@phdthesis{19271, abstract = {The medial habenula (MHb) is implicated in regulating emotional responses to aversive events. Studies in zebrafish have identified a remarkable morphological left-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian MHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in modulating fear responses. However, there is little evidence for structural or functional lateralization in the mammalian MHb-IPN pathway. Here, I investigated the synaptic properties of the left and right MHb afferents to the IPN in mice and addressed whether these synaptic connections selectively influence the expression of conditioned fear in mice. My findings reveal that each individual IPN neuron receives inputs from both left and right MHb. Electrophysiological recordings from the same postsynaptic IPN neurons demonstrate that the left MHb-originating synapses exhibit lower release probability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated potentiation compared to the right MHb-originating synapses. Interestingly, chemogenetic inhibition of cholinergic neurons in the left but not the right MHb significantly attenuated cue-dependent fear recall. Furthermore, conditional deletion of GABABR in the left MHb interfered with the recall of cued fear memory, whereas that in the right MHb neurons spared fear memory expression. Collectively, I demonstrate a functional asymmetry of the MHb in mice, revealing a predominant role for GABABR-mediated signaling in the left MHb-IPN pathway in the modulation of fear memories. These findings suggest that lateralized pathways could represent a fundamental principle in the neural regulation of emotion across species.}, author = {Önal, Hüseyin C}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula}}, doi = {10.15479/AT-ISTA-19271}, year = {2025}, } @phdthesis{19302, abstract = {Social interaction networks of insect colonies facilitate efficient information exchange and demonstrate adaptive changes to mitigate disease transmission. While circadian rhythms influence individual behaviour, their role in shaping colony-level defences against pathogens remains unexplored. Here, we investigate whether social networks of the black garden ant, Lasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability when colonies are exposed to a pathogen during the day or the night. We first establish baseline daily variations in activity and network dynamics in pathogen-free colonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we examine pathogen-induced changes in sanitary care and network dynamics by exposing foragers to a natural pathogen (Metarhizium brunneum) during either the day or the night. Individual pathogen loads were measured after a nine-hour post-exposure period to evaluate transmission outcomes. Our results demonstrate that diurnal ant colonies maintain robust circadian patterns in network properties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care irrespective of exposure timing, prioritising the protection of the valuable colony centre consisting of nurses and the queen. These findings underscore the robustness and adaptability of ant colonies in balancing circadian rhythms with effective social immune responses.}, author = {Sartoris, Linda}, issn = {2663-337X}, pages = {85}, publisher = {Institute of Science and Technology Austria}, title = {{The effect of circadian rhythm on organisational immunity of ant colonies}}, doi = {10.15479/AT-ISTA-19302}, year = {2025}, } @phdthesis{19386, abstract = {Crustaceans are a large group of arthropods with a great diversity of species and different types of sex determination systems and reproductive modes (Subramoniam, 2017). This makes them a great model for exploring the evolution of sex chromosomes and sexual dimorphism and investigating the evolutionary mechanisms driving and maintaining the diversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a branchiopod crustacean, are well suited for such explorations, as they have both highly dimorphic traits and closely related sexual and asexual species. Although brine shrimp are known to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex chromosomes are still not well characterized at the genomic level, the sex-determination gene is unknown, and it is still unclear whether the same sex chromosomes as shared by the different species. The first part of this thesis was to characterize the Z and W chromosomes in Artemia using an array of methods, from generating multiple chromosome and contig level genome assemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer based approaches. The second part tackles the conservation of the cell type specific regulatory pathways in the female reproductive system between Artemia and Drosophila, and the expression of the Z-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show that germline cells lack dosage compensation, with a subset of cells showing evidence of extreme repression of the Z chromosome. With multiple sexual species and several asexual lineages of parthenogenetic females that produce rare males at low frequencies, Brine shrimp present the perfect opportunity to explore the transition to asexuality and shed light on the prerequisites and repercussions of the form of modified meiosis maintaining the asexual lineages. The last chapter is an investigation of the molecular pathways involved in asexual reproduction in Artemia using newly generated single nucleus RNAseq and WGS data and previously published data. }, author = {Elkrewi, Marwan N}, isbn = {9783990780534}, issn = {2663-337X}, pages = {170}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp}}, doi = {10.15479/AT-ISTA-19386}, year = {2025}, } @phdthesis{19431, abstract = {Gene expression is crucial for cell differentiation, development and survival of organisms. It consists of several steps, starting with transcription that is mediated by RNA polymerases. These are protein machineries transcribing and producing different types of RNAs. Although, the individual steps of transcription by RNA polymerase II (Pol II) as well as the structure of Pol II has been extensively studied, surprisingly, there is still little known about its regulation and assembly in cytoplasm. Among the proteins that are important in biogenesis of Pol II are RNA polymerase II associating proteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups were shown to take essential part in assembly of Pol II. The aim of this project was to deepen our knowledge in regulation of Pol II in the cytoplasm as well as the proteins involved in this process. Techniques of structural biology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners. This study shows for the first time the structure of cytoplasmic Pol II at high resolution. The structure also reveals proteins interacting with Pol II in cytoplasm, namely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state. Furthermore, GDOWN1 and RPAP2 make steric clashes with various transcription factors bound to Pol II during different stages of transcription. Even though GPN1 and GPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of the complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes these proteins on Pol II and several experiments suggest that they interact with the clamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or partially open state. Based on these results I propose a novel model of regulation of Pol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm and doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus. This research contributes to the current knowledge of molecular mechanisms of Pol II regulation in cytoplasm.}, author = {Hlavata, Annamaria}, isbn = {978-3-99078-055-8}, issn = {2663-337X}, pages = {83}, publisher = {Institute of Science and Technology Austria}, title = {{Regulation of Cytoplasmic RNA Polymerase II}}, doi = {10.15479/10.15479/AT-ISTA-19431}, 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{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{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}, } @phdthesis{19836, abstract = {Over the past century, researchers have been fascinated by the quantum nature of the physical world, initially striving to understand its fundamental principles and consequences, and eventually progressing toward engineering systems that can control and manipulate quantum properties. Today, we stand at the dawn of the quantum technology era. While some quantum technologies follow well-defined roadmaps, others are still in the exciting and uncertain early stages of development. In the fields of quantum computing and quantum simulation, research is being conducted across a wide variety of platforms. Each of these demonstrates control over quantum properties but also faces challenges in scaling up to the level of a mature technology. This thesis explores some of the fundamental properties of hole spin qubits in planar germanium. Semiconductor spin qubits are considered strong candidates for the realization of quantum processors, owing to their long relaxation and coherence times, as well as their compatibility with existing semiconductor industry infrastructure. Among these, hole spin qubits in planar germanium are particularly promising. Their advantages include a large effective mass, which eases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit interaction, which enables fast and purely electrical control. However, spin-orbit coupling also introduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip tunneling, which might cause that the quantization axes are not aligned. In this thesis, we investigate the tilt between the quantization axes of two hole spins hosted in a double quantum dot as a function of both the magnetic field direction and various electrostatic configurations, demonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove to be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the physics governing spin qubit behavior. }, author = {Saez Mollejo, Jaime}, issn = {2663-337X}, pages = {175}, publisher = {Institute of Science and Technology Austria}, title = {{Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning }}, doi = {10.15479/AT-ISTA-19836}, year = {2025}, } @phdthesis{20449, abstract = {Males and females of many species differ in morphology, physiology, and behavior. In taxa with genetic sex determination, sexual differentiation arises largely from sex-biased gene expression, which varies across tissues, developmental stages, and lineages. Increasing evidence highlights chromatin configuration, which can exist in open or closed states, and can be shaped by sex-determination path ways, as a key regulatory layer of this dimorphism. Degeneration of the Y or W chromosome further contributes to sex -specific differences by altering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these imbalances, many eukaryotes have independently evolved dosage compensation mechanisms, often mediated through chromatin -level regulation. In this thesis, we investigate the evolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana and Cameraria ohridella , with a particular focus on the extent of dosage compensation following gene loss in the heterogametic sex and the potential chromatin-based mechanisms underlying this process. We further characterize sex -biased gene expression and its regulation through histone modifications. Our analyses also reveal that the A. franciscana genome is highly repetitive, with many genes containing intronic transposable elements. We find that enrichment of histonemo difications associated with constitutive heterochromatin, positively correlates with variation in gene expression levels. Collectively, these findings underscore role of chromatin regulation in shaping the evolution of sex chromosomes and sexual differentiation. }, author = {Bett, Vincent K}, issn = {2663-337X}, pages = {114}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution and regulation of the Z chromosome}}, doi = {10.15479/AT-ISTA-20449}, year = {2025}, } @phdthesis{19993, abstract = {Ants are frequently challenged by different pathogens, which they counter with individual and collective responses. Usually, the pathogens like fungi or viruses are solitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These entomopathogenic nematodes are active parasites with an own behavior and chasing pray. In the first chapter, we investigated the basic biology of the host-pathogen relationship. We tested different ant life stages and found that adult ants display defense behaviors and are generally resistant to nematode infection, whereas brood is highly susceptible. In the case of worker pupae, we found a slight protective effect of the cocoon. When larvae are accompanied by adults, meaning a queen or a group of workers, survival is significantly enhanced. Moreover, we found that nematodes can transmit from infected cadavers to healthy worker larvae, confirming a transmissible disease in ants. Again, worker presence significantly reduces transmission risk. In the end, we were also able to disentangle the pathogen system and investigate the pathogenic effect of the bacterial and nematode components. In the second chapter, we studied the effect of multiple infections in adult queens and queen larvae. By multiple exposures in the mode of coinfection and superinfections, we wanted to assess the detrimental effect of combined fungal and nematode exposure to better understand how the pathogens interact with each other in an ant host. We found instances where combined exposure lead to higher mortality in a given time frame in both, adult queens and queen larvae. Overall entomopathogenic nematodes are a promising model to study worm infections in ants which extend our knowledge on collective disease defense.}, author = {Strahodinsky, Florian}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Social immunity in a tri-partite host-pathogen relationship}}, doi = {10.15479/AT-ISTA-19993}, year = {2025}, } @phdthesis{19906, abstract = {Flows of ordinary fluids such as water or air transition from laminar to turbulent motion as the velocity increases. This simple dependence of the flow state solely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here various different instabilities and turbulent states can arise at low and even vanishing inertia, while high inertia turbulence counterintuitively is suppressed and its drag strongly reduced. We here show in experiments of a viscoelastic model fluid that the phenomena observed at low and high inertia have a common origin and that the same dynamical state, elasto-inertial turbulence, persists across four orders of magnitude in Reynolds number, ranging from very low inertia, all the way to high inertia Maximum drag reduction (MDR) asymptote. We also explore the transitions from Newtonian turbulence to MDR, and specific cases of flow at high polymer concentrations, exploring the relationship between flow at these wide range of control parameters. }, author = {Suresh, Sarath S}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote}}, doi = {10.15479/AT-ISTA-19906}, year = {2025}, } @phdthesis{20470, abstract = {Systems design has classically relied on composable systems, in which individual subsystems have defined inputs, outputs, and interactions with each other; however, attempts at designing complex systems in synthetic biology has often run in to issues of crosstalk and interference, given that these systems must function within the context of the host. In nature, mobile genetic elements are systems that have evolved to travel between hosts, and thus appear to be a good candidate with which to evaluate composability. Selecting temperate phages as a model system, I used mathematical modelling to identify sources of information that temperate phages should respond to. I found that essential proteins of temperate phages can interfere with potential hosts, indicating limitations to composability. I also designed a lysogeny reporter construct and characterize its behavior across various laboratory and environmental strains, finding differences in phage lambda lysogens, and potential interference from prophages that already exist within the environmental strains. Although the information gathered is not conclusive, it suggests that composability is not a key property of temperate phages, implying that biological systems may not be composable, and that other system design principles should be considered when designing synthetic systems.}, author = {Wu, Bryan}, issn = {2663-337X}, pages = {102}, publisher = {Institute of Science and Technology Austria}, title = {{An examination on phages as a naturally composable system}}, doi = {10.15479/AT-ISTA-20470}, year = {2025}, } @phdthesis{20694, abstract = {Understanding the mechanisms underlying speciation is a central aim of evolutionary biology. A persistent challenge in the field is to identify loci that contribute to reproductive isolation, while disentangling signals of selection from demography, linkage and intrinsic genomic features. Traditional population genomic approaches that rely on site-based statistics in arbitrary fixed windows face inherent limitations, as they conflate historical and contemporary processes of divergence and overlook haplotype structure. Recent advances in whole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now offer the opportunity to study genealogical relationships explicitly, revealing how lineages coalesce and recombine through time. By directly analysing haplotype clustering by species or phenotype and their patterns of coalescence, ARG-based methods show promise for diagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene flow, and tracing their evolutionary history. In this thesis, I explore the utility of genealogical approaches for studying species divergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks through the structure of the ARG, using simulations and empirical data to highlight how genealogical processes generate rich and often overlooked haplotypic patterns. In chapter 3, I examine the genomic basis of a key evolutionary innovation in marine snails Littorina. These snails offer a unique opportunity to study an innovation because they include a very recent transition from egg-laying to live bearing, yet snails with the different reproductive modes are not reciprocally monophyletic. I exploited this by using topology clustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or haplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying to live-bearing involves multiple, live-bearer-specific sweeps. Chapter 4 establishes a population-scale, phased genomic resource for Antirrhinum majus, using cost-effective haplotagging, then optimizes imputation from low-coverage data against high-accuracy KASP sequencing to maximize sequence completeness with modest accuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing strategy combines molecular phasing with statistical phasing to generate phased whole genome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing costs. In chapter 5, I analyse hybridising populations from two replicate hybrid zones to find a parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape driven by variation in demographic history. While outlier genome scans of FST failed to dissect the causes of differentiation, ARG-based topology clustering revealed a reuse of colour associated haplotypes across hybrid zones. In addition to the biological insight, this chapter also presents a comparison of the latest ARG inference tools, showing that signals of Abstract viii topological clustering qualitatively agree between methods, despite differences in the tree sequences. Next, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I integrated genome-wide association studies of floral pigmentation with genealogical inference, to test for additional colour loci, and confirm the effect of previously described loci. This work demonstrates that flower colour variation is driven by a small number of large effect loci, while also hinting at the presence of a new candidate regulatory factor. Finally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of speciation around Rosea/Eluta to understand its evolutionary origins. My results show that it consists of 5 highly divergent loci, each of which is associated with flower colour. Using patterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps and a persistent localized barrier to gene flow within an otherwise permeable genome. Together, these chapters add to the increasing pool of studies using genealogical approaches to complement and extend site-based statistics to use haplotype structures in speciation research. By tracking haplotypes directly and connecting genealogical clustering to population processes, ARG-based inference promises to provide new insights into how local selective pressures, demographic history, and long-term barriers interact to shape the genomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about the benefits of using genealogical inference to learn more than what site-based statistics could tell us.}, author = {Pal, Arka}, issn = {2663-337X}, pages = {268}, publisher = {Institute of Science and Technology Austria}, title = {{Using genealogies to study the genomic basis of species divergence}}, doi = {10.15479/AT-ISTA-20694}, year = {2025}, } @phdthesis{20563, abstract = {The theory of optimal transport provides an elegant and powerful description of many evolution equations as gradient flows. The primary objective of this thesis is to adapt and extend the theory to deal with important equations that are not covered by the classical framework, specifically boundary value problems and kinetic equations. Additionally, we establish new results in periodic homogenization for discrete dynamical optimal transport and in quantization of measures. Section 1.1 serves as an invitation to the classical theory of optimal transport, including the main definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the main results of this thesis, outline the motivations, and review the current state of the art. In Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet boundary conditions. We construct a time-discrete scheme involving a modification of the Wasserstein distance and, under weak assumptions, prove its convergence to a solution of this boundary value problem. In dimension 1, we show that this solution is a gradient flow in a suitable space of measures. Chapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory of optimal transport to describe and study particle systems at the mesoscopic scale. We prove adapted versions of some fundamental theorems, including the Benamou–Brenier formula and the identification of absolutely continuous curves of measures. Chapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical transportation functionals on periodic graphs in the large-scale limit when the cost functional is asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge to 1-Wasserstein distances constructed from crystalline norms on R d . Chapter 5 concerns optimal empirical quantization: the problem of approximating a measure by the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein distance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for the minimal error as n tends to infinity. }, author = {Quattrocchi, Filippo}, issn = {2663-337X}, keywords = {optimal transport, kinetic equations, boundary value problems, quantization, gradient flows, homogenization}, pages = {240}, publisher = {Institute of Science and Technology Austria}, title = {{Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures}}, doi = {10.15479/AT-ISTA-20563}, year = {2025}, } @unpublished{20569, abstract = {This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.}, author = {Brigati, Giovanni and Maas, Jan and Quattrocchi, Filippo}, booktitle = {arXiv}, keywords = {optimal transport, kinetic theory, second-order discrepancy, Vlasov equation, Wasserstein splines.}, title = {{Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures}}, doi = {10.48550/arXiv.2502.15665}, year = {2025}, } @phdthesis{20798, 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{20777, author = {Zivadinovic, Predrag}, issn = {2663-337X}, pages = {104}, publisher = {Institute of Science and Technology Austria}, title = {{Scale-free activity as a basis for spatial learning and memory in the brain}}, doi = {10.15479/AT-ISTA-20777}, year = {2025}, } @article{12846, abstract = {We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.}, author = {Chern, Albert and Ishida, Sadashige}, issn = {2470-6566}, journal = {SIAM Journal on Applied Algebra and Geometry}, number = {3}, pages = {782--796}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Area formula for spherical polygons via prequantization}}, doi = {10.1137/23M1565255}, volume = {8}, year = {2024}, }