@phdthesis{14821, abstract = {The hippocampus is central to memory formation, storage and retrieval over many timescales. Neurons in this brain area are highly selective to spatial position as well as to many other variables of the environment. It is believed that the selectivity patterns of hippocampal neurons reflect the structure of tasks an animal performs. However, especially at timescales longer than a few minutes or hours it is not fully known how these representations evolve, nor how they map to behaviour in the process. In this thesis, I monitored the evolution of hippocampal representations in a novel spatial-associative memory task for rats. Reward locations were associated with global sensory cues (i.e. context); animals had to remember the associations and dig for food in those locations only. I used in vivo electrophysiology to record the activity of the hippocampus dorsal CA1 neurons during the learning period of a few days. I report here a novel and simple method to classify behaviour performance to account for individual variability in learning speed and spurious performance unrelated to true task rule learning. Using this classification I was then able to investigate neural responses on different stages of learning matched across animals. On the first day of learning, I observed a fast formation of single-cell selectivity to task variables which remained stable over days. I also observed that reward tuning was not a single process but dependent on task-related cognitive load. At the population level, a linear decoding approach revealed a hierarchy in the representation of task variables that changed with learning. In the high-dimensional space of population activity, the representation of contexts was specific to each position in the maze, and could thus be better decoded if the position was known. The decoding of position did not improve with knowledge of other variables. As learning progressed, the hippocampal code underwent a reorganisation of high-variance directions in population activity, identified by principal component analysis. I found that dominant dimensions started carrying increasing amounts of information about task context specifically at those positions where it mattered for task performance. When I contrasted this with variables less relevant to task performance (e.g. movement direction), I did not observe differences in decoding quality over positions nor a reduction of dimensionality with learning. Overall, the largest changes in CA1 neural response with task learning happened in a matter of a few trials; over days, changes undetectable in single-cell statistics were responsible for re-structuring the hierarchy of neural representations at the population level; these changes were task-specific and reflected different stages of learning. This indicates that complex task learning may involve different magnitudes of response modulation in CA1, which happen at specific time scales linked to behaviour.}, author = {Chiossi, Heloisa}, issn = {2663-337X}, pages = {89}, publisher = {Institute of Science and Technology Austria}, title = {{Adaptive hierarchical representations in the hippocampus}}, doi = {10.15479/at:ista:14821}, year = {2024}, } @phdthesis{18129, abstract = {State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate for qubits due to their long coherence, tunability, control, and readout. However, their natural coupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours. Long-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a coherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of high-impedance resonators to compensate for this has gained significant attention in the past decade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not exceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The large kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude enhancement. However, fully exploiting the potential of disordered or granular superconductors is challenging as their impedances close to the superconductor-to-insulator transition are difficult to control reproducibly. We report on the realization of a wireless ohmmeter which allows in situ resistance measurements during film deposition and, therefore, indirect control of the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators with characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due to the large sheet kinetic inductance of up to 3 nH □−1 . By integrating an 8 kW resonator with a germanium double QD, we demonstrate a strong charge-photon coupling with the highest rate reported, 566 MHz. The demonstrated method and grAl properties make these resonators suitable for boosting the spin-photon coupling strength, a crucial requirement for fast, high-fidelity, long-distance two-qubit gates. }, author = {Janik, Marian}, issn = {2663-337X}, pages = {164}, publisher = {Institute of Science and Technology Austria}, title = {{Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors}}, doi = {10.15479/at:ista:18129}, year = {2024}, } @phdthesis{15101, abstract = {The coupling between presynaptic Ca2+ channels and release sensors is a key factor that determines speed and efficacy of synapse transmission. At some excitatory synapses, channel–sensor coupling becomes tighter during development, and tightening is often associated with a switch in the reliance on different Ca2+ channel subtypes. However, the coupling topography at many synapses remains unknown, and it is unclear how it changes during development. To address this question, we analyzed the coupling configuration at the cerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages, combining biophysical analysis, structural analysis, and modeling. Quantal analysis of BC–PC indicated that release probability decreased, while the number of functional sites increased during development. Although transmitter release persistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects of the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased during development, indicative of tightening of source-sensor coupling. Furthermore, presynaptic action potentials became shorter during development, suggesting reduced efficacy of Ca2+ channel activation. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. The number of functional release sites correlated better with the AZ number early in development, but match better with the Ca2+ channel cluster number at later stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.}, author = {Chen, JingJing}, issn = {2663-337X}, pages = {84}, publisher = {Institute of Science and Technology Austria}, title = {{Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse}}, doi = {10.15479/at:ista:15101}, year = {2024}, } @phdthesis{17881, abstract = {This work can be broadly classified into the study of critical phenomena in a one dimensional array of Josephson junctions. While we study quantum criticality when the array is in thermal equilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the array at a critical non-zero bias. This work furthers our knowledge in understanding quantum critical behaviour at finite temperatures in a one dimensional Josephson array, while also establishing relaxation behaviour dual to that observed in a single Josephson junction. Chapter 1 briefly introduces the model to understand superconductor-insulator phase transition in a one dimensional Josephson array and points out the state of the field from where we started our zero-bias experiments. In this context it discusses the phase-charge duality observed in a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the ground for our non-equilibrium study of the array. Chapter 2 shows the experimental setup and the chip layout of the device we measured. In chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads to a regime of superconductivity at high temperature, arising from the melted zero-temperature insulator. Our results quantitatively explain the low-temperature onset of superconductivity in nominally insulating regimes, and the transition to the strongly insulating phase. We further present, to our knowledge, the first understanding of the onset of anomalous-metallic resistance saturation [30]. This work demonstrates a non-trivial interplay between thermal effects and quantum criticality. A practical consequence is that, counterintuitively, the coherence of high-impedance quantum circuits is expected to be stabilized by thermal fluctuations. In chapter 4, we show relaxation oscillations in a current-biased one dimensional array of Josephson junctions. These oscillations are well described by a circuit model, dual to the ordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in current plateaux. The relaxation step is found to obey a characteristic self-consistent relation, suggesting that it is governed by overheating effects. Chapter 5 describes the various checks and analysis we performed to support our conclusions made in chapters 3 and 4. Finally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic simulations we performed to fabricate our devices.}, author = {Mukhopadhyay, Soham}, isbn = {978-3-99078-043-5}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Thermal effects in one dimensional Josephson chains}}, doi = {10.15479/at:ista:17881}, year = {2024}, } @phdthesis{18531, abstract = {Sex chromosomes and autosomes exhibit very different evolutionary dynamics. The Y chromosome usually degenerates, leaving many X-linked loci hemizygous in males. Since recessive X-linked mutations are always exposed to selection in males, selection is more efficient on the X chromosome than on autosomes on recessive mutations, leading to faster adaptation on the X chromosome than other genomic regions, if beneficial mutations are on average recessive (known as the Faster-X effect). In the presence of the functional, but non-recombining gametolog on the Y (as is often the case in young non-recombining regions), recessive mutations are sheltered from selection on the X chromosome. We model this scenario and show that the efficiency of selection is reduced on diploid X loci due to sheltering by the Y chromosome. Reduced efficiency of selection leads to slower adaptation and increased accumulation of deleterious mutations (Slower-X effect). We extended this model to explore the effect of sex-specific selection on degeneration of sex chromosomes, showing theoretically that male-limited genes degenerate on the X chromosome and female-biased genes degenerate on the Y chromosome. This prediction depends on the effective population size and the mutation rate, explaining the variety of sex chromosome degeneration patterns observed in nature. To test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the ZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very young non-recombining region with non-degenerated W. Diploid Z-linked genes have higher ratios of non-synonymous to synonymous polymorphisms than autosomal genes, supporting reduced efficiency of selection on the diploid Z region. These results provide evidence of sheltering by the W chromosome, a mechanism that could contribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary patterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young (diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. }, author = {Mrnjavac, Andrea}, issn = {2663-337X}, keywords = {Sex chromosomes, evolution, selection, sheltering}, pages = {181}, publisher = {Institute of Science and Technology Austria}, title = {{Early stages of sex chromosome evolution}}, doi = {10.15479/at:ista:18531}, year = {2024}, } @phdthesis{18661, abstract = {Across the tree of life, distinct designs of cellular membranes have evolved that are both stable and flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids that self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess both bilayer and double-headed, monolayer spanning bolalipids. This composition is believed to enable extremophile archaea to survive harsh environments. Here, through the creation of a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of bolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble bilayer membranes as they can adopt U-shaped conformations to enable higher curvatures. Conversely, rigid bolalipid molecules, like those found in archaea at higher temperatures, preferentially take on a straight conformation to self-assemble into liquid membranes that are stable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly, however, our analysis reveals that it is possible to achieve the best of both worlds – membranes that are fluid, stable at high temperatures and flexible enough to be reshaped without leaking – through the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally, the curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive conformation can also enable high rigidity at low curvatures while softening at high curvatures, making the membrane effectively a plastic material. Taken together, our study compares the different membrane designs across the tree of life and indicates how combining lipids can be used to resolve trade-offs when generating membranes for (bio)technological applications. }, author = {Santana de Freitas Amaral, Miguel}, isbn = {978-3-99078-046-6}, issn = {2663-337X}, pages = {57}, publisher = {Institute of Science and Technology Austria}, title = {{Archaeal membranes : In silico modelling and design}}, doi = {10.15479/at:ista:18661}, year = {2024}, } @phdthesis{18104, abstract = {We introduce a new all-electric platform, that strong couples light to mechanical motion by ensuring that the external environmental coupling dominates over internal mechanical dissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which a metallized silicon nitride membrane is fipped on top of the device under test. This everyday electromechanical device can be operated at low or room temperature and has 10000× lower insertion loss than a comparable commercial quartz crystal, achieves a position imprecision matching state-of-the-art optical interferometer, and enables remote cooling of mechanical motion. The spatial properties of higher order mechanical modes are a promising feature for reconstructing unknown charge distributions. }, author = {Puglia, Denise}, issn = {2663-337X}, pages = {63}, publisher = {Institute of Science and Technology Austria}, title = {{Everyday electromechanics: Capacitive strong coupling to mechanical motion}}, doi = {10.15479/at:ista:18104}, year = {2024}, } @phdthesis{18642, abstract = {This thesis consists of two pieces of work in the broader feld of computational biology, both of which are methods for the analysis of large scale biological data, implemented in efcient software. Chapter 2 introduces a statistical software for causal discovery and inference from observed genetic marker and phenotypic trait data. We explore in simulation how well the method can fne-map genetic efects, fnd the correct causal structure among tens of traits and millions of genetic markers, and infer the causal efect size for the discovered causal relations. We then apply the method to 8 million markers and 17 traits from the UK Biobank and show that many relationships found with other methods are likely due to the efects of hidden confounders. Chapter 3 describes how this method can be applied to longitudinal data. I show how one can incorporate the background knowledge present in the known order of measurements to improve the accuracy of the causal discovery process, and explore the method’s ability to identify age specifc genetic efects, and how the error rates of this recovery are infuenced by missing data due to diferent censoring mechanisms. Chapter 4 introduces a statistical software for the comparison of chromatin contact maps based on the structural similarity index. We explore the robustness of the method to noise and size diferences of the compared maps, show how it can measure evolutionary conservation of topological features by providing a similarity ranking of syntenic regions, and fnally how it can detect alterations in 3D genome structure due to genetic mutations in samples of medical relevance. }, author = {Machnik, Nick N}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Algorithms for causal learning and comparative analysis for genomic data}}, doi = {10.15479/at:ista:18642}, year = {2024}, } @phdthesis{18574, abstract = {Biological vision is unlike a camera; rather than transmitting light information faithfully, early visual circuits process the visual scene to convey only the relevant information in an efficient manner. Consequentially, the nature of this visual processing then depends on what is the relevant information in a scene and on the notion of efficiency. In this work, I study how visual processing is modulated by two different variations in the visual scene. First, I discovered that in the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual field have differences in the center surround structure of their receptive fields. Comparison with models of efficient coding show that this adaptation likely evolved to cope with the brightness gradient from the sky to the ground that is pervasive in natural scenes. In the second project, I study how the downstream neurons in the Superior Colliculus dynamically change their temporal selectivity depending on the ambient luminance and behavioral state. As the scene gets darker or when the animal is is less aroused, the neuronal responses get laggier, while still maintaining their relative timing with respect to the population. Overall, this work emphasises the need to understand visual processing in the context of specific demands of the animal in its the environment. The adaptive changes in the visual system, from the retinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological vision optimizes the processing of visual information. }, author = {Gupta, Divyansh}, isbn = {978-3-99078-050-3}, issn = {2663-337X}, pages = {86}, publisher = {Institute of Science and Technology Austria}, title = {{Visual adaptations to natural statistics}}, doi = {10.15479/at:ista:18574}, year = {2024}, } @phdthesis{18471, abstract = {Spatial omics technologies are enriching our understanding of complex biological samples, by allowing us to study their molecular composition while preserving the spatial relationships between molecules in their native context. As the field continues to advance, there are technical challenges that need to be addressed in order to take full advantage of the spatial capabilities of these methods. In this work, I present two technical developments that I established for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the spatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain transcriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it with stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a spatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse brain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which provides an unbiased morphological readout by labeling the extracellular domain. I successfully established this method, which we call CATS-MERFISH-ExM, to work with thick mouse brain slices, being able to extract transcriptomics information with 3D tissue context. CATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular distribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific transcriptome. This method provides integrated information on cellular structure and transcriptomes in situ, and could potentially be applied with other modalities, opening new avenues for scientific discovery. }, author = {Agudelo Duenas, Nathalie}, isbn = {978-3-99078-044-2}, issn = {2663-337X}, pages = {97}, publisher = {Institute of Science and Technology Austria}, title = {{Visualizing the neuronal transcriptional landscape with tissue context}}, doi = {10.15479/at:ista:18471}, year = {2024}, } @phdthesis{12716, abstract = {The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process. Our knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.}, author = {Burnett, Laura}, issn = {2663-337X}, pages = {178}, publisher = {Institute of Science and Technology Austria}, title = {{To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism}}, doi = {10.15479/at:ista:12716}, year = {2023}, } @phdthesis{14547, abstract = {Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation. Despite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood. In this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. The second focuses on a technological application, a gate-tunable Josephson parametric amplifier. In the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well. We embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance. The behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \pm ip$ pairing in InAs. Measuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory. We observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory. In contrast, the data can be captured quantitatively by fitting to a two-component model. We find the evidence of the intraband $p \pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\mathrm{T}$. From the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined. By systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle. Strong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data. In the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element. The device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator. By applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz. Modelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage. We observed gate-tunable Kerr nonlinearity qualitatively in line with expectation. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency. In general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared. The noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier. As a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account. We found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.}, author = {Phan, Duc T}, issn = {2663-337X}, keywords = {superconductor-semiconductor, superconductivity, Al, InAs, p-wave, superconductivity, JPA, microwave}, pages = {80}, publisher = {Institute of Science and Technology Austria}, title = {{Resonant microwave spectroscopy of Al-InAs}}, doi = {10.15479/14547}, year = {2023}, } @phdthesis{14058, abstract = {Females and males across species are subject to divergent selective pressures arising from di↵erent reproductive interests and ecological niches. This often translates into a intricate array of sex-specific natural and sexual selection on traits that have a shared genetic basis between both sexes, causing a genetic sexual conflict. The resolution of this conflict mostly relies on the evolution of sex-specific expression of the shared genes, leading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought to evolve via modifications of the genetic networks ultimately linked to sex-determining transcription factors. Although much empirical and theoretical evidence supports this standard picture of the molecular basis of sexual conflict resolution, there still are a few open questions regarding the complex array of selective forces driving phenotypic di↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis. First, how do patterns of phenotypic sexual dimorphism vary within populations, as a response to the temporal and spatial changes in sex-specific selective forces? To tackle this question, I analyze the patterns of sex-specific phenotypic variation along three life stages and across populations spanning the whole geographical range of Rumex hastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis. Second, how do gene expression patterns lead to phenotypic dimorphism, and what are the molecular mechanisms underlying the observed transcriptomic variation? I address this question by examining the sex- and tissue-specific expression variation in newly-generated datasets of sex-specific expression in heads and gonads of Drosophila melanogaster. I additionally used two complementary approaches for the study of the genetic basis of sex di↵erences in gene expression in the second and third Chapters of the thesis. Third, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual dimorphism? I develop models of sex-specific stabilizing selection, mutation and drift to formalize common intuition regarding the patterns of covariation between intersex correlation and sexual dimorphism in the fourth Chapter of the thesis. Alltogether, the work described in this PhD thesis provides useful insights into the links between genetic, transcriptomic and phenotypic layers of sex-specific variation, and contributes to our general understanding of the dynamics of sexual dimorphism evolution.}, author = {Puixeu Sala, Gemma}, isbn = {978-3-99078-035-0}, issn = {2663-337X}, pages = {230}, publisher = {Institute of Science and Technology Austria}, title = {{The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation}}, doi = {10.15479/at:ista:14058}, year = {2023}, } @phdthesis{12885, abstract = {High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. }, author = {Calcabrini, Mariano}, isbn = {978-3-99078-028-2}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Nanoparticle-based semiconductor solids: From synthesis to consolidation}}, doi = {10.15479/at:ista:12885}, year = {2023}, } @phdthesis{12732, abstract = {Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices. Going beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium. In this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models. In particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models. Using tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods. In this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges. Inspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect. In the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model. The system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping. We show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon. We further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes. The study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times. This work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies. Next, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density. This feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies. The time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities. Our results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument. To support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied. In the last Chapter of this Thesis, we address the topic of many-body localization proximity effect. We study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons. The interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques. Our simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong. We furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory. Finally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.}, author = {Brighi, Pietro}, issn = {2663-337X}, pages = {158}, publisher = {Institute of Science and Technology Austria}, title = {{Ergodicity breaking in disordered and kinetically constrained quantum many-body systems}}, doi = {10.15479/at:ista:12732}, year = {2023}, } @phdthesis{12826, abstract = {During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. Firstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations. Secondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns. Taken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.}, author = {Pokusaeva, Victoria}, issn = {2663-337X}, pages = {106}, publisher = {Institute of Science and Technology Austria}, title = {{Neural control of optic flow-based navigation in Drosophila melanogaster}}, doi = {10.15479/at:ista:12826}, year = {2023}, } @phdthesis{13286, abstract = {Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices.}, author = {Valentini, Marco}, issn = {2663-337X}, pages = {184}, publisher = {Institute of Science and Technology Austria}, title = {{Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium}}, doi = {10.15479/at:ista:13286}, year = {2023}, } @phdthesis{14374, abstract = {Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary. BCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries. For Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary. Second, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality. In the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.}, author = {Roos, Barbara}, issn = {2663-337X}, pages = {206}, publisher = {Institute of Science and Technology Austria}, title = {{Boundary superconductivity in BCS theory}}, doi = {10.15479/at:ista:14374}, year = {2023}, } @phdthesis{14539, abstract = {Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal verification and control of finite state stochastic systems, a subfield of formal methods also known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively less attention. However, infinite state stochastic systems commonly arise in practice. For instance, probabilistic models that contain continuous probability distributions such as normal or uniform, or stochastic dynamical systems which are a classical model for control under uncertainty, both give rise to infinite state systems. The goal of this thesis is to contribute to laying theoretical and algorithmic foundations of fully automated formal verification and control of infinite state stochastic systems, with a particular focus on systems that may be executed over a long or infinite time. We consider formal verification of infinite state stochastic systems in the setting of static analysis of probabilistic programs and formal control in the setting of controller synthesis in stochastic dynamical systems. For both problems, we present some of the first fully automated methods for probabilistic (a.k.a. quantitative) reachability and safety analysis applicable to infinite time horizon systems. We also advance the state of the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems. Finally, for formal controller synthesis in stochastic dynamical systems, we present a novel framework for learning neural network control policies in stochastic dynamical systems with formal guarantees on correctness with respect to quantitative reachability, safety or reach-avoid specifications. }, author = {Zikelic, Dorde}, isbn = {978-3-99078-036-7}, issn = {2663-337X}, pages = {256}, publisher = {Institute of Science and Technology Austria}, title = {{Automated verification and control of infinite state stochastic systems}}, doi = {10.15479/14539}, year = {2023}, } @phdthesis{14587, abstract = {This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations. First, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids. The core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting. This thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift. In the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem. At last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.}, author = {Marveggio, Alice}, issn = {2663-337X}, pages = {228}, publisher = {Institute of Science and Technology Austria}, title = {{Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences}}, doi = {10.15479/at:ista:14587}, year = {2023}, }