@phdthesis{21863, abstract = {Atoms and photons, two things so different but yet so alike. The former, the building block of matter, something we learn about in school and imagine it as some tiny marbles encircled by other tinier marbles. The latter, an electromagnetic wave, a light particle or an excitation of the electromagnetic field. Quantum mechanics tells us about the properties of these two entities. And even if it sounds, looks and writes counter-intuitive, it has proven right for over a century now. In this work, I elaborate on how we tested the laws of quantum mechanics and how we used them learn more about the tiny building blocks of nature and the fields they use to talk to each other. The atoms we use, are artificial. Superconducting qubits, small electrical circuits with quantized energy levels behave like electrons that transition between different orbitals in an atom. One of the qubits' advantages, is also a big disadvantage. We design the circuits' energy levels and fabricate them in a cleanroom. This allows for arbitrary spaced energy levels but in contrast to real atoms, prevents two superconducting qubits from being alike. Still, this qubit platform is one of the frontrunners for future quantum computing technology and testing fundamental physics due to their scalability. We interface superconducting qubits, which operate in the GHz regime, with microwave photons. We use 3D aluminum cavities as mediators between qubits and photons. The cavities allow for non-destructive readout of the qubit state, they shield the qubits from noise at the qubit frequency and they give us an easy way to frequency-tune these joint systems. We need to operate superconducting qubits and their cavities at millikelvin temperatures in dilution refrigerators. At higher temperatures, superconductivity suffers and even worse, the environment is filled with thermal noise photons. This poses a fundamental limitation on the scalability of superconducting qubit devices. Also connecting multiple devices in different fridges does not work over room temperature links because the microwave photons used for this purpose will be covered in noise and the quantum information they carry, will be unusable. Infrared photons do not suffer from this noise problem since there are close to zero thermal noise photons at their frequencies at room temperature. We cannot simply interface superconducting devices with optical photons due their frequency mismatch and the destructive effect of optical photons on superconductors. Therefore, we use microwave-to-optics transducers that allow to convert microwave photons into optical ones and vice-versa. The transducers that we use are macroscopic electro-optic transducers using the Pockels effect in a disk-shaped Lithium Niobate whispering gallery mode resonator. By using a strong optical pump, photons from the two frequency domains experience a beam-splitter interaction and get converted from one to the other. We measure the generated optical photons using elaborate optical setups, optical heterodyning and single photon detectors to gain knowledge about the qubit state or the converted microwave photons. Bridging the microwave and the optical world allows us to take advantage of both of their strengths but it also requires deep knowledge about both of their working principles. In this work, we describe two experiments that our group conducted to showcase the opportunities that arise from interfacing superconducting qubits with optical photons but also the pitfalls, one may encounter on the way. In the first experiment, we managed to all-optically read out a superconducting qubit. We show that the assignment fidelity, the probability that a measurement of the qubit state matches the prepared state, is close to equal for all-optical, microwave-to-optics and conventional microwave readout. We show T1 and T2 measurements for all three readout types and give an analysis of the noise caused by the optics. Finally, we show that the infrared light does not affect the qubit performance in a negative way but that the heating it causes does. This is an important insight that we used in the next experiment. The second experiment is the upconversion of itinerant single microwave photons to the optical domain. We show that we can generate single microwave photons from a qubit-cavity system. We upconvert these single photons, measure them with a single photon detector and reconstruct their shape. By conducting a single photon Rabi measurement, we show correlations between the microwave and the optical domain. And by thorough signal-to-noise measurements and noise analysis, we find that we can generate single infrared photons with high signal-to-noise ratio 5.1 and low transducer added noise (<0.012 quanta). We show that this measurement creates a path towards entanglement of a superconducting qubit and an optical photon and what parameters need to be improved to achieve it. Additionally, this experiment is a proof of principle for an on-demand infrared single photon source. More generally, it allows to link microwave quantum technology in general to the optical domain.}, author = {Werner, Thomas}, issn = {2663-337X}, keywords = {Superconducting qubits, Quantum optics, Single photons and quantum effects, Nonlinear optics}, pages = {97}, publisher = {Institute of Science and Technology Austria}, title = {{Interfacing superconducting qubits with optical photons}}, doi = {10.15479/AT-ISTA-21863}, year = {2026}, } @phdthesis{19048, abstract = {Rotations are found in physics problems at all scales: from spatial motion of celestial bodies, to transitions between quantum states of atoms and molecules. Mathematically, they represent a fundamental class of transformations and symmetries. Unlike spatial displacements, rotational transformations in three-dimensional space are non-commutative: the result of applying a sequence of rotations depends on the order of these operations. This feature makes the emergent physics that involves rotations rather intricate, but instrumental for studies of highly-interconnected many-body systems. In the presence of an environment, rotational properties of an object change, due to the interaction with particles of the environment. Owing to the complexity of this interaction, it can be engineered to exhibit certain properties of interest. In this Thesis, we examine several scenarios of how the rotational behavior of an impurity can be modified by interactions with its environment.}, author = {Maslov, Mikhail}, issn = {2663-337X}, pages = {86}, publisher = {Institute of Science and Technology Austria}, title = {{Emergent physics of rotating quantum impurities in many-body environments}}, doi = {10.15479/at:ista:19048}, year = {2025}, } @phdthesis{20467, author = {Miteva, Florianne E}, issn = {2663-337X}, pages = {99}, publisher = {Institute of Science and Technology Austria}, title = {{The role of cyclooxygenase 1 on microglial response to inflammatory stressors}}, doi = {10.15479/AT-ISTA-20467}, year = {2025}, } @phdthesis{20607, author = {Mondal, Soumyadip}, isbn = {978-3-99078-071-8}, issn = {2663-337X}, pages = {71}, publisher = {Institute of Science and Technology Austria}, title = {{Oxygen and sulfur redox : Conversion kinetics and phase equilibria}}, doi = {10.15479/AT-ISTA-20607}, year = {2025}, } @phdthesis{18871, abstract = {"Can we do this with a new type of computer - a quantum computer?". This famous quotation of the brilliant Richard Feynman within a conference talk on "Simulating physics with computers.” is often reverently praised as the origin of the field of quantum computing. The idea was to use quantum mechanical systems itself to simulate "Nature", which is inherently quantum mechanical. Now, 43 years later, the theoretical framework of how such a computer can operate has been developed. Two main important concepts for a potential quantum supremacy, superposition and entanglement, have been exploited to design quantum algorithms to significantly speed up certain tasks. Yet, the specific hardware implementation is still far from being certain, in fact the race between the most promising platforms such as superconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well as spin qubits has recently intensified. If one also includes the most mature applications of quantum communication technologies, secure quantum key distribution and quantum random number generators, as part of a quantum information technology ecosystem, we are confronted with a plethora of different materials, concepts, and also operation frequencies. While superconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5 GHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum computing operate with light in the infrared or visible range. Consequently, a quantum frequency converter or microwave-optic transducer is required to interface the different frequency domains or establish a long-range network connection with suitable telecom fibers. In fact, the combination of different frequency regimes is also an essential part in our classical modern communication network, where computations are performed in electrical circuits and the information exchange over longer distances happens via optical fibers. However, the specific challenges specific to building a quantum computer, also apply to the development of such a quantum frequency transducer: 1) As we deal with single excitations as the carrier of information, i.e. the smallest possible quantity, the signal can easily be corrupted by other noise sources which needs to be avoided by all means. This is also the reason why microwave quantum computers operate at temperature environments close to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The frequency interface generally needs to preserve the phase of the signal as an essential part of the quantum state. And 3) Quantum signals cannot be copied which would be a typical strategy to account for errors in classical computers. And finally, there is a challenge specific to microwave-optic transducers: While quantum computers are operating in one specific frequency domain, microwave-optic transducers combine microwave and optical fields in one device. This results in the particular challenge that high-energy optical radiation, which is usually well-shielded from superconducting microwave quantum processors, are now an essential part of the device. The concomitant optical radiation in the operating transducer will inevitably have a detrimental effect on the superconducting microwave components. Together with the requirement of minimal background noise for quantum-limited operation as described above, v heating from the absorption of optical photons within the same device where single microwave excitations are processed forms a formidable challenge. This thesis aims to address this challenge by developing microwave-optic transducers where the impact of optical absorption on superconducting circuits in general and superconducting qubits specifically can be mitigated. In our first approach, we developed a compact device with optimized interaction strengths between the different frequency domains. This minimizes the optical powers used for transducer operation and thus the optical absorption heating. This work was - to the best of our knowledge - the first comprehensive noise study, in an integrated microwave-optic transducer. Unfortunately, we saw that the optical absorption heating added noise way above a single excitation. Consequently, a potential quantum signal would have been buried in the noise, added by the transduction. Building on this insight, we utilized a three-dimensional microwave-optic transducer instead of an integrated device. The larger heat capacity of the macroscopic device with a size of a few millimeters can absorb a larger fraction of the optical heating before it increases the temperature of the device. This allowed us to interface the transducer directly with a superconducting qubit to readout the qubit state in a novel all-optical manner. We showed that the microwave-optic transducer can be operated in a regime in which optical fields don’t harm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic transducers in conjunction with microwave quantum processors and brings the integration and seamless orchestration of different frequency components in a quantum network a step closer. }, author = {Arnold, Georg M}, issn = {2663-337X}, pages = {135}, publisher = {Institute of Science and Technology Austria}, title = {{Microwave-optic interconnects for superconducting circuits}}, doi = {10.15479/at:ista:18871}, year = {2025}, } @phdthesis{19533, abstract = {This thesis explores advancements in quantum remote sensing and non-equilibrium phase transitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing. In the first project, I experimentally studied photon blockade breakdown as a dissipative phase transition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic limit, we demonstrated that the observed bistability is a genuine signature of a first-order phase transition in this system. This work provides insight into non-equilibrium quantum dynamics and phase transitions in driven-dissipative open quantum systems. The second project focuses on the experimental realization of a phase-conjugate receiver for quantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy environments using entangled light. While an ideal spontaneous parametric down-conversion (SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical illumination, no such ideal receiver exists. Instead, we explore an experimental realization of a phase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a Josephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled signal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate key experimental limitations that constrain practical QI performance, contributing to the development of quantum-enhanced sensing. Additionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These methods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been essential in data acquisition, noise filtering, and correlation analysis across multiple research projects. Although not real-time, these DSP techniques significantly enhance the accuracy of quantum measurements. Overall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic limit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver for QI. These findings contribute to quantum metrology, particularly for weak signal detection and remote sensing in noisy environments. }, author = {Sett, Riya}, issn = {2663-337X}, keywords = {phase transition, open quantum system, phase diagram, cavity quantum electrodynamics, superconducting qubits, semiclassical physics, quantum optics, josephson junction, parametric converter, phase conjugation, quantum radar, quantum entanglement, correlation, quantum sensing}, pages = {109}, publisher = {Institute of Science and Technology Austria}, title = {{ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime}}, doi = {10.15479/AT-ISTA-19533}, year = {2025}, } @phdthesis{14711, abstract = {In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies. For species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges as well as in highly fragmented populations. In this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters. Chapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate. In chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist. The focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts. Chapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence. Overall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.}, author = {Olusanya, Oluwafunmilola O}, issn = {2663-337X}, pages = {183}, publisher = {Institute of Science and Technology Austria}, title = {{Local adaptation, genetic load and extinction in metapopulations}}, doi = {10.15479/at:ista:14711}, year = {2024}, } @phdthesis{12900, abstract = {About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. Quantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. Till date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. After decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. Optical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. In this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. With this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. }, author = {Sahu, Rishabh}, isbn = {978-3-99078-030-5}, issn = {2663-337X}, keywords = {quantum optics, electrooptics, quantum networks, quantum communication, transduction}, pages = {190}, publisher = {Institute of Science and Technology Austria}, title = {{Cavity quantum electrooptics}}, doi = {10.15479/at:ista:12900}, year = {2023}, } @phdthesis{13175, abstract = {About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. Quantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. Till date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. After decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. Optical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. In this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. With this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. }, author = {Sahu, Rishabh}, isbn = {978-3-99078-030-5}, issn = {2663-337X}, keywords = {quantum optics, electrooptics, quantum networks, quantum communication, transduction}, pages = {202}, publisher = {Institute of Science and Technology Austria}, title = {{Cavity quantum electrooptics}}, doi = {10.15479/at:ista:13175}, year = {2023}, } @phdthesis{11473, abstract = {The polaron model is a basic model of quantum field theory describing a single particle interacting with a bosonic field. It arises in many physical contexts. We are mostly concerned with models applicable in the context of an impurity atom in a Bose-Einstein condensate as well as the problem of electrons moving in polar crystals. The model has a simple structure in which the interaction of the particle with the field is given by a term linear in the field’s creation and annihilation operators. In this work, we investigate the properties of this model by providing rigorous estimates on various energies relevant to the problem. The estimates are obtained, for the most part, by suitable operator techniques which constitute the principal mathematical substance of the thesis. The first application of these techniques is to derive the polaron model rigorously from first principles, i.e., from a full microscopic quantum-mechanical many-body problem involving an impurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas in the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak interactions as a low-energy effective theory for this problem. In the second part, we investigate rigorously the ground state of the model at fixed momentum and for large values of the coupling constant. Qualitatively, the system is expected to display a transition from the quasi-particle behavior at small momenta, where the dispersion relation is parabolic and the particle moves through the medium dragging along a cloud of phonons, to the radiative behavior at larger momenta where the polaron decelerates and emits free phonons. At the same time, in the strong coupling regime, the bosonic field is expected to behave purely classically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to be asymptotically equal to the one obtained from the semiclassical counterpart of the problem, first studied by Landau and Pekar in the 1940s. For polaron models with regularized form factors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear function of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove that for a large window of momenta below the radiation threshold, the energy-momentum relation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the Landau–Pekar effective mass, as expected. For the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is of the optical type and the form factor is formally UV–singular due to the nature of the point charge-dipole interaction, we are able to give the corresponding upper bound. In contrast to the regular case, this requires the inclusion of the quantum fluctuations of the phonon field, which makes the problem considerably more difficult. The results are supplemented by studies on the absolute ground-state energy at strong coupling, a proof of the divergence of the effective mass with the coupling constant for a wide class of polaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model and the application of the techniques used for its removal for the energy estimates. }, author = {Mysliwy, Krzysztof}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Polarons in Bose gases and polar crystals: Some rigorous energy estimates}}, doi = {10.15479/at:ista:11473}, year = {2022}, } @article{11951, abstract = {The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.}, author = {Ben Simon, Yoav and Käfer, Karola and Velicky, Philipp and Csicsvari, Jozsef L and Danzl, Johann G and Jonas, Peter M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory}}, doi = {10.1038/s41467-022-32559-8}, volume = {13}, 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{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{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}, } @article{9329, abstract = {Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events. New method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold. Results: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency. Comparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy. Conclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.}, author = {Zhang, Xiaomin and Schlögl, Alois and Vandael, David H and Jonas, Peter M}, issn = {1872-678X}, journal = {Journal of Neuroscience Methods}, number = {6}, publisher = {Elsevier}, title = {{MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo}}, doi = {10.1016/j.jneumeth.2021.109125}, volume = {357}, year = {2021}, } @article{9778, abstract = {The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.}, author = {Vandael, David H and Okamoto, Yuji and Jonas, Peter M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {general physics and astronomy, general biochemistry, genetics and molecular biology, general chemistry}, number = {1}, publisher = {Springer}, title = {{Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses}}, doi = {10.1038/s41467-021-23153-5}, volume = {12}, year = {2021}, } @article{10816, abstract = {Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.}, author = {Guzmán, José and Schlögl, Alois and Espinoza Martinez, Claudia and Zhang, Xiaomin and Suter, Benjamin and Jonas, Peter M}, issn = {2662-8457}, journal = {Nature Computational Science}, keywords = {general medicine}, number = {12}, pages = {830--842}, publisher = {Springer Nature}, title = {{How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network}}, doi = {10.1038/s43588-021-00157-1}, volume = {1}, year = {2021}, } @article{8001, abstract = {Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network.}, author = {Vandael, David H and Borges Merjane, Carolina and Zhang, Xiaomin and Jonas, Peter M}, issn = {10974199}, journal = {Neuron}, number = {3}, pages = {509--521}, publisher = {Elsevier}, title = {{Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation}}, doi = {10.1016/j.neuron.2020.05.013}, volume = {107}, year = {2020}, } @phdthesis{8386, abstract = {Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical quantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures— our design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints were taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.}, author = {Zhang, Ran}, issn = {2663-337X}, pages = {148}, publisher = {Institute of Science and Technology Austria}, title = {{Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability}}, doi = {10.15479/AT:ISTA:8386}, year = {2020}, } @unpublished{9750, abstract = {Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.}, author = {Slovakova, Jana and Sikora, Mateusz K and Caballero Mancebo, Silvia and Krens, Gabriel and Kaufmann, Walter and Huljev, Karla and Heisenberg, Carl-Philipp J}, booktitle = {bioRxiv}, pages = {41}, title = {{Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion}}, doi = {10.1101/2020.11.20.391284}, year = {2020}, }