@phdthesis{11626,
  abstract     = {Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.},
  author       = {Gallei, Michelle C},
  isbn         = {978-3-99078-019-0},
  issn         = {2663-337X},
  pages        = {248},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana}},
  doi          = {10.15479/at:ista:11626},
  year         = {2022},
}

@phdthesis{10799,
  abstract     = {Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the
sake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range
of training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the
data they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.},
  author       = {Konstantinov, Nikola H},
  isbn         = {978-3-99078-015-2},
  issn         = {2663-337X},
  keywords     = {robustness, fairness, machine learning, PAC learning, adversarial learning},
  pages        = {176},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Robustness and fairness in machine learning}},
  doi          = {10.15479/at:ista:10799},
  year         = {2022},
}

@phdthesis{10759,
  abstract     = {In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data.},
  author       = {Rzadkowski, Wojciech},
  issn         = {2663-337X},
  pages        = {120},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Analytic and machine learning approaches to composite quantum impurities}},
  doi          = {10.15479/at:ista:10759},
  year         = {2022},
}

@phdthesis{12390,
  abstract     = {The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that
is broken on the level of the corresponding effective theory. In particular we are going to
investigate translation-invariant Bose gases in the mean field limit, effectively described by
the Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively
described by the Pekar functional. The latter is a model describing the interaction between a
charged particle and the optical modes of a polar crystal. Regarding the former, we assume in
addition that the particles in the gas are unconfined, and typically we will consider particles
that are subject to an attractive interaction. In both cases the ground state energy of the
Hamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on
the contrary there exists a whole invariant orbit of minimizers for the corresponding effective
functionals. Both, the absence of proper eigenstates and the broken symmetry of the effective
theory, make the study significantly more involved and it is the content of this thesis to
develop a frameworks which allows for a systematic way to circumvent these issues.
It is a well-established result that the ground state energy of Bose gases in the mean field limit,
as well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is
to leading order given by the minimal energy of the corresponding effective theory. As part
of this thesis we identify the sub-leading term in the expansion of the ground state energy,
which can be interpreted as the quantum correction to the classical energy, since the effective
theories under consideration can be seen as classical counterparts.
We are further going to establish an asymptotic expression for the energy-momentum relation
of the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,
this asymptotic expression agrees with the energy-momentum relation of a free particle having
an effectively increased mass, and we find that this effectively increased mass agrees with the
conjectured value in the physics literature.
In addition we will discuss two unrelated papers written by the author during his stay at ISTA
in the appendix. The first one concerns the realization of anyons, which are quasi-particles
acquiring a non-trivial phase under the exchange of two particles, as molecular impurities.
The second one provides a classification of those vector fields defined on a given manifold
that can be written as the gradient of a given functional with respect to a suitable metric,
provided that some mild smoothness assumptions hold. This classification is subsequently
used to identify those quantum Markov semigroups that can be written as a gradient flow of
the relative entropy.
},
  author       = {Brooks, Morris},
  issn         = {2663-337X},
  pages        = {196},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Translation-invariant quantum systems with effectively broken symmetry}},
  doi          = {10.15479/at:ista:12390},
  year         = {2022},
}

@phdthesis{12358,
  abstract     = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and
visual complexity. The small-scale interactions of yarns colliding with and pulling on each
other result in drastically different large-scale stretching and bending behavior, introducing
anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this
complexity and match the quality of real fabric, it may be too computationally expensive for
large fabrics. On the other hand, continuum-based approaches do not need to discretize the
cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the
large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,
we discuss three methods to try and bridge the gap between small-scale and large-scale yarn
mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively
fitting yarn parameters to physical measurements of real fabric.
To start, we present a method for animating yarn-level cloth effects using a thin-shell solver.
We first use a large number of periodic yarn-level simulations to build a model of the potential
energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The
resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics
and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of
full yarn-level simulation.
While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack
the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate
yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware
fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are
able to reproduce effects such as knit loops tightening under stretching at negligible cost.
Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,
based on the mechanical response of fabrics in the real world. We compile a database from
physical tests of several knitted fabrics used in the textile industry spanning diverse physical
properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized
shell models to speed up computation and adding some small-but-necessary extensions to
yarn-level models used in computer graphics.
},
  author       = {Sperl, Georg},
  isbn         = {978-3-99078-020-6},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}},
  doi          = {10.15479/at:ista:12103},
  year         = {2022},
}

@phdthesis{11196,
  abstract     = {One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). 
	In addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.
},
  author       = {Kim, Olena},
  issn         = {2663-337X},
  pages        = {132},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses}},
  doi          = {10.15479/at:ista:11196},
  year         = {2022},
}

@phdthesis{10727,
  abstract     = {Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).
In the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.
In the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.
First, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.
In the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.},
  author       = {Metzler, Sina},
  issn         = {2663-337X},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Pathogen-mediated sexual selection and immunization in ant colonies}},
  doi          = {10.15479/AT:ISTA:10727},
  year         = {2022},
}

@phdthesis{11879,
  abstract     = {As the overall global mean surface temperature is increasing due to climate change, plant
adaptation to those stressful conditions is of utmost importance for their survival. Plants are
sessile organisms, thus to compensate for their lack of mobility, they evolved a variety of
mechanisms enabling them to flexibly adjust their physiological, growth and developmental
processes to fluctuating temperatures and to survive in harsh environments. While these unique
adaptation abilities provide an important evolutionary advantage, overall modulation of plant
growth and developmental program due to non-optimal temperature negatively affects biomass
production, crop productivity or sensitivity to pathogens. Thus, understanding molecular
processes underlying plant adaptation to increased temperature can provide important
resources for breeding strategies to ensure sufficient agricultural food production.
An increase in ambient temperature by a few degrees leads to profound changes in organ growth
including enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and
cotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,
one of the best-studied growth hormones, plays an essential role in this process by direct
activation of transcriptional and non-transcriptional processes resulting in elongation growth
(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature
(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key
components of the polar auxin transport (PAT) machinery, which controls the amount and
direction of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,
PIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT
through either chemical or genetic means dramatically affecting the adaptive responses to hAT.
Intriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether
and how PINs at the level of expression adapt to fluctuation in temperature is scarcely
understood.
With genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN
auxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via
adjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we
identified three Zinc-Finger (ZF) transcription factors as novel molecular components of the
thermo-regulatory network, which through negative regulation of PIN transcription adjust the
transport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the
negative feedback loop attenuating the activity of the thermo-sensing pathway to restrain
exaggerated growth and developmental responses to hAT.},
  author       = {Artner, Christina},
  isbn         = {978-3-99078-022-0},
  issn         = {2663-337X},
  keywords     = {high ambient temperature, auxin, PINs, Zinc-Finger proteins, thermomorphogenesis, stress},
  pages        = {128},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature}},
  doi          = {10.15479/at:ista:11879},
  year         = {2022},
}

@phdthesis{12364,
  abstract     = {Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders characterized by behavioral symptoms such as problems in social communication and interaction, as
well as repetitive, restricted behaviors and interests. These disorders show a high degree
of heritability and hundreds of risk genes have been identifed using high throughput
sequencing technologies. This genetic heterogeneity has hampered eforts in understanding
the pathogenesis of ASD but at the same time given rise to the concept of convergent
mechanisms. Previous studies have identifed that risk genes for ASD broadly converge
onto specifc functional categories with transcriptional regulation being one of the biggest
groups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory
consequences of some of them in the context of neurodevelopment.
First, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead
to perturbations of gene regulatory programs in early cell fate specifcation. In addition,
adult animals display abnormal learning behavior which is mirrored at the transcriptional
level by altered activity dependent regulation of postsynaptic gene expression. Lastly,
we link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR
complex.
Second, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral
organoids we demonstrate profound changes in the developmental trajectories of both
inhibitory and excitatory neurons using single cell RNA-sequencing. While the former
were generated earlier in CHD8+/- organoids, the generation of the latter was shifted to
later times in favor of a prolonged progenitor expansion phase and ultimately increased
organoid size.
Finally, by modeling heterozygous mutations for four ASD associated chromatin modifers,
ASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of
regulatory convergence across three of those genes. We observe a shift from dorsal cortical
excitatory neuron fates towards partially ventralized cell types resembling cells from the
lateral ganglionic eminence. As this project is still ongoing at the time of writing, future
experiments will aim at elucidating the regulatory mechanisms underlying this shift with
the aim of linking these three ASD risk genes through biological convergence.},
  author       = {Dotter, Christoph},
  issn         = {2663-337X},
  pages        = {152},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder}},
  doi          = {10.15479/at:ista:12094},
  year         = {2022},
}

@phdthesis{11393,
  abstract     = {AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is
implicated in complex processes such as learning and memory and various neurological
diseases. These receptors are composed of different subunits and the subunit composition can
affect channel properties, receptor trafficking and interaction with other associated proteins.
Using the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for
electron microscopy I investigated the number, density, and localization of AMPAR subunits,
GluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse
hippocampus. I have found that the immunogold labeling for all of these subunits in the
postsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual
increase from the pyramidal cell soma towards the distal part of stratum radiatum. The densities
of extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,
while the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those
for other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their
densities were higher in the periphery than center of synapses. In contrast, the GluA3-
containing receptors were more centrally localized compared to the GluA1- and GluA2-
containing receptors.
The hippocampus plays a central role in learning and memory. Contextual learning has been
shown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.
However, proximodistal heterogeneity of this plasticity and particular contribution of different
AMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a
hippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an
increase in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.
The intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred
pattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but
not stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings
further contribute to our understanding of how specific hippocampal subregions and AMPA
receptor subunits are involved in physiological learning.
Although the immunolabeling results above shed light on subunit-specific plasticity in
AMPAR distribution, no tools to visualize and study the subunit composition at the single
channel level in situ have been available. Electron microscopy with conventional immunogold
labeling approaches has limitations in the single channel analysis because of the large size of
antibodies and steric hindrance hampering multiple subunit labeling of single channels. I
managed to develop a new chemical labeling system using a short peptide tag and small
synthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to
proteins of interest (reactive tag system). I additionally made substantial progress into adapting
this system for AMPA receptor subunits.},
  author       = {Jevtic, Marijo},
  issn         = {2663-337X},
  pages        = {108},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus}},
  doi          = {10.15479/at:ista:11393},
  year         = {2022},
}

@phdthesis{12366,
  abstract     = {Recent substantial advances in the feld of superconducting circuits have shown its
potential as a leading platform for future quantum computing. In contrast to classical
computers based on bits that are represented by a single binary value, 0 or 1, quantum
bits (or qubits) can be in a superposition of both. Thus, quantum computers can store
and handle more information at the same time and a quantum advantage has already
been demonstrated for two types of computational tasks. Rapid progress in academic
and industry labs accelerates the development of superconducting processors which may
soon fnd applications in complex computations, chemical simulations, cryptography, and
optimization. Now that these machines are scaled up to tackle such problems the questions
of qubit interconnects and networks becomes very relevant. How to route signals on-chip
between diferent processor components? What is the most efcient way to entangle
qubits? And how to then send and process entangled signals between distant cryostats
hosting superconducting processors?
In this thesis, we are looking for solutions to these problems by studying the collective
behavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable
directional scattering of microwave photons from a pair of qubits in a waveguide. Such a
device can route microwave photons on-chip with a high diode efciency. Then we focus
on studying ultra-strong coupling regimes between light (microwave photons) and matter
(superconducting qubits), a regime that could be promising for extremely fast multi-qubit
entanglement generation. Finally, we show coherent pulse storage and periodic revivals
in a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage
device could be used as part of a quantum repeater that is needed for longer-distance
quantum communication.
The achieved high degree of control over multi-qubit ensembles highlights not only the
beautiful physics of circuit quantum electrodynamics, it also represents the frst step
toward new quantum simulation and communication methods, and certain techniques
may also fnd applications in future superconducting quantum computing hardware.
},
  author       = {Redchenko, Elena},
  isbn         = {978-3-99078-024-4},
  issn         = {2663-337X},
  pages        = {168},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Controllable states of superconducting Qubit ensembles}},
  doi          = {10.15479/at:ista:12132},
  year         = {2022},
}

@phdthesis{11932,
  abstract     = {The ability to form and retrieve memories is central to survival. In mammals, the hippocampus
is a brain region essential to the acquisition and consolidation of new memories. It is also
involved in keeping track of one’s position in space and aids navigation. Although this
space-memory has been a source of contradiction, evidence supports the view that the role of
the hippocampus in navigation is memory, thanks to the formation of cognitive maps. First
introduced by Tolman in 1948, cognitive maps are generally used to organize experiences in
memory; however, the detailed mechanisms by which these maps are formed and stored are not
yet agreed upon. Some influential theories describe this process as involving three fundamental
steps: initial encoding by the hippocampus, interactions between the hippocampus and other
cortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how
the investigation of cognitive maps of space helped to shed light on each of these three memory
processes.
The first study included in this thesis deals with the initial encoding of spatial memories in
the hippocampus. Much is known about encoding at the level of single cells, but less about
their co-activity or joint contribution to the encoding of novel spatial information. I will
describe the structure of an interaction network that allows for efficient encoding of noisy
spatial information during the first exploration of a novel environment.
The second study describes the interactions between the hippocampus and the prefrontal
cortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert
with the hippocampus, is involved in various processes, including memory storage and spatial
navigation. Nonetheless, the detailed mechanisms by which PFC receives information from the
hippocampus are not clear. I will show how a transient improvement in theta phase locking of
PFC cells enables interactions of cell pairs across the two regions.
The third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around
goal locations, a correlate of learning, can shed light on the transition from short- to long-term
spatial memories and the speed of consolidation in different brain areas.
The studies included in this thesis represent the main scientific contributions of my Ph.D. They
involve statistical analyses and models of neural responses of cells in different brain areas of
rats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings
on principles of memory formation and retention, including the mechanisms, the speed, and
the duration of these processes.},
  author       = {Nardin, Michele},
  issn         = {2663-337X},
  pages        = {136},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{On the encoding, transfer, and consolidation of spatial memories}},
  doi          = {10.15479/at:ista:11932},
  year         = {2022},
}

@phdthesis{11193,
  abstract     = {The infiltration of immune cells into tissues underlies the establishment of tissue-resident
macrophages and responses to infections and tumors. However, the mechanisms immune
cells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.
In this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to
overcome the tissue barrier of the germband in the embryo. One strategy is the strengthening
of the actin cortex through developmentally controlled transcriptional regulation induced by
the Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces
expression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the
activated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical
strength allows hemocytes to overcome the physical resistance of the surrounding tissue and
translocate their nucleus to move forward. This mechanism affects the speed of migration
when hemocytes face a confined environment in vivo.
Another aspect of the invasion process is the initial step of the leading hemocytes entering
the tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel
subpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads
penetration into the germband. Hemocytes that are deficient in BMP signaling activation
show impaired persistence at the tissue entry, while their migration speed remains
unaffected.
This suggests that there might be different mechanisms controlling immune cell migration
within the confined environment in vivo, one of these being the general ability to overcome
the resistance of the surrounding tissue and another affecting the order of hemocytes that
collectively invade the tissue in a stream of individual cells.
Together, my findings provide deeper insights into transcriptional changes in immune
cells that enable efficient tissue invasion and pave the way for future studies investigating the
early colonization of tissues by macrophages in higher organisms. Moreover, they extend the
current view of Drosophila immune cell heterogeneity and point toward a potentially
conserved role for canonical BMP signaling in specifying immune cells that lead the migration
of tissue resident macrophages during embryogenesis.},
  author       = {Wachner, Stephanie},
  issn         = {2663-337X},
  pages        = {170},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells}},
  doi          = {10.15479/at:ista:11193},
  year         = {2022},
}

@phdthesis{12378,
  abstract     = {Environmental cues influence the highly dynamic morphology of microglia. Strategies to 
characterize these changes usually involve user-selected morphometric features, which 
preclude the identification of a spectrum of context-dependent morphological phenotypes. 
Here, we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,
overcomes feature-selection bias and minimizes biological variability. 
First, with MorphOMICs we derive the morphological spectrum of microglia across seven 
brain regions during postnatal development and in two distinct Alzheimer’s disease 
degeneration mouse models. We uncover region-specific and sexually dimorphic
morphological trajectories, with females showing an earlier morphological shift than males in 
the degenerating brain. Overall, we demonstrate that both long primary- and short terminal 
processes provide distinct insights to morphological phenotypes. Moreover, using machine 
learning to map novel condition on the spectrum, we observe that microglia morphologies 
reflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control 
morphologies.
Next, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of 
microglial morphological spectrum in the retina, covering postnatal development and rd10 
degeneration. Here, following photoreceptor death, microglia assume an early developmentlike morphology. Finally, we map microglial morphology following optic nerve crush on the 
retinal spectrum and observe a layer- and sex-dependent response. 
Overall, MorphOMICs opens a new perspective to analyze microglial morphology across 
multiple conditions, and provides a novel tool to characterize microglial morphology beyond 
the traditionally dichotomized view of microglia.},
  author       = {Colombo, Gloria},
  issn         = {2663-337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes}},
  doi          = {10.15479/at:ista:12378},
  year         = {2022},
}

@phdthesis{12401,
  abstract     = {Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which
is the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.
Recent studies indicate a crucial role of the tumor microenvironment in malignant
transformation and metastasis. Studying cancer cell invasion and detachments quantitatively in
the context of its physiological microenvironment is technically challenging. Especially, precise
control of microenvironmental properties in vivo is currently not possible. Here, I studied the
role of microenvironment geometry in the invasion and detachment of cancer cells from the
bulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic
devices to mimic a pseudo 3D extracellular matrix environment, where I was able to
quantitatively tune the geometrical configuration of the microenvironment and follow tumor
cells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable
software application to automatically analyze and visualize particle tracking data.
Quantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments
showed that heterogeneity in the microenvironment promotes faster invasion and more
frequent detachment of cells. These observations correlated with overall higher speed of cells at
the edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially
passed through larger pores, thus invading areas of least resistance and generating finger-like
invasive structures. The detachments occurred mostly at the tips of these structures.
To investigate the potential mechanism, we established a two dimensional model to simulate
active Brownian particles representing the cell nuclei dynamics. These simulations backed our in
vitro observations without the need of precise fitting the simulation parameters. Our model
suggests the importance of the pore heterogeneity in the direction perpendicular to the
orientation of bias field (lateral heterogeneity), which causes the interface roughening.},
  author       = {Tasciyan, Saren},
  issn         = {2663-337X},
  pages        = {105},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Role of microenvironment heterogeneity in cancer cell invasion}},
  doi          = {10.15479/at:ista:12401},
  year         = {2022},
}

@phdthesis{9022,
  abstract     = {In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.
In the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time
(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.
In the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result
improves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.},
  author       = {Cipolloni, Giorgio},
  issn         = {2663-337X},
  pages        = {380},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Fluctuations in the spectrum of random matrices}},
  doi          = {10.15479/AT:ISTA:9022},
  year         = {2021},
}

@phdthesis{10030,
  abstract     = {This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning
non-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.},
  author       = {Portinale, Lorenzo},
  issn         = {2663-337X},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Discrete-to-continuum limits of transport problems and gradient flows in the space of measures}},
  doi          = {10.15479/at:ista:10030},
  year         = {2021},
}

@phdthesis{9733,
  abstract     = {This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.},
  author       = {Feliciangeli, Dario},
  issn         = {2663-337X},
  pages        = {180},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The polaron at strong coupling}},
  doi          = {10.15479/at:ista:9733},
  year         = {2021},
}

@phdthesis{10199,
  abstract     = {The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.},
  author       = {Toman, Viktor},
  issn         = {2663-337X},
  keywords     = {concurrency, verification, model checking},
  pages        = {166},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Improved verification techniques for concurrent systems}},
  doi          = {10.15479/at:ista:10199},
  year         = {2021},
}

@phdthesis{10007,
  abstract     = {The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis.},
  author       = {Hensel, Sebastian},
  issn         = {2663-337X},
  pages        = {300},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Curvature driven interface evolution: Uniqueness properties of weak solution concepts}},
  doi          = {10.15479/at:ista:10007},
  year         = {2021},
}