@phdthesis{17133, abstract = {An ideal quantum computer relies on qubits capable of performing fast gate operations and maintaining strong interconnections while preserving their quantum coherence. Since the inception of experimental eforts toward building a quantum computer, the community has faced challenges in engineering such a system. Among the various methods of implementing a quantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds, with the state-of-the-art reaching a coherence of a few milliseconds. However, achieving simultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits with high coherence require isolation from the environment, while fast operation necessitates strong coupling of the qubit. This thesis approaches this issue by proposing the idea of engineering superconducting qubits capable of transitioning between operating in a protected regime, where the qubit is completely isolated from the environment, and coupling to the communication channels as needed. In this direction, we use the geometric superinductor to scan the parameter space of rf-SQUID devices, searching for a regime where we can take the qubit protection to its extreme. This leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1 and EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier separating the local ground states of each quantum well. In this regime, although it is anticipated that the two quantum wells would be isolated from each other, we observe single fuxon tunneling between them. The interplay of the cavity photons and the fuxon transition forms a rich physical system, containing resonance conditions that allow the preparation of the fuxon ground or excited states. This enables us to study the relaxation rate of such transition and show that it can be as large as 3.6 hours. Dynamically controlling the barrier height between the two quantum wells allows for controllable coupling, which scales exponentially, for a qubit encoded in two fuxon states. The 0-π qubit is one of the very few known superconducting circuit types that ofers exponential protection from both relaxation and dephasing simultaneously. However, this qubit is not exempt from the fact that such protection comes at the expense of complex readout and control. In this thesis, we propose a way to controllably break the circuit symmetry, the key reason for the protection, to momentarily restore the ability to control and manipulate the qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental since they lead to coupling of the protected state to the thermally occupied parasitic mode of the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies and show that this can be used as a tunable coupler between the protected states. In the future, this should allow to perform gate operations by dynamically controlling the asymmetry instead of driving the protected transition with microwave pulses. Therefore, we believe that the proposed method can make the use of protected qubits more practical in experimental realizations of quantum computing.}, author = {Hassani, Farid}, isbn = {978-3-99078-040-4}, issn = {2663-337X}, keywords = {Quantum information, Qubits, Superconducting devices}, pages = {161}, publisher = {Institute of Science and Technology Austria}, title = {{Superconducting qubits capable of dynamic switching between protected and high-speed control regimes}}, doi = {10.15479/at:ista:17133}, year = {2024}, } @phdthesis{18135, abstract = {This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ and the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\rho^{2+2/d}$ with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \rho^2$ with an error smaller than $a_s \rho^2 (a_s\rho^{1/3})^{1-\eps}$ for any $\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. These asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis. In the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\Xi(T=0)/T_c$ approaches a universal constant $\pi e^{-\gamma}\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$.}, author = {Lauritsen, Asbjørn Bækgaard}, isbn = {978-3-99078-042-8}, issn = {2663-337X}, pages = {353}, publisher = {Institute of Science and Technology Austria}, title = {{Energies of dilute Fermi gases and universalities in BCS theory}}, doi = {10.15479/at:ista:18135}, year = {2024}, } @phdthesis{18076, abstract = {The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge spin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track to enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for such hybrid quantum circuits. In this thesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.}, author = {Sagi, Oliver}, issn = {2663-337X}, pages = {111}, publisher = {Institute of Science and Technology Austria}, title = {{Hybrid circuits on planar Germanium}}, doi = {10.15479/at:ista:18076}, year = {2024}, } @phdthesis{17206, abstract = {Males and females exhibit numerous differences, from the initial stages of sex determination to the development of secondary sexual characteristics. In Drosophila, these differences have been thoroughly studied. Extensive research has been performed to understand the role and molecular mode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal (Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to create sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is alternative splicing, the mechanism through which genes can produce multiple transcripts with distinct properties and functions. The primary switch sex-determining gene Sxl is a good example of the role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines the male or female form of the protein, which in turn switches on either the male or female developmental pathway. The genes that act upstream of Sxl and determine which form is expressed - the counter genes - have received less attention. This thesis addresses two critical questions about the molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms in male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary parameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in Drosophila-related species is investigated, shedding light on potential changes leading to their incorporation into the sex-determination pathway. For the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male midguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique transcript identifiers for each sequence of exons and introns in the read, enabling detailed comparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more pervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males), especially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive splice forms, suggesting most female exclusive splice forms originate there. Genome location and gene age were also correlated with the number of splice forms per gene. In particular, the X and 4th chromosomes (Muller elements A and F) showed more splice forms per gene than other chromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene than younger genes. Our results suggest that alternative splicing is more prevalent than previously believed, with numerous female-exclusive forms, age, and location playing significant roles in shaping its prevalence. For the counter genes analyses, we combined published gene expression, genomic, and gene interaction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus, Caenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra macrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite (her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster, which are most of the counter genes identified in the C. capitata genome. Their expression patterns during early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn, gro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between the species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn interactions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da, da-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were recruited by ancestral characteristics, primarily during embryogenesis. The conserved expression, location, and interactions of counter genes suggest serendipitous recruitment of such genes instead of a change in those characteristics as they were recruited for this function. }, author = {Raices, Julia}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination}}, doi = {10.15479/at:ista:17206}, year = {2024}, } @phdthesis{18101, abstract = {The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the Spumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the human immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which are regularly used as model systems to study the retroviral life cycle. The main structural component of the retroviruses, is the Gag protein and its truncation derivatives occurring during viral maturation. Orthoretroviral Gag assemblies have been extensively studied to understand the interactions that confer stability and morphology to viral particles. The Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae. Its members, the Foamy viruses (FV), share most of the conventional features found in retroviruses. However, they also possess multiple characteristics that make them unique. In particular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag architecture deviates from the canonical domain arrangement in FV. They also exhibit a peculiar particle morphology, having no apparent immature state and a seemingly icosahedral mature particle. Due to this, many fundamental questions on FV structural assembly mechanisms remain open. To answer these questions, was the main focus of this thesis. Mainly, it is not known how FV assemble their core in a virus particle and what are the important assembly interaction sites within said core. What is the minimum assembly competent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be interesting to know what is the evolutionary relationship between FV and the rest of the retrotranscribing elements, from a structural point of view? To answer these questions, membrane-enveloped mammalian cell-derived FV virus-like particles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested these FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with earlier observations. To further evaluate FV Gag assembly competence and morphology, the first bacterial cell-derived in vitro VLP assembly system was designed and optimized. Using this system with different truncation variants, the minimum assembly competent domain of FV Gag was found to be the putative CA300-477 domain. Varying VLP morphologies were also observed and strongly suggested residues upstream of CA300-477 play a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal assembly competent domain. This revealed an unexpectedly unique non-canonical assembly architecture. Three novel lattice stabilizing interfaces were described which proved to be as unique as the lattice arrangement. Comparison to a newly published FV CA core structure revealed the CA-CA interactions in the atypical assembly do not recapitulate what is described for the FV core lattice. However, the new in vitro VLP assembly system obtained in this thesis also provides an exciting opportunity to study still unresolved FV assembly features in a potentially facilitated approach compared to conventional methods. In summary, this work provided a deeper understanding of the basic FV Gag assembly unit, as well as presenting the first FV Gag-derived in vitro VLP assembly system. This system reveals a novel and unique assembly architecture among retroviral in vitro assemblies.}, author = {Porley, Dario J}, isbn = {978-3-99078-041-1}, issn = {2663-337X}, pages = {131}, publisher = {Institute of Science and Technology Austria}, title = {{Structural characterization of spumavirus capsid assemblies}}, doi = {10.15479/at:ista:18101}, year = {2024}, } @phdthesis{17465, abstract = {In the modern age of machine learning, artificial neural networks have become an integral part of many practical systems. One of the key ingredients of the success of the deep learning approach is recent computational advances which allowed the training of models with billions of parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a challenge for the theoretical analysis of modern models since “classical” statistical wisdom is no longer applicable. In this view, it is paramount to extend or develop new machinery that will allow tackling the neural network analysis under new challenging asymptotic regimes, which is the focus of this thesis. Large neural network systems are usually optimized via “local” search algorithms, such as stochastic gradient descent (SGD). However, given the high-dimensional nature of the parameter space, it is a priori not clear why such a crude “local” approach works so remarkably well in practice. We take a step towards demystifying this phenomenon by showing that the landscape of the SGD training dynamics exhibits a few beneficial properties for the optimization. First, we show that along the SGD trajectory an over-parameterized network is dropout stable. The emergence of dropout stability allows to conclude that the minima found by SGD are connected via a continuous path of small loss. This in turn means that the high-dimensional landscape of the neural network optimization problem is provably not so unfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD for an over-parameterized network tends to find solutions that are functionally more “simple”. This in turn means that the SGD minima are more robust, since a less complicated solution will less likely overfit the data. More formally, for a prototypical example of a wide two-layer ReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in its choice of an interpolating solution. Namely, at convergence the neural network implements a piece-wise linear function with the number of linear regions depending only on the amount of training data. This is in contrast to a “smooth”-like behaviour which one would expect given such a severe over-parameterization of the model. Diverging from the generic supervised setting of classification and regression problems, we analyze an auto-encoder model that is commonly used for representation learning and data compression. Despite the wide applicability of the auto-encoding paradigm, the theoretical understanding of their behaviour is limited even in the simplistic shallow case. The related work is restricted to extreme asymptotic regimes in which the auto-encoder is either severely over-parameterized or under-parameterized. In contrast, we provide a tight characterization for the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the input dimension and the size of the compressed representation obey the same asymptotics. We also show that gradient-based methods are able to find a globally optimal solution and that the predictions made for Gaussian data extrapolate beyond - to the case of compression of natural images. Next, we relax the Gaussian assumption and study more structured input sources. We show that the shallow model is sometimes agnostic to the structure of the data vii which results in a Gaussian-like behaviour. We prove that making the decoding component slightly less shallow is already enough to escape the “curse” of Gaussian performance. }, author = {Shevchenko, Aleksandr}, issn = {2663-337X}, pages = {232}, publisher = {Institute of Science and Technology Austria}, title = {{High-dimensional limits in artificial neural networks}}, doi = {10.15479/at:ista:17465}, year = {2024}, } @phdthesis{17119, abstract = {Genomes are shaped by natural selection at the level of the organism, as genomic variants that have a beneficial effect on the viability or fecundity of their carriers are on average expected to be passed on to more offspring than less beneficial alleles. However, selection also favors genomic variants that drive their own transmission to the next generation above the mendelian expectation of 50 percent in heterozygotes, even if these self-promoting variants are less beneficial to the organism than other variants at the same locus. Such variants, called meiotic drivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As meiotic drivers often require multiple genes and sequences for transmission ratio distortion, they are often found in regions of low recombination, such as inversions, which prevent their recombination with the non-driving homologous regions. Reduced recombination rates are expected to lead to the accumulation of deleterious mutations, which may affect hundreds of genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of self-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has systematically investigated the level of degeneration on a meiotic driver. Further, the low rates of recombination between driving and non-driving haplotypes have limited the power of traditional genetic studies in uncovering the gene content of meiotic drivers, and made the the identification of the genes causing transmission ratio distortion difficult. After an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that make use of next generation sequencing data to characterize the sequence and expression evolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is transmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents a comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of sequence degeneration counteracted by occasional recombination with the non-driving homolog over large parts of the meiotic driver, proposing an explanation for its long-term survival. Chapter 3 investigates the sequence and expression evolution of genes on the t-haplotype, and finds widespread expression and copy number changes and signs of less efficient purifying selection compared to the genes on the non-driving homolog. Further, this chapter finds candidates for involvment in drive: two positively selected genes on the t-haplotype, and the discovery of a t-specific gene duplicate, which was gained from another chromosome, and which acquired novel sequence and testis-specific expression on the t-haplotype. Finally, Chapter 4 provides unprecedented insights into the gene expression landscape in testes of t-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the comparison of expression in spermatids carrying or not carrying the t-haplotype as well as the timing of t-haplotype-induced expression changes along spermatogenesis. This study shows the timing of previously found drive-associated genes, and uncovers novel candidate genes and biological processes that may underlie the complex biology of transmission ratio distortion of the t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in the context of the current state of meiotic drive research.}, author = {Kelemen, Réka K}, isbn = {978-3-99078-039-8}, issn = {2663-337X}, keywords = {meiotic driver, neofunctionalization, single nucleus sequencing}, pages = {105}, publisher = {Institute of Science and Technology Austria}, title = {{Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver}}, doi = {10.15479/at:ista:17119}, year = {2024}, } @phdthesis{18477, abstract = {ADAR1 is broadly expressed across various tissues and is vital in regulating pathways associated with innate immune responses. ADAR1 marks double-stranded RNA as "self" through its A-to-I editing activity, effectively repressing autoimmunity and maintaining immune tolerance. This editing process has been detected at millions of sites across the human genome. However, the mechanism underlying ADAR1's substrate selectivity properties remains largely unclear, with much of the current knowledge derived from comparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex with its RNA substrates and applying a combination of biochemical techniques and structural studies using CryoEM, we aim to gain a more comprehensive understanding of the substrate selectivity characteristics of ADAR1. In this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the first report in the literature to achieve high protein purity and activity. This advancement enabled the investigation of complex formation between ADAR1 and various RNA substrates, leading to the identification of optimal conditions for preparing the cryoEM sample. However, despite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the desired quality, highlighting the need for similar rigorous optimization of the RNA substrates to facilitate structural studies of the ADAR1-RNA complex. The study was complemented by AlphaFold predictions, which provided some insights into this mechanism. Moreover, during this project I established a collaboration with a research group focused on studying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it was further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific oysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to significant losses in oyster populations globally. I successfully purified oyster ADAR and prepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology capable of detecting modified nucleotides without the need for reverse transcription. The collaborators initiated optimization of this nanopore-based approach. However, current technological limitations still constrain the reliable detection of modified nucleotides. The project also examined the impact of RNA editing on RNA binding and filament formation by MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target of ADAR1's editing activity is RNA derived from repetitive elements present in the genome, particularly Alu elements forming double-stranded RNA. When unedited, these RNA sequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with Alu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well understood. The interaction between MDA5 and Alu elements, was successfully established. This was achieved through the testing of different RNA variants and the evaluation of filament formation using binding techniques and electron microscopy imaging. This groundwork has set the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I editing on the binding properties of MDA5 with Alu RNA were investigated. Given the recent research that has provided new insights into MDA5's interaction with dsRNA, it is essential to revise the experimental setup to integrate these findings before moving forward with the CryoEM sample analysis.}, author = {Kaczmarek, Beata M}, isbn = {978-3-99078-045-9}, issn = {2663-337X}, pages = {124}, publisher = {Institute of Science and Technology Austria}, title = {{Biochemical and structural insights into ADAR1 RNA editing}}, doi = {10.15479/at:ista:18477}, year = {2024}, } @phdthesis{17319, abstract = {This thesis comprises two distinct projects, each offering unique insights into fundamental cellular processes. While distinct in their focus, these different perspectives have a common theme: chemiosmotic theory and utilisation of the proton gradient for driving the essential processes like auxin efflux and ATP synthesis, effectively bridging the membrane protein structure and function from the realms of plant biology and cellular bioenergetics. The first project of this thesis centres on the characterisation of PIN proteins, a class of transmembrane transporters pivotal in the regulation of auxin transport and distribution in plants. PINs form a conserved and phylogenetically abundant group of transporters present in land plants and certain algae. Despite their great importance, they were one of the few elusive proteins essential for plant development not to be structurally and mechanistically characterised since their discovery almost 30 years ago. This work aimed to uncover the structural and functional dynamics of the PIN protein-mediated auxin transport using an array of experimental techniques, including protein purification, biochemical assays and structural analysis. Through an exhaustive screening process that took several years and included testing different PIN homologues, expression systems, constructs, and purification conditions, we developed a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein. Moreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8 exhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0) being optimal for the stability of the protein. Using SEC-MALS and crosslinking, we determined that PIN8 forms dimers, which was confirmed by our structural studies. We obtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures, our map implies major pH-dependent conformational changes and possibly utilisation of the proton gradient in the transport mechanism. The subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental to cellular energy metabolism. Through an approach integrating biochemical assays and structural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP synthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using submitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to published data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions. Moreover, we found that yaku´amide inhibitory activity is proton motive force (pmf) dependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained maps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å, 8 State 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps; however, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on the protein due to either resolution limits or suboptimal binding of the inhibitor.}, author = {Lukic, Kristina}, issn = {2663-337X}, pages = {224}, publisher = {Institute of Science and Technology Austria}, title = {{Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B}}, doi = {10.15479/at:ista:17319}, year = {2024}, } @phdthesis{17346, abstract = {Acquiring, retaining, and retrieving information over a wide range of timescales are crucial functions of the brain. The successful processing of memories affects many aspects of our lives and enables us and many other organisms to operate in a complex environment and to interact with it. In this context, the hippocampus and functionally connected brain areas, such as the prefrontal cortex, are central and have been subject to intensive research in the past decades. Storage of memories is believed to rely on distributed neural activity within these neural circuits. Additionally, neural memory traces of recent experience are reinstated during periods of rest or sleep. These reactivations are thought to play an outstanding role in the consolidation of memories and potentially facilitate the transfer of information from the hippocampus to cortical areas for long-term storage and integration into existing knowledge. However, there is growing evidence that memory-related neural representations in the hippocampus are not as stable as initially thought and that they change even in the absence of learning. It has been suggested that these changes reflect the accumulation of experience, but the influence of interspersed consolidation periods has not been considered. Previous studies have analyzed consolidation periods by detecting activity that strongly resembled neural activity during the acquisition of memory. Besides being often limited to only non-rapid eye movement (NREM) sleep, the used approaches were not capable of tracking changes in neural representations over extended temporal periods. More fluid representations do not only challenge our understanding of how information is stored, but they also affect the transfer of information between brain areas during the consolidation process. For this thesis, I investigated the evolution of memory-related activity during sleep periods expected to be involved in consolidation in the hippocampus and between the hippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus gradually transformed during prolonged periods of sleep and inactivity. In the beginning, neural activity strongly resembled acquisition activity, whereas, with the progression of time, it became more similar to the subsequent recall activity. NREM periods drove this process, while rapid-eye movement (REM) periods showed a resetting effect. This reactivation drift was due to firing rate changes of a subset of cells and mirrored the representational changes from the acquisition to the recall. A stable subset of cells withstood the drift and maintained their activity. Therefore, my results indicate that memory-related representations undergo spontaneous modifications during consolidation periods and that these changes are predictive of representational drift. Furthermore, I found that the amount of change in the neural activity during subsequent sleep periods was biased by prior behavioral performance. Observed changes in the hippocampus and the prefrontal cortex were synchronized and increased after poor performance, highlighting a potential role in the exchange of information. Low-variance vii periods with distinct, more stable activity from a subset of cells significantly contributed to the heightened synchrony between both areas. Hence, interleaved phases of more stable neural activity could facilitate the information transfer between brain areas. In conclusion, my investigations underline the fluidity of memory-related representations and assign a prominent role to sleep reactivation periods in their evolution. In addition, I identified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling and integrating findings from both spontaneous and behaviorally-related representational changes in functionally related brain areas will help to broaden our understanding of how knowledge is stored, maintained, updated, and transferred between brain areas.}, author = {Bollmann, Lars}, issn = {2663-337X}, keywords = {Memory, Hippocampus, Consolidation}, pages = {103}, publisher = {Institute of Science and Technology Austria}, title = {{Stability and change in the memory system during rest}}, doi = {10.15479/at:ista:17346}, year = {2024}, } @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}, }