@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. }, 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}, } @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{20607, author = {Mondal, Soumyadip}, isbn = {978-3-99078-071-8}, issn = {2663-337X}, pages = {71}, publisher = {Institute of Science and Technology Austria}, title = {{Oxygen and sulfur redox: Conversion kinetics and phase equilibria}}, doi = {10.15479/AT-ISTA-20607}, year = {2025}, } @phdthesis{20811, abstract = { This thesis is organized into two parts, each comprising two chapters: Chapter 1 and 2 offer models for the evolution of vaccine resistance in response to diverse vaccination strategies. Chapter 3 and 4 review the statistics of records, their connection to models of innovation and an application to the cultural evolution of sports. In chapter 1 we present a modelling study from 2021 on the evolution of SARS-CoV-2. At that time the vaccine-resistant Omicron variant had not yet evolved. In our model we consider a population that is becoming vaccinated over time, while a pathogen is spreading in the population and eventually becoming resistant to the vaccine. We explore effective pharmaceutical and non-pharmaceutical interventions to prevent the emergence of vaccine resistance. In chapter 2 we model a particular set of complex vaccination strategies, mosaic and pyramid vaccination, where an immunologically diverse portfolio of vaccines is considered. We find that a bet-hatching strategy, in which vaccine types are distributed in the population, is effective at hindering the evolution of vaccine resistance if mutation rates are high. In chapter 3 we switch gears and present a review on the statistics of records. We highlight similarities and analogies to other models in the fields of statistical physics, evolution and innovation. This offers interesting complimentary perspectives on well-known models. In chapter 4 we apply models of record statistics and innovation to study cultural evolution in sport. We propose a model of sport evolution that combines deterministic improvements in performance and stochastic bursts of improvements due to innovation. }, author = {Rella, Simon}, issn = {2663-337X}, pages = {95}, publisher = {Institute of Science and Technology Austria}, title = {{Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation}}, doi = {10.15479/AT-ISTA-20811}, 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{20203, abstract = {Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon.}, author = {Sobarzo Ponce, Juan Carlos A}, isbn = {978-3-99078-062-6}, issn = {2663-337X}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges}}, doi = {10.15479/AT-ISTA-20203}, year = {2025}, } @phdthesis{20371, abstract = {Quantum mechanics reveals a world that defies classical determinism, where uncertainty, superposition, and fluctuations are fundamental aspects. Engineering devices that harness these quantum features requires not only precision, but also a deep understanding of how they interact with their surrounding environment. Superconducting circuits, which exploit macroscopic quantum coherence in low-loss superconducting materials, provide a scalable platform for implementing such systems. Among the critical elements in these circuits, superinductors—high-impedance, dissipation-free inductive components—play a central role by suppressing charge fluctuations. They allow quantum states to be delocalized in phase space, protect qubits from environmental noise, and facilitate access to phenomena such as dual Josephson physics and ultra-strong coupling regimes. This thesis explores two complementary implementations of high-impedance circuits: geometric superinductors, demonstrating that high impedance can be achieved beyond kinetic inductance, and Josephson junction chains, used to investigate both microwave mode properties and DC transport across the superconductor-to-insulator transition. Part I addresses geometric superinductors. Contrary to the common belief that high-impedance superconducting circuits require kinetic inductance, we demonstrate that purely geometric designs can achieve characteristic impedance exceeding the resistance quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors achieve enhanced self-inductance, creating a reliable platform for qubits and resonators. Modeling, simulation, fabrication, and characterization confirm that these elements behave as superinductor. With low loss, high linearity, and minimal stray capacitance, these elements are reproducible, free of uncontrolled tunneling events, and capable of strong magnetic coupling. This establishes geometric superinductors as robust, single-wave-function superconducting devices suitable for hardware protected qubits and hybrid systems. Part II presents classical numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps. The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive environment with a parasitic capacitance. Part III extends the investigation of high characteristic-impedance circuit elements to one-dimensional Josephson junction chains, which act as a quantum simulator for many-body physics and the superconductor–insulator transition. Different devices are realized on both sides of the DC phase transition, showing either a supercurrent branch or Coulomb blockade at zero bias. The effect of the crossover on microwave modes, however, remains insufficiently investigated. Studying these modes provides insight into the interplay between disorder and phase-slip events. Small differences in circuit component sizes determine which side of the transition a device falls on, making these results relevant not only for fundamental understanding but also for the design of quantum devices, emphasizing the crucial role of the electromagnetic environment in stabilizing and controlling fragile quantum states. Together, these results illustrate how carefully engineered high characteristic-impedance elements provide a link between macroscopic circuits and the inherently uncertain quantum world, enabling experiments that probe, control, and ultimately exploit quantum fluctuations for applications in quantum information, metrology, solid state physics and beyond. }, author = {Trioni, Andrea}, isbn = {978-3-99078-067-1}, issn = {2663-337X}, pages = {202}, publisher = {Institute of Science and Technology Austria}, title = {{High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains}}, doi = {10.15479/AT-ISTA-20371}, year = {2025}, } @phdthesis{20339, abstract = {This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights. We first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations. In the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D. }, author = {Tasinato, Gianluca}, issn = {2663-337X}, pages = {106}, publisher = {Institute of Science and Technology Austria}, title = {{Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems}}, doi = {10.15479/AT-ISTA-20339}, year = {2025}, } @phdthesis{20234, abstract = {Game Theory is the mathematical formalization of social dynamics - systems where agents interact over time and the evolution of the state of the system depends on the decisions of every player. This thesis takes the perspective of a single player and focuses on what they can guarantee in the worst case over the behavior of other players. In other words, we consider that the objective of every other player in the game is exactly the opposite to the player. We focus on sustained interactions over time, where the players repeatedly obtain quantitative rewards over time, and they are interested in maximizing their long-term performance. Formally, this thesis focuses on zero-sum games with the liminf average objective. Two fundamental questions that Game Theory aims to answer are the following. 1. How much can a player guarantee to obtain after the interaction? 2. How to act in order to obtain the previously mentioned guarantee? These questions are formalized by the concepts of "value" and "optimal strategies". We study their properties on games that exhibit one or more of the following properties. 1. Partial Observation: the players can not perfectly observe the current state of the system during the game. We consider the model of (finite) Partially Observable Markov Decision Processes and prove that finite-memory strategies are sufficient to approximately guarantee the value. 2. Perturbed Description: the formal description of the game is perturbed by a small parameter. We consider the model of (finite) Perturbed Matrix Games, and provide algorithms to check various robustness properties and to compute the parameterized value and optimal strategies. 3. Stochastic Transitions: the actions of the players determine the behavior of the evolution of the system, described as a probability distribution over the next state. We consider the model of (finite) Perturbed Stochastic Games and provide formulas for the marginal value. 4. Infinite States: the system can be in infinitely many states. We consider the model of Random Dynamic Games on a class of infinite graphs, prove the existence of the value, and quantify the concentration of finite-horizon values.}, author = {Saona Urmeneta, Raimundo J}, issn = {2663-337X}, pages = {125}, publisher = {Institute of Science and Technology Austria}, title = {{Robustness of solutions in game theory: Values and strategies in partially observable, perturbed, stochastic, and infinite games}}, doi = {10.15479/AT-ISTA-20234}, year = {2025}, } @phdthesis{19540, abstract = {This thesis deals with several different models for complex quantum mechanical systems and is structured in three main parts. In Part I, we study mean field random matrices as models for quantum Hamiltonians. Our focus lies on proving concentration estimates for resolvents of random matrices, so-called local laws, mostly in the setting of multiple resolvents. These estimates have profound consequences for eigenvector overlaps and thermalization problems. More concretely, we obtain, e.g., the optimal eigenstate thermalization hypothesis (ETH) uniformly in the spectrum for Wigner matrices, an optimal lower bound on non-Hermitian eigenvector overlaps, and prethermalization for deformed Wigner matrices. In order to prove our novel multi-resolvent local laws, we develop and devise two main methods, the static Psi-method and the dynamical Zigzag strategy. In Part II, we study Bardeen-Cooper-Schrieffer (BCS) theory, the standard mean field microscopic theory of superconductivity. We focus on asymptotic formulas for the characteristic critical temperature and energy gap of a superconductor and prove universality of their ratio in various physical regimes. Additionally, we investigate multi-band superconductors and show that inter-band coupling effects can only enhance the critical temperature. In Part III, we study quantum lattice systems. On the one hand, we show a strong version of the local-perturbations-perturb-locally (LPPL) principle for the ground state of weakly interacting quantum spin systems with a uniform on-site gap. On the other hand, we introduce a notion of a local gap and rigorously justify response theory and the Kubo formula under the weakened assumption of a local gap. Additionally, we discuss two classes of problems which do not fit into the three main parts of the thesis. These are deformational rigidity of Liouville metrics on the torus and relativistic toy models of particle creation via interior-boundary-conditions (IBCs). }, author = {Henheik, Sven Joscha}, isbn = {978-3-99078-057-2}, issn = {2663-337X}, pages = {720}, publisher = {Institute of Science and Technology Austria}, title = {{Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems}}, doi = {10.15479/AT-ISTA-19540}, year = {2025}, } @phdthesis{20357, author = {Ruzickova, Natalia}, isbn = {978-3-99078-066-4}, issn = {2663-337X}, keywords = {gene regulation, networks, omnigenic model, pancreas, collective behaviour}, pages = {156}, publisher = {Institute of Science and Technology Austria}, title = {{Effect propagation in biological networks}}, doi = {10.15479/AT-ISTA-20357}, year = {2025}, } @phdthesis{20074, abstract = {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. In 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. In 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. In 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 = {Hübschmann, Verena}, isbn = {978-3-99078-060-2}, issn = {2663-337X}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Human microglia impact neuronal development in retinal organoids}}, doi = {10.15479/AT-ISTA-20074}, year = {2025}, } @phdthesis{20147, abstract = {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. In 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. }, author = {Sarac, Naci E}, issn = {2663-337X}, pages = {149}, publisher = {Institute of Science and Technology Austria}, title = {{A monitoring-oriented theory and classification of quantitative specifications}}, doi = {10.15479/AT-ISTA-20147}, year = {2025}, } @phdthesis{20167, author = {Schön, Hanna}, isbn = {978-3-99078-061-9}, issn = {2663-337X}, pages = {171}, publisher = {Institute of Science and Technology Austria}, title = {{The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs}}, doi = {10.15479/AT-ISTA-20167}, 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}, } @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{20212, author = {Miranda, Osvaldo}, isbn = {978-3-99078-063-3}, issn = {2663-337X}, keywords = {Pten, mtor, cortical development, MADM, Mapk}, pages = {119}, publisher = {Institute of Science and Technology Austria}, title = {{Unraveling the role of Pten in cortical stem cell lineage progression using MADM}}, doi = {10.15479/AT-ISTA-20212}, year = {2025}, } @phdthesis{20798, abstract = {Atom interferometers measure the relative phase shifts between coherent matter-wave paths that arise from interactions with external fields or inertial forces. Due to their exceptional phase sensitivity, atom interferometers became an essential tool for precision measurements and fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial navigation. However, their measurement precision is limited by quantum projection noise, which arises from the Heisenberg uncertainty principle, preventing the measurement of atomic states with absolute precision. The generation of entanglement between the atoms offers a path to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s phase sensitivity beyond classical measurement bounds. This thesis reports on the development of an atom interferometer experiment designed to realize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms. The experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder interferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is centered on a triangular optical cavity that mediates all relevant atom-light interactions. The cavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling to perform interferometry on a continuously trapped atomic ensemble. The thesis elaborates on the fundamental theoretical framework, the cavity design, and the full optical setup, including the detailed configuration of the developed laser stabilization methods. Experimentally, continuous loading methods were explored, resulting in an accumulation of up to 4 × 106 atoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift compensation method developed for continuous loading was further applied for in-trap cooling to 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control was verified via observation of microwave-driven Rabi oscillations, and used to characterize atom-cavity coupling. These presented results establish the experimental groundwork for the future development of cavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry.}, author = {Wald, Sebastian}, isbn = {978-3-99078-075-6}, issn = {2663-337X}, keywords = {entanglement-enhanced atom interferometry, cavity QED, spin-squeezing, dipole trap, quantum optics}, pages = {152}, publisher = {Institute of Science and Technology Austria}, title = {{Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry}}, doi = {10.15479/AT-ISTA-20798}, year = {2025}, } @phdthesis{18871, abstract = {"Can we do this with a new type of computer - a quantum computer?". This famous quotation of the brilliant Richard Feynman within a conference talk on "Simulating physics with computers.” is often reverently praised as the origin of the field of quantum computing. The idea was to use quantum mechanical systems itself to simulate "Nature", which is inherently quantum mechanical. Now, 43 years later, the theoretical framework of how such a computer can operate has been developed. Two main important concepts for a potential quantum supremacy, superposition and entanglement, have been exploited to design quantum algorithms to significantly speed up certain tasks. Yet, the specific hardware implementation is still far from being certain, in fact the race between the most promising platforms such as superconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well as spin qubits has recently intensified. If one also includes the most mature applications of quantum communication technologies, secure quantum key distribution and quantum random number generators, as part of a quantum information technology ecosystem, we are confronted with a plethora of different materials, concepts, and also operation frequencies. While superconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5 GHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum computing operate with light in the infrared or visible range. Consequently, a quantum frequency converter or microwave-optic transducer is required to interface the different frequency domains or establish a long-range network connection with suitable telecom fibers. In fact, the combination of different frequency regimes is also an essential part in our classical modern communication network, where computations are performed in electrical circuits and the information exchange over longer distances happens via optical fibers. However, the specific challenges specific to building a quantum computer, also apply to the development of such a quantum frequency transducer: 1) As we deal with single excitations as the carrier of information, i.e. the smallest possible quantity, the signal can easily be corrupted by other noise sources which needs to be avoided by all means. This is also the reason why microwave quantum computers operate at temperature environments close to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The frequency interface generally needs to preserve the phase of the signal as an essential part of the quantum state. And 3) Quantum signals cannot be copied which would be a typical strategy to account for errors in classical computers. And finally, there is a challenge specific to microwave-optic transducers: While quantum computers are operating in one specific frequency domain, microwave-optic transducers combine microwave and optical fields in one device. This results in the particular challenge that high-energy optical radiation, which is usually well-shielded from superconducting microwave quantum processors, are now an essential part of the device. The concomitant optical radiation in the operating transducer will inevitably have a detrimental effect on the superconducting microwave components. Together with the requirement of minimal background noise for quantum-limited operation as described above, v heating from the absorption of optical photons within the same device where single microwave excitations are processed forms a formidable challenge. This thesis aims to address this challenge by developing microwave-optic transducers where the impact of optical absorption on superconducting circuits in general and superconducting qubits specifically can be mitigated. In our first approach, we developed a compact device with optimized interaction strengths between the different frequency domains. This minimizes the optical powers used for transducer operation and thus the optical absorption heating. This work was - to the best of our knowledge - the first comprehensive noise study, in an integrated microwave-optic transducer. Unfortunately, we saw that the optical absorption heating added noise way above a single excitation. Consequently, a potential quantum signal would have been buried in the noise, added by the transduction. Building on this insight, we utilized a three-dimensional microwave-optic transducer instead of an integrated device. The larger heat capacity of the macroscopic device with a size of a few millimeters can absorb a larger fraction of the optical heating before it increases the temperature of the device. This allowed us to interface the transducer directly with a superconducting qubit to readout the qubit state in a novel all-optical manner. We showed that the microwave-optic transducer can be operated in a regime in which optical fields don’t harm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic transducers in conjunction with microwave quantum processors and brings the integration and seamless orchestration of different frequency components in a quantum network a step closer. }, author = {Arnold, Georg M}, issn = {2663-337X}, pages = {135}, publisher = {Institute of Science and Technology Austria}, title = {{Microwave-optic interconnects for superconducting circuits}}, doi = {10.15479/at:ista:18871}, year = {2025}, } @phdthesis{19745, abstract = {Cell migration is a crucial process in animal development and maintenance. It is incredibly heterogeneous, with different cell types utilizing fundamentally distinct migration strategies. The strategies also depend on the cellular microenvironment, where cells can switch between migration modes as they encounter new environmental cues. In this thesis, we investigated how dendritic cells adapt their migration strategy when encountering geometrically, mechanically and chemically distinct environments. When dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast and directional amoeboid manner. In this migration strategy, extracellular proteolysis and integrin-mediated adhesions are dispensable. Instead, the cells use topography of the environment to propel their cell body forward. To migrate efficiently in the maze of different pore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and use it to gauge the pores to identify the path of least resistance. Our aim was to identify whether dendritic cells adapt their migration strategy when encountering asymmetrical transitions into much denser environments with limited choice of large pores. In such invasive transitions it is unclear if the cells can cross tight pores without the use of adhesions and extracellular proteolysis and whether they maintain the nucleus in the cell front. Using various cell migration assays such as fibrous 3D collagen gels, geometrically defined microchannels with constrictions and simplistic under agarose migration assay, we provide a comprehensive characterization of invasive migration of dendritic cells. We show that during invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell body into the dense environment. In collagen gels, we show that dendritic cells can invade without proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading to a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is required. This contractile force is simultaneously necessary for reverting the nucleus back to the cell front after invasion and maintaining this positioning during permissive migration. A functional role of the reorientation was uncovered in the first collaboration project. A prominent central actin pool was identified around the MTOC, especially pronounced in dense and compressive environments. The actin pool was shown to generate pushing forces to dilate the space for cell translocation. These forces are only necessary in non-permissive environments, where the nucleus reorients to the cell rear, allowing the actin pool to generate space. In permissive environments where space generation is dispensable, the MTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more actin to be incorporated into the lamellipodium, speeding up migration. In the second collaboration project, we investigated the effects of distinct chemical environments on dendritic cell migration. The strikingly persistent migration of these cells was explained by their ability to modulate and even self-generate chemokine gradients. This allows the cells to migrate faster and more persistent in uniform chemokine fields compared to imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial player in this process, both sensing the signal and internalizing the chemokine to create a sink.}, author = {Canigova, Nikola}, isbn = {978-3-99078-058-9}, issn = {2663-337X}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Adaptive strategies of dendritic cell migration in response to environmental cues}}, doi = {10.15479/AT-ISTA-19745}, year = {2025}, }