire populations to extinction. Here, we investigate this eco-evolutionary feedback in a metapopulation consisting of local demes connected via migration, with individuals subject to deleterious mutation at a large number of loci. We first analyze the determinants of load under soft selection, where population sizes are fixed, and then build on this to understand hard selection, where population sizes and load coevolve. We show that under soft selection, very little gene flow (less than one migrant per generation) is enough to prevent fixation of deleterious alleles. By contrast, much higher levels of migration are required to mitigate load and prevent extinction when selection is hard, with critical migration thresholds for metapopulation persistence increasing sharply as the genome-wide deleterious mutation rate becomes comparable to the baseline population growth rate. Moreover, critical migration thresholds are highest if deleterious mutations have intermediate selection coefficients but lower if alleles are predominantly recessive rather than additive (due to more efficient purging of recessive load within local populations). Our analysis is based on a combination of analytical approximations and simulations, allowing for a more comprehensive understanding of the factors influencing load and extinction in fragmented populations.}, author = {Olusanya, Oluwafunmilola O and Khudiakova, Kseniia and Sachdeva, Himani}, issn = {1537-5323}, journal = {The American Naturalist}, number = {6}, pages = {617--636}, publisher = {University of Chicago Press}, title = {{Genetic load, eco-evolutionary feedback, and extinction in metapopulations}}, doi = {10.1086/735562}, volume = {205}, year = {2025}, } @misc{21668, abstract = {This artifact allows to review and reproduce the experiments from the paper *A Revised Practitioner's Guide to MDP Model Checking Algorithms*. The package contains all original logfiles and derived data used to generate the plots as in the paper. Furthermore, the artifact contains the model checking tools `Storm` and `mcsta` in the version exercised in the paper, the used Docker container, as well as benchmark instances and execution scripts to reproduce the experiments. See also the artifact of the conference paper: https://zenodo.org/records/7509474}, author = {Hartmanns, Arnd and Junges, Sebastian and Quatmann, Tim and Weininger, Maximilian}, publisher = {Zenodo}, title = {{Benchmark data for the revised practitioner's guide to MDP model checking algorithms}}, doi = {10.5281/ZENODO.14500423}, year = {2025}, } @unpublished{20982, abstract = {Plant cells respond to a wide range of stimuli through intracellular calcium (Ca2+) signaling. Cyclic nucleotide-gated channels (CNGCs) are a major class of plant Ca2+ channels, with 20 homologs in Arabidopsis. These tetrameric plasma membrane proteins act downstream of diverse signals, such as phytohormones, extracellular damage, cell wall integrity or temperature. Here, we identify a class of plant-specific proteins, Armadillo Repeat Only (ARO), as essential regulators of possibly all plant CNGCs. Abrogation of functional sporophytic AROs results in a phenotypic pattern strongly reminiscent of CNGC dysfunction, including defects in root gravitropism, root hair growth and morphology, stomatal movement, and responses to extracellular ATP and the phytohormone auxin. aro2/3/4 mutants are fully resistant to the toxic effects caused by overexpression of CNGCs. AROs colocalize and physically interact with multiple CNGCs and modulate CNGC-dependent currents in Xenopus oocytes. Structural modeling and site-directed mutagenesis reveal AROs tetramer formation surrounding the CNGC channel, interacting via its IQ domain. Taken together, plant CNGC channels don’t act alone, but in a larger complex - channelosome, first of a kind in plants.}, author = {Kulich, Ivan and Oulehlová, Denisa and Vladimirtsev, Dmitrii and Zou, Minxia and Lileikyte, Edita and Bondar, Alexey and Kulichová, Katarína and Janda, Martin and Iakovenko, Oksana and Neubergerová, Michaela and Studtrucker, Tanja and Pleskot, Roman and Dietrich, Petra and Fendrych, Matyas and Friml, Jiří}, booktitle = {bioRxiv}, title = {{Armadillo repeat only proteins are required for the function of plant CNGC channels}}, doi = {10.1101/2025.01.06.631460}, year = {2025}, } @article{20260, abstract = {The medial axis of a set consists of the points in the ambient space without a unique closest point in the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a skeleton topologically equivalent to the original set. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities, various prunings of the medial axis have been proposed in the computational geometry community. Here, we examine one type of pruning, called burning. Because of the good experimental results it was hoped that the burning method of simplifying the medial axis would be stable. In this work, we show a simple example that dashes such hopes. Based on Bing’s house with two rooms, we demonstrate an isotopy of a shape where the medial axis goes from collapsible to non-collapsible. More precisely, we consider the standard deformation retract from the closed ball to Bing’s house with two rooms, but stop just short of the point where Bing’s house becomes two dimensional. This way we obtain an isotopy from the 3-ball to a thickened version of Bing’s house. Under this isotopy, the medial axis goes from collapsible to non-collapsible. We stress that this isotopy can be made generic, in the sense of singularity theory, as developed by Arnol’d and Thom.}, author = {Chambers, Erin Wolf and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs}, issn = {2730-9657}, journal = {La Matematica}, pages = {811--828}, publisher = {Springer Nature}, title = {{Burning or collapsing the medial axis is unstable}}, doi = {10.1007/s44007-025-00170-0}, volume = {4}, year = {2025}, } @inproceedings{20819, abstract = {Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for -means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success.}, author = {Scott, Jonathan A and Lampert, Christoph and Saulpic, David}, booktitle = {42nd International Conference on Machine Learning}, issn = {2640-3498}, location = {Vancouver, Canada}, pages = {53757--53790}, publisher = {ML Research Press}, title = {{Differentially private federated k-means clustering with server-side data}}, volume = {267}, year = {2025}, } @unpublished{21207, abstract = {Personalized federated learning has emerged as a popular approach to training on devices holding statistically heterogeneous data, known as clients. However, most existing approaches require a client to have labeled data for training or finetuning in order to obtain their own personalized model. In this paper we address this by proposing FLowDUP, a novel method that is able to generate a personalized model using only a forward pass with unlabeled data. The generated model parameters reside in a low-dimensional subspace, enabling efficient communication and computation. FLowDUP's learning objective is theoretically motivated by our new transductive multi-task PAC-Bayesian generalization bound, that provides performance guarantees for unlabeled clients. The objective is structured in such a way that it allows both clients with labeled data and clients with only unlabeled data to contribute to the training process. To supplement our theoretical results we carry out a thorough experimental evaluation of FLowDUP, demonstrating strong empirical performance on a range of datasets with differing sorts of statistically heterogeneous clients. Through numerous ablation studies, we test the efficacy of the individual components of the method.}, author = {Zakerinia, Hossein and Scott, Jonathan A and Lampert, Christoph}, booktitle = {arXiv}, title = {{Federated learning with unlabeled clients: Personalization can happen in low dimensions}}, doi = {10.48550/ARXIV.2505.15579}, year = {2025}, } @unpublished{21050, abstract = {In 1873, James C. Maxwell conjectured that the electric field generated by $n$ point charges in generic position has at most $(n-1)^2$ isolated zeroes. The first (non-optimal) upper bound was only obtained in 2007 by Gabrielov, Novikov and Shapiro, who also posed two additional interesting conjectures. In this article, we give the best upper bound known to date on the number of zeroes of the electric field, and construct a counterexample to a conjecture of Gabrielov, Novikov and Shapiro that the number of equilibria cannot exceed those of the distance function defined by the unit point charges. Finally, we note that it is quite possible that Maxwell's quadratic upper bound is not tight, so it is prudent to find smaller bounds. Hence, we also explore examples and construct configurations of charges achieving the highest ratios of the number of electric field zeroes by point charges found to this day.}, author = {Edelsbrunner, Herbert and Fillmore, Christopher D and Olivera, Gonçalo}, booktitle = {arXiv}, title = {{Counting equilibria of the electrostatic potential}}, doi = {10.48550/ARXIV.2501.05315}, year = {2025}, } @phdthesis{19684, abstract = {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. Initially, 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. In 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. In 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. Finally, 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.}, author = {Yalniz, Gökhan}, issn = {2663-337X}, pages = {155}, publisher = {Institute of Science and Technology Austria}, title = {{Transition to turbulence : Data-, solution-, and pattern-driven approaches}}, doi = {10.15479/AT-ISTA-19684}, year = {2025}, } @article{19795, abstract = {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.}, author = {Vorlaufer, Jakob and Semenov, Nikolai and Kreuzinger, Caroline and Javoor, Manjunath and Zens, Bettina and Agudelo Duenas, Nathalie and Tavakoli, Mojtaba and Suplata, Marek and Jahr, Wiebke and Lyudchik, Julia and Wartak, Andreas and Schur, Florian Km and Danzl, Johann G}, issn = {2667-0747}, journal = {Biophysical Reports}, number = {2}, publisher = {Elsevier}, title = {{Image-based 3D active sample stabilization on the nanometer scale for optical microscopy}}, doi = {10.1016/j.bpr.2025.100211}, volume = {5}, year = {2025}, } @phdthesis{18979, abstract = {Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA. The first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue. The aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor. We describe a construction of a chromatic alpha complex, which enables efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline. The second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory. In the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot.}, author = {Draganov, Ondrej}, issn = {2663-337X}, keywords = {topological data analysis, chromatic point set, alpha complex, persistent homology, six pack, sheaf, microlocal discrete Morse, injective resolution, collapse, knot, discrete Morse theory}, pages = {140}, publisher = {Institute of Science and Technology Austria}, title = {{Structures and computations in topological data analysis}}, doi = {10.15479/at:ista:18979}, year = {2025}, } @phdthesis{20206, abstract = {The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. The spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains. We have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions. }, author = {Vorlaufer, Jakob}, issn = {2663-337X}, pages = {107}, publisher = {Institute of Science and Technology Austria}, title = {{Construction of a cryo-super-resolution microscope to guide in situ structure analysis}}, doi = {10.15479/AT-ISTA-20206}, year = {2025}, } @phdthesis{19722, author = {Inumella, Syamala}, isbn = {978-3-99078-059-6}, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of microtubule reorganization in elongating root epidermal cells}}, doi = {10.15479/AT-ISTA-19722}, year = {2025}, } @phdthesis{19395, abstract = {Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development. One particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions. Like other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation. In this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network. Given the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism. These findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood.}, author = {Monzer, Aline}, issn = {2663-337X}, pages = {160}, publisher = {Institute of Science and Technology Austria}, title = {{Cell-Surface Auxin Signaling: Linking molecular pathways to plant development}}, doi = {10.15479/AT-ISTA-19395}, year = {2025}, } @unpublished{19398, abstract = {Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.}, author = {Monzer, Aline and Mazur, Ewa and Rodriguez Solovey, Lesia and Gallei, Michelle C and Zou, Minxia and Smejkal, Michael and Cervenova, Ema and Friml, Jiří}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}}, doi = {10.1101/2025.02.28.640727}, year = {2025}, } @phdthesis{19393, abstract = {Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta. While most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined. In this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems. We begin by establishing a theoretical bridge between periodically kicked rotors and "crystalline" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear molecules provide an ideal experimental platform due to their abovementioned precise controllability. The core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through molecular alignment and rotational level populations. These findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental physics and developing quantum technologies.}, author = {Karle, Volker}, issn = {2663-337X}, pages = {192}, publisher = {Institute of Science and Technology Austria}, title = {{Non-equilibrium topological phases with periodically driven molecules and quantum rotors}}, doi = {10.15479/AT-ISTA-19393}, year = {2025}, } @phdthesis{20138, abstract = {The evolution shapes the world around us. Not 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. Many models describe these dynamics. This thesis examines the role of the structure in the models of selection. The population structure is represented as a graph or a network, and each vertex is occupied by one individual. Every individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors. The evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness. The role of the networks is widely examined in the literature. The structures that promote the spread of the desired type compared to the structureless case are called amplifiers. The existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified. Moreover, 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. This thesis explores the role of structure in evolution from many perspectives. First, it introduces different models and various choices that can be made in the models of evolution. It highlights the role of the structure in the real world and how this is reflected in these models. Then, it describes the previous results and open problems. Second, 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. This is an important contribution to the robustness of the amplification. Third, the thesis determines the complexity of spatial games. These are processes where the fitness comes from a game, and the strength of selection is high. It shows that determining the fate of cooperation in these games is a PSPACE-complete problem. Fourth, the thesis describes the amplifier of cooperation for spatial games. This is the first amplifier in this setting. Fifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity. In this setting, the fitness depends not only on the type of the individual but also on the occupied vertex. The chapter determines the relationship between the interactions of vertices of different types and the coexistence time. Sixth, 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. Finally, the thesis presents conclusions and outlines the directions for future work. }, author = {Svoboda, Jakub}, issn = {2663-337X}, pages = {167}, publisher = {Institute of Science and Technology Austria}, title = {{Structural properties of games on graphs}}, doi = {10.15479/AT-ISTA-20138}, year = {2025}, } @phdthesis{20117, author = {Wang, Yiqun}, issn = {2663-337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{The role of dynamin related protein 2A in cytokinin regulated plant growth and development}}, doi = {10.15479/AT-ISTA-20117}, year = {2025}, } @phdthesis{20276, abstract = {Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations either preserve the intrinsic material geometry (e.g., folding paper) or modify it through localized contraction. Once transformed, the 3D shape can be further controlled to achieve a target functionality. A key challenge is to take the material specifications and the actuation process as input to automatically design the target 3D shape and its functionality. This thesis presents two novel computational pipelines for the design and control of shape-morphing structures used to create functional prototypes. The first pipeline borrows from the art of origami to fold paper into intricate shapes and applies this principle to make 3D lighting displays. We introduce, PCBend a computational design approach that covers a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize cut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and fabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated standard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs are cut along the contour and folded onto a 3D-printed support. The 3D lighting display is then controlled to display complex surface light patterns. Creating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion or require multiple patches, which are unsuitable for fabrication pipelines that rely on folding non-stretchable materials. We reinforce such fabrication pipelines by providing a geometric relaxation to the problem, where the input shape is modified to admit overlap-free unfolding. The second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s blueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots using modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable artificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is altered to enable untethered actuation through infrared radiation, allowing active control of individual muscles and their corresponding bones. The combined motion of individual bones defines the robot’s overall shape and functionality. Our proposed system significantly expands both the design and control spaces of soft robots, which we harness using our computational design tools. We build several physical robots that exhibit complex shape morphing and varied terrain navigation, showcasing the versatility of our pipeline. This thesis explores applications ranging from intricate light patterns displayed on 3D shapes formed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit shape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform passive structures into functional prototypes.}, author = {Bhargava, Manas}, isbn = {978-3-99078-065-7}, issn = {2663-337X}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{Design and control of deformable structures: From PCB lighting displays to elastomer robots}}, doi = {10.15479/AT-ISTA-20276}, year = {2025}, } @phdthesis{19759, abstract = {Despite generating remarkable results in various computer vision tasks, deep learning comes with some surprising shortcomings. For example, tiny perturbations, often imperceptible to the human eye, can completely change the predictions of image classifiers. Despite a decade of research, the field has made limited progress in developing image classifiers that are both accurate and robust. This thesis aims to address this gap. As our first contribution, we aim to simplify the process of training certifiably robust image classifiers. We do this by designing a convolutional layer that does not require executing an iterative procedure in every forward pass, but relies on an explicit bound instead. We also propose a loss function that allows optimizing for a particular margin more precisely. Next, we provide an overview and comparison of various methods that create robust image classifiers by constraining the Lipschitz constant. This is important since generally longer training times and more parameters improve the performance of robust classifiers, making it challenging to determine the most practical and effective methods from existing literature. In 1-Lipschitz classification, the performance of current methods is still much worse than what we expect on the simple tasks we consider. Therefore, we next investigate potential causes of this shortcoming. We first consider the role of the activation function. We prove a theoretical shortcoming of the commonly used activation function, and provide an alternative without it. However this theoretical improvement does barely translate to the empirical performance of robust classifiers, suggesting a different bottleneck. Therefore, in the final chapter, we study how the performance depends on the amount of training data. We prove that in the worst case, we might require far more data to train a robust classifier compared to a normal one. We furthermore find that the amount of training data is a key determinant of the performance current methods achieve on popular datasets. Additionally, we show that linear subspaces exist with tiny data variance, and yet we can still train very accurate classifiers after projecting into those subspaces. This shows that on the datasets considered, enforcing robustness in classification makes the task strictly more challenging. -----------------“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.” }, author = {Prach, Bernd}, issn = {2663-337X}, pages = {84}, publisher = {Institute of Science and Technology Austria}, title = {{Robust image classification with 1-Lipschitz networks}}, doi = {10.15479/10.15479/at-ista-19759}, year = {2025}, }