@phdthesis{20551, abstract = {The space of codimension-2 shapes, such as curves in 3D and surfaces in 4D, is an infinite-dimensional manifold. This thesis explores geometric structures and dynamics on this space, with emphasis on their implications for physics, particularly hydrodynamics. Our investigation ranges from theoretical studies of infinite-dimensional symplectic and prequantum geometry to numerical computation of the time evolution of shapes. The thesis presents four main contributions. In the first part, we introduce implicit representations of codimension-2 shapes using a class of complex-valued functions, and prove that the space of these implicit representations forms a prequantum bundle over the codimension-2 shape space. This reveals a new geometric interpretation of the canonical symplectic structure on the codimension-2 shape space. In the second part, we use implicit representations to develop a simulation method for the dynamics of space curves. To handle chaotic systems such as vortex filaments in hydrodynamics, we exploit the infinite degrees of freedom, hidden in both the configuration and dynamics of implicit representations. In the third part, we introduce new symplectic structures on the space of space curves, which generalize the only previously known symplectic structure on this space, allowing for new Hamiltonian dynamics of space curves. In the fourth part, we apply a symplectic viewpoint to a differential geometric problem with practical applications. We derive a new area formula for spherical polygons via prequantization. }, author = {Ishida, Sadashige}, isbn = {978-3-99078-070-1}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{Symplectic-prequantum structures and dynamics on the codimension-2 shape space}}, doi = {10.15479/AT-ISTA-20551}, year = {2025}, } @phdthesis{20575, abstract = {This thesis deals with eigenvalue and eigenvector universality results for random matrix ensembles equipped with non-trivial spatial structure. We consider both mean-field models with a general variance profile (Wigner-type matrices) and correlation structure (correlated matrices) among the entries, as well as non-mean-field random band matrices with bandwidth W >> N^(1/2). To extract the universal properties of random matrix spectra and eigenvectors, we obtain concentration estimates for their resolvent, the local laws, which generalize the celebrated Wigner semicircle law for a broad class of random matrices to much finer spectral scales. The local laws hold for both a single resolvent as well as for products of multiple resolvents, known as resolvent chains, and express the remarkable approximately-deterministic behavior of these objects down to the microscopic scale. Our primary tool for establishing the local laws is the dynamical Zigzag strategy, which we develop in the setting of spatially-inhomogeneous random matrices. Our proof method systematically addresses the challenges arising from non-trivial spatial structures and is robust to all types of singularities in the spectrum, as we demonstrate in the correlated setting. Furthermore, we incorporate the analysis of the deterministic resolvent chain approximations into the dynamical framework of the Zigzag strategy, synthesizing a unified toolkit for establishing multi-resolvent local laws. Using these methods, we prove complete eigenvector delocalization, the Eigenstate Thermalization Hypothesis, and Wigner-Dyson universality in the bulk for random band matrices down to the optimal bandwidth W >> N^(1/2). For mean-field ensembles, we establish universality of local eigenvalue statistics at the cups for random matrices with correlated entries, and the Eigenstate Thermalization Hypothesis for Wigner-type matrices in the bulk of the spectrum. Finally, this thesis also contains other applications of the multi-resolvent local laws to spatially-inhomogeneous random matrices, obtained prior to the development of the Zigzag strategy. In particular, we provide a complete analysis of mesoscopic linear-eigenvalue statistics of Wigner-type matrices in all spectral regimes, including the novel cusps, and rigorously establish the prethermalization phenomenon for deformed Wigner matrices. The main body of this thesis consists of seven research papers (listed on page xi), each presented in a separate chapter with its own introduction and all relevant context, suitable to be read independently. We ask the reader’s indulgence for the repetitions in the historical overviews and other minor redundancies that remain among the chapters as a result. The overall Introduction, preceding the chapters, provides a condensed, informal summary of the main ideas and concepts at the core of these works. }, author = {Riabov, Volodymyr}, isbn = {978-3-99078-064-0}, issn = {2663-337X}, pages = {436}, publisher = {Institute of Science and Technology Austria}, title = {{Universality in random matrices with spatial structure}}, doi = {10.15479/AT-ISTA-20575}, 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{20737, author = {Casado Polanco, Raquel}, isbn = {978-3-99078-072-5}, issn = {2663-337X}, keywords = {NOTCH, radial glial progenitor, lineage progression, cortical development}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Role of NOTCH signaling in radial glial progenitor lineage progression}}, doi = {10.15479/AT-ISTA-20737}, year = {2025}, } @phdthesis{20741, abstract = {Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. Firstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. Next, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. Finally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. }, author = {Kojic, Marko}, isbn = {978-3-99078-073-2}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria}}, doi = {10.15479/AT-ISTA-20741}, 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{20364, author = {Giannini, Caterina}, issn = {2663-337X}, keywords = {Auxin Signaling, Plant Development}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}}, doi = {10.15479/AT-ISTA-20364}, year = {2025}, } @phdthesis{20441, abstract = {Epithelial spreading plays a pivotal role in the development of organisms especially those such as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the substantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium with cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the cells show tissue-scale mechanosensation with mechanisms such as direct mechanical control over the axis of cell division. Cytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating mechanical stability but also helping facilitate the mechanosensitive response of the cell. Mechanosenstivity displayed by intermediate filaments is due not just to their interesting physical properties but also to their interactions with other cytoskeletal elements such as actin and microtubules. Keratin is the predominant intermediate filament expressed in the EVL. It expresses concomitantly with the gastrulation movements of the developing embryo. Our work focuses on understanding the role and dynamics of the keratin cytoskeletal network in modulating the physical aspects of EVL spreading. We demonstrated with the combination of physical characterisation and manipulations of the EVL, utilising a variety of biophysical tools and microscopy, the mechanistic role of keratin in tissue spreading. Generating novel genetic morphants and mutants, we probe the effect that the loss of the keratin network has on the physiology of the epithelium and the developing embryo. We show that the changing organisation of the keratin network is important for changing EVL physical properties as the stress imposed on the EVL increases during epiboly. By modelling the epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into a mechanical loop to the maturation of the keratin network and hence affect the mechanics of the epithelium. However, unlike what would be predicted by the effect of intermediate filaments in acting as a security belt and increasing the resistance of the epithelium, we observe that loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the YSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation in a keratin-dependent manner. Furthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into the mechanisms underlying the organisation and distribution of keratin. Interestingly, the phenotype observed upon this loss of microtubules shows that keratins interact with the nucleus through microtubular interactions. Together with these diverse observations, we describe the mechanosensory feedback between resilience and that is critical for uniform and robust spreading of the epithelium.}, author = {Naik, Suyash}, isbn = {978-3-99078-069-5}, issn = {2663-337X}, pages = {105}, publisher = {Institute of Science and Technology Austria}, title = {{Keratins act as global coordinators of tissue spreading through mechanosensitive feedback}}, doi = {10.15479/AT-ISTA-20441}, year = {2025}, } @phdthesis{19478, author = {Chen, Huihuang}, issn = {2663-337X}, pages = {118}, publisher = {Institute of Science and Technology Austria}, title = {{The cAMP second messenger in auxin signalling}}, doi = {10.15479/AT-ISTA-19478}, year = {2025}, } @phdthesis{20920, abstract = {Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality. The only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T). The iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \pi. Given \pi, the output of VDF can be verified in time much less than T. We first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications. Secondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources. We then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions). Finally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory. Together, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications.}, author = {Hoffmann, Charlotte}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Theory and applications of verifiable delay functions}}, doi = {10.15479/AT-ISTA-20920}, year = {2025}, } @phdthesis{20556, abstract = {Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality. The only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T). The iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \pi. Given \pi, the output of VDF can be verified in time much less than T. We first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications. Secondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources. We then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions). Finally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory. Together, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications.}, author = {Hoffmann, Charlotte}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Theory and applications of verifiable delay functions}}, doi = {10.15479/AT-ISTA-20556}, 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{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{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{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}, } @phdthesis{19456, abstract = {Making decisions requires flexibly adapting to changing environments, a process that depends on accurately interpreting current contingencies and integrating them with past experience. Two brain regions are particularly critical for this process, the medial prefrontal cortex (mPFC) and the hippocampus. Using contextual information from the hippocampus, the mPFC selects relevant cognitive frameworks and suppresses irrelevant ones to guide appropriate actions. Several studies have shown that some mPFC pyramidal neurons become spatially tuned when spatial information is required to guide goal-directed behavior. However, the role of prefrontal spatial representations in learning and decision making is not well understood. This work aims to characterize the role of mPFC spatial tuning in supporting a contextual association task. Rats were trained to learn two cue–location associations on a radial arm maze over multiple days, while we simultaneously recorded from dorsal CA1 of the hippocampus and the prelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and prefrontal pyramidal neurons that “flicker” between multiple spatial representations on different trials, suggesting dynamic, context-dependent coding. This flickering may provide a substrate for how the network reorganizes in response to task demands, likely by enabling the flexible evaluation of competing representations. }, author = {Cumpelik, Andrea D}, isbn = {978-3-99078-056-5}, issn = {2663-337X}, keywords = {neuroscience, decision making, learning, cognitive flexibility, medial prefrontal cortex, hippocampus, electrophysiology}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{The role of prefrontal spatial coding in supporting a contextual association task}}, doi = {10.15479/AT-ISTA-19456}, year = {2025}, } @phdthesis{19533, abstract = {This thesis explores advancements in quantum remote sensing and non-equilibrium phase transitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing. In the first project, I experimentally studied photon blockade breakdown as a dissipative phase transition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic limit, we demonstrated that the observed bistability is a genuine signature of a first-order phase transition in this system. This work provides insight into non-equilibrium quantum dynamics and phase transitions in driven-dissipative open quantum systems. The second project focuses on the experimental realization of a phase-conjugate receiver for quantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy environments using entangled light. While an ideal spontaneous parametric down-conversion (SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical illumination, no such ideal receiver exists. Instead, we explore an experimental realization of a phase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a Josephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled signal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate key experimental limitations that constrain practical QI performance, contributing to the development of quantum-enhanced sensing. Additionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These methods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been essential in data acquisition, noise filtering, and correlation analysis across multiple research projects. Although not real-time, these DSP techniques significantly enhance the accuracy of quantum measurements. Overall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic limit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver for QI. These findings contribute to quantum metrology, particularly for weak signal detection and remote sensing in noisy environments. }, author = {Sett, Riya}, issn = {2663-337X}, keywords = {phase transition, open quantum system, phase diagram, cavity quantum electrodynamics, superconducting qubits, semiclassical physics, quantum optics, josephson junction, parametric converter, phase conjugation, quantum radar, quantum entanglement, correlation, quantum sensing}, pages = {109}, publisher = {Institute of Science and Technology Austria}, title = {{ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime}}, doi = {10.15479/AT-ISTA-19533}, year = {2025}, } @phdthesis{19722, abstract = {As root epidermal cells progress from a phase of elongation to differentiation, their cortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The hormone cytokinin, a key regulator of root development, facilitates these cytoskeletal changes. However, the molecular mechanisms underlying hormone-mediated MT reorientation during root development are still unknown. Here, we find that MT reorientation in root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell differentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s association with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end created by katanin-mediated severing at crossovers. Notably, our findings suggest that dynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning of the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets of cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1 association in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it increases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives MT reorganization during cell development by simultaneously modulating several microtubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool during this process.}, 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{19763, abstract = {Pattern formation in developing organs is controlled by morphogens. These signalling molecules form concentration gradients across tissues, thereby providing positional information that instructs the pattern of cell differentiation. Morphogen gradients are highly dynamic in space and time. Many factors such as morphogen production, spreading, degradation, cellular rearrangements and others could contribute to changes in the gradient shape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear. We studied the dynamics of morphogen signalling and tissue patterning in the developing vertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor subtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are established and interpreted to ensure ordered cell specification is poorly understood. To address this question, we developed a 2D embryonic stem cell differentiation system that captures key features of dorsal neural tube development. In this system, differentiated colonies display remarkable self-organised pattern formation in response to uniformly applied BMP ligand. We established a method of differentiating the colonies using microfabricated stencils, which allowed us to control the initial size and shape of colonies without confining cell migration and colony growth. This led to highly reproducible pattern formation that facilitates quantification. Using this approach, we observed striking two-phase temporal dynamics of BMP signalling in our colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies, subsequently disappears and is re-established again in the second phase. By combining our quantitative data with a data-driven theoretical model, we uncovered a temporal relay mechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is controlled by fast tissue-autonomous negative feedback that restricts the duration of the initial response to BMP. The early BMP activity gradient moreover controls the spatial organisation of the cell type pattern: the absence of a first phase results in disordered cell type pattern. The second phase is controlled by slow positive regulation of BMP signalling by the transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the second phase of BMP signalling via positive feedback on LMX1A. Altogether, the mechanism that we uncovered ensures the coupling of sequential developmental events, making pattern formation spatially and temporally organised. Furthermore, this mechanism allows the BMP signalling pathway to be reused in different contexts – first for the establishment of the neural plate border, and subsequently for dorsal neural progenitor patterning. Our study supports a general developmental principle in which multiple morphogens interact with transcriptional networks resulting in complex spatiotemporal signalling dynamics that ultimately drive organised pattern formation.}, author = {Rus, Stefanie}, issn = {2663-337X}, pages = {129}, publisher = {Institute of Science and Technology Austria}, title = {{Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube}}, doi = {10.15479/AT-ISTA-19763}, year = {2025}, }