@phdthesis{19393,
  abstract     = {Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.
While most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.
In this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.
We begin by establishing a theoretical bridge between periodically kicked rotors and "crystalline" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear
molecules provide an ideal experimental platform due to their abovementioned precise controllability.
The core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through
molecular alignment and rotational level populations.
These findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental
physics and developing quantum technologies.},
  author       = {Karle, Volker},
  issn         = {2663-337X},
  pages        = {192},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Non-equilibrium topological phases with periodically driven molecules and quantum rotors}},
  doi          = {10.15479/AT-ISTA-19393},
  year         = {2025},
}

@phdthesis{20735,
  abstract     = {Left–right alternation is a defining feature of spinal locomotor circuits, yet the level of neuronal
detail required to generate and maintain this pattern remains unclear. This thesis investigates how
models spanning multiple levels of abstraction—from biophysically detailed Hodgkin–Huxley (HH)
neurons to adaptive integrate–and–fire (I&F) formulations and synfire-chain modules—can account
for the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole. The guiding
hypothesis is that a small set of neuronal mechanisms is sufficient to reproduce the essential features
of rhythmic alternation, and that moving between modeling scales helps distinguish core principles
from biological detail.
A minimal bilateral HH network comprising only four canonical neuron classes—excitatory
descending interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory
interneurons (aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce
experimentally observed firing modes, the model demonstrated that rebound-prone dIN excitability,
contralateral inhibition and modest electrical coupling are sufficient to generate stable alternating
activity, even in very small networks. These results motivated the transition to simpler models
capable of efficient analysis and scaling.
Adaptive exponential I&F (AdEx) neurons were calibrated to physiological recordings using
simulation-based inference, yielding tonic and phasic/rebound templates that preserved the key
dynamical signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying
single-spike responses and rebound firing in dINs. At network level, the I&F models robustly
reproduced left–right alternation, while highlighting constraints on synaptic kinetics and adaptation
needed to avoid multi-spike responses.
Finally, a synfire-chain framework provided a complementary, timing-centric perspective, demonstrating how precise spike synchrony, synaptic delays and minimal inhibitory coupling can generate
alternating left–right sequences in a feedforward setting. Together, these approaches converge on a
common conclusion: rebound-prone ipsilateral excitation combined with precisely timed contralateral inhibition constitutes a sufficient substrate for alternating spinal rhythms.
By integrating bottom-up and top-down modeling strategies, this thesis provides a unified, extensible framework for studying spinal pattern generation. The results show that essential locomotor
dynamics can be captured across multiple abstraction levels, offering both mechanistic insight and
practical tools for future data-driven investigations of spinal circuit development, robustness and
modulation.},
  author       = {Wilson, Alexia C},
  issn         = {2791-4585},
  pages        = {110},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog}},
  doi          = {10.15479/AT-ISTA-20735},
  year         = {2025},
}

@unpublished{21398,
  abstract     = {Seymour's decomposition theorem is a hallmark result in matroid theory presenting a structural characterization of the class of regular matroids. Formalization of matroid theory faces many challenges, most importantly that only a limited number of notions and results have been implemented so far. In this work, we formalize the proof of the forward (composition) direction of Seymour's theorem for regular matroids. To this end, we develop a library in Lean 4 that implements definitions and results about totally unimodular matrices, vector matroids, their standard representations, regular matroids, and 1-, 2-, and 3-sums of matrices and binary matroids given by their standard representations. Using this framework, we formally state Seymour's decomposition theorem and implement a formally verified proof of the composition direction in the setting where the matroids have finite rank and may have infinite ground sets.},
  author       = {Dvorak, Martin and Figueroa-Reid, Tristan and Hamadani, Rida and Hwang, Byung-Hak and Karunus, Evgenia and Kolmogorov, Vladimir and Meiburg, Alexander and Nelson, Alexander and Nelson, Peter and Sandey, Mark and Sergeev, Ivan},
  booktitle    = {arXiv},
  title        = {{Composition direction of Seymour's theorem for regular matroids — Formally verified}},
  doi          = {10.48550/arXiv.2509.20539},
  year         = {2025},
}

@phdthesis{20811,
  abstract     = {	This thesis is organized into two parts, each comprising two chapters: Chapter 1 and 2 offer models for the evolution of vaccine resistance in response to diverse vaccination strategies. Chapter 3 and 4 review the statistics of records, their connection to models of innovation and an application to the cultural evolution of sports.
	In chapter 1 we present a modelling study from 2021 on the evolution of SARS-CoV-2. At that time the vaccine-resistant Omicron variant had not yet evolved. In our model we consider a population that is becoming vaccinated over time, while a pathogen is spreading in the population and eventually becoming resistant to the vaccine. We explore effective pharmaceutical and non-pharmaceutical interventions to prevent the emergence of vaccine resistance. 
	In chapter 2 we model a particular set of complex vaccination strategies, mosaic and pyramid vaccination, where an immunologically diverse portfolio of vaccines is considered. We find that a bet-hatching strategy, in which vaccine types are distributed in the population, is effective at hindering the evolution of vaccine resistance if mutation rates are high. 
	In chapter 3 we switch gears and present a review on the statistics of records. We highlight similarities and analogies to other models in the fields of statistical physics, evolution and innovation. This offers interesting complimentary perspectives on well-known models. 
	In chapter 4 we apply models of record statistics and innovation to study cultural evolution in sport. We propose a model of sport evolution that combines deterministic improvements in performance and stochastic bursts of improvements due to innovation. },
  author       = {Rella, Simon},
  issn         = {2663-337X},
  pages        = {95},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation}},
  doi          = {10.15479/AT-ISTA-20811},
  year         = {2025},
}

@phdthesis{20276,
  abstract     = {Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations
either preserve the intrinsic material geometry (e.g., folding paper) or modify it through
localized contraction. Once transformed, the 3D shape can be further controlled to achieve a
target functionality. A key challenge is to take the material specifications and the actuation
process as input to automatically design the target 3D shape and its functionality. This thesis
presents two novel computational pipelines for the design and control of shape-morphing
structures used to create functional prototypes.
The first pipeline borrows from the art of origami to fold paper into intricate shapes and
applies this principle to make 3D lighting displays. We introduce, PCBend a computational
design approach that covers a surface with individually addressable RGB LEDs, effectively
forming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize
cut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and
fabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated
standard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs
are cut along the contour and folded onto a 3D-printed support. The 3D lighting display is
then controlled to display complex surface light patterns.
Creating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion
or require multiple patches, which are unsuitable for fabrication pipelines that rely on folding
non-stretchable materials. We reinforce such fabrication pipelines by providing a geometric
relaxation to the problem, where the input shape is modified to admit overlap-free unfolding.
The second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s
blueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots
using modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable
artificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is
altered to enable untethered actuation through infrared radiation, allowing active control of
individual muscles and their corresponding bones. The combined motion of individual bones
defines the robot’s overall shape and functionality. Our proposed system significantly expands
both the design and control spaces of soft robots, which we harness using our computational
design tools. We build several physical robots that exhibit complex shape morphing and varied
terrain navigation, showcasing the versatility of our pipeline.
This thesis explores applications ranging from intricate light patterns displayed on 3D shapes
formed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit
shape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform
passive structures into functional prototypes.},
  author       = {Bhargava, Manas},
  isbn         = {978-3-99078-065-7},
  issn         = {2663-337X},
  pages        = {96},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Design and control of deformable structures: From PCB lighting displays to elastomer robots}},
  doi          = {10.15479/AT-ISTA-20276},
  year         = {2025},
}

@phdthesis{20203,
  abstract     = {Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon.},
  author       = {Sobarzo Ponce, Juan Carlos A},
  isbn         = {978-3-99078-062-6},
  issn         = {2663-337X},
  pages        = {96},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges}},
  doi          = {10.15479/AT-ISTA-20203},
  year         = {2025},
}

@article{18565,
  abstract     = {We present a computational approach for unfolding 3D shapes isometrically into the plane as a single patch without overlapping triangles. This is a hard, sometimes impossible, problem, which existing methods are forced to soften by allowing for map distortions or multiple patches. Instead, we propose a geometric relaxation of the problem: We modify the input shape until it admits an overlap‐free unfolding. We achieve this by locally displacing vertices and collapsing edges, guided by the unfolding process. We validate our algorithm quantitatively and qualitatively on a large dataset of complex shapes and show its proficiency by fabricating real shapes from paper.},
  author       = {Bhargava, Manas and Schreck, Camille and Freire, M. and Hugron, P. A. and Lefebvre, S. and Sellán, S. and Bickel, Bernd},
  issn         = {1467-8659},
  journal      = {Computer Graphics Forum},
  keywords     = {fabrication, single patch unfolding, mesh simplification},
  number       = {1},
  publisher    = {Wiley},
  title        = {{Mesh simplification for unfolding}},
  doi          = {10.1111/cgf.15269},
  volume       = {44},
  year         = {2025},
}

@phdthesis{20371,
  abstract     = {Quantum mechanics reveals a world that defies classical determinism, where uncertainty, superposition, and fluctuations are fundamental aspects. Engineering devices that harness these quantum features requires not only precision, but also a deep understanding of how they interact with their surrounding environment. Superconducting circuits, which exploit
macroscopic quantum coherence in low-loss superconducting materials, provide a scalable platform for implementing such systems. Among the critical elements in these circuits, superinductors—high-impedance, dissipation-free inductive components—play a central role by suppressing charge fluctuations. They allow quantum states to be delocalized in phase space, protect qubits from environmental noise, and facilitate access to phenomena such as dual Josephson physics and ultra-strong coupling regimes. 
This thesis explores two complementary implementations of high-impedance circuits: geometric superinductors, demonstrating that high impedance can be achieved beyond kinetic inductance,
and Josephson junction chains, used to investigate both microwave mode properties and DC transport across the superconductor-to-insulator transition. 
Part I addresses geometric superinductors. Contrary to the common belief that high-impedance superconducting circuits require kinetic inductance, we demonstrate that purely geometric designs can achieve characteristic impedance exceeding the resistance quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors achieve enhanced self-inductance, creating a reliable platform for qubits and resonators. Modeling, simulation, fabrication, and
characterization confirm that these elements behave as superinductor. With low loss, high linearity, and minimal stray capacitance, these elements are reproducible, free of uncontrolled tunneling events, and capable of strong magnetic coupling. This establishes geometric superinductors as robust, single-wave-function superconducting devices suitable for hardware protected qubits and hybrid systems.
Part II presents classical numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps. The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive environment with a parasitic capacitance.
Part III extends the investigation of high characteristic-impedance circuit elements to one-dimensional Josephson junction chains, which act as a quantum simulator for many-body physics and the superconductor–insulator transition. Different devices are realized on both sides of the DC phase transition, showing either a supercurrent branch or Coulomb blockade at zero bias. The effect of the crossover on microwave modes, however, remains insufficiently investigated. Studying these modes provides insight into the interplay between disorder and phase-slip events. Small differences in circuit component sizes determine which side of the transition a device falls on, making these results relevant not only for fundamental understanding but also for the design of quantum devices, emphasizing the crucial role of the
electromagnetic environment in stabilizing and controlling fragile quantum states. 
Together, these results illustrate how carefully engineered high characteristic-impedance elements provide a link between macroscopic circuits and the inherently uncertain quantum world, enabling experiments that probe, control, and ultimately exploit quantum fluctuations for applications in quantum information, metrology, solid state physics and beyond.

},
  author       = {Trioni, Andrea},
  isbn         = {978-3-99078-067-1},
  issn         = {2663-337X},
  pages        = {202},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains}},
  doi          = {10.15479/AT-ISTA-20371},
  year         = {2025},
}

@phdthesis{20339,
  abstract     = {This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights.

We first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations.

In the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D.
},
  author       = {Tasinato, Gianluca},
  issn         = {2663-337X},
  pages        = {106},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems}},
  doi          = {10.15479/AT-ISTA-20339},
  year         = {2025},
}

@phdthesis{19540,
  abstract     = {This thesis deals with several different models for complex quantum mechanical systems and is structured in three main parts. 
	
In Part I, we study mean field random matrices as models for quantum Hamiltonians. Our focus lies on proving concentration estimates for resolvents of random matrices, so-called local laws, mostly in the setting of multiple resolvents. These estimates have profound consequences for eigenvector overlaps and thermalization problems. More concretely, we obtain, e.g., the optimal eigenstate thermalization hypothesis (ETH) uniformly in the spectrum for Wigner matrices, an optimal lower bound on non-Hermitian eigenvector overlaps, and prethermalization for deformed Wigner matrices.	In order to prove our novel multi-resolvent local laws, we develop and devise two main methods, the static Psi-method and the dynamical Zigzag strategy. 
	
In Part II, we study Bardeen-Cooper-Schrieffer (BCS) theory, the standard mean field microscopic theory of superconductivity. We focus on asymptotic formulas for the characteristic critical temperature and energy gap of a superconductor and prove universality of their ratio in various physical regimes. Additionally, we investigate multi-band superconductors and show that inter-band coupling effects can only enhance the critical temperature. 
	
In Part III, we study quantum lattice systems. On the one hand, we show a strong version of the local-perturbations-perturb-locally (LPPL) principle for the ground state of weakly interacting quantum spin systems with a uniform on-site gap. On the other hand, we introduce a notion of a local gap and rigorously justify response theory and the Kubo formula under the weakened assumption of a local gap. 
	
Additionally, we discuss two classes of problems which do not fit into the three main parts of the thesis. These are deformational rigidity of Liouville metrics on the torus and relativistic toy models of particle creation via interior-boundary-conditions (IBCs).  },
  author       = {Henheik, Sven Joscha},
  isbn         = {978-3-99078-057-2},
  issn         = {2663-337X},
  pages        = {720},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems}},
  doi          = {10.15479/AT-ISTA-19540},
  year         = {2025},
}

@misc{20641,
  abstract     = {Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. },
  author       = {Becker, Lea Marie and Schanda, Paul},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes"}},
  doi          = {10.15479/AT-ISTA-20641},
  year         = {2025},
}

@article{20926,
  abstract     = {Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs.},
  author       = {Kim, Dongjin and Wang, Xiaoyu and Vargas, Santiago and Zhong, Peichen and King, Daniel S. and Inizan, Theo Jaffrelot and Cheng, Bingqing},
  issn         = {1549-9626},
  journal      = {Journal of Chemical Theory and Computation},
  number       = {24},
  pages        = {12709--12724},
  publisher    = {American Chemical Society},
  title        = {{A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials}},
  doi          = {10.1021/acs.jctc.5c01400},
  volume       = {21},
  year         = {2025},
}

@phdthesis{20074,
  abstract     = {Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. 
In chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. 
In chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. 
In summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.},
  author       = {Hübschmann, Verena},
  isbn         = {978-3-99078-060-2},
  issn         = {2663-337X},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Human microglia impact neuronal development in retinal organoids}},
  doi          = {10.15479/AT-ISTA-20074},
  year         = {2025},
}

@article{20342,
  abstract     = {Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata.},
  author       = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E},
  issn         = {1860-5974},
  journal      = {Logical Methods in Computer Science},
  number       = {2},
  publisher    = {EPI Sciences},
  title        = {{Safety and liveness of quantitative properties and automata}},
  doi          = {10.46298/lmcs-21(2:2)2025},
  volume       = {21},
  year         = {2025},
}

@phdthesis{20147,
  abstract     = {Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.

In this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.


},
  author       = {Sarac, Naci E},
  issn         = {2663-337X},
  pages        = {149},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A monitoring-oriented theory and classification of quantitative specifications}},
  doi          = {10.15479/AT-ISTA-20147},
  year         = {2025},
}

@phdthesis{20167,
  author       = {Schön, Hanna},
  isbn         = {978-3-99078-061-9},
  issn         = {2663-337X},
  pages        = {171},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs}},
  doi          = {10.15479/AT-ISTA-20167},
  year         = {2025},
}

@article{20538,
  abstract     = {In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins.},
  author       = {Knödlstorfer, Sonja and Toscano, Giorgia and Ptaszek, Aleksandra L. and Kontaxis, Georg and Napoli, Federico and Schneider, Jakob and Maier, Katharina and Kapitonova, Anna and Lichtenecker, Roman J. and Schanda, Paul and Konrat, Robert},
  issn         = {1089-8638},
  journal      = {Journal of Molecular Biology},
  number       = {23},
  publisher    = {Elsevier},
  title        = {{A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0}},
  doi          = {10.1016/j.jmb.2025.169465},
  volume       = {437},
  year         = {2025},
}

@phdthesis{19395,
  abstract     = {Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.
One particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.
Like other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.
In this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.
Given the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.
These findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood.},
  author       = {Monzer, Aline},
  issn         = {2663-337X},
  pages        = {160},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Cell-surface auxin signaling: Linking molecular pathways to plant development}},
  doi          = {10.15479/AT-ISTA-19395},
  year         = {2025},
}

@unpublished{19398,
  abstract     = {Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.},
  author       = {Monzer, Aline and Mazur, Ewa and Rodriguez Solovey, Lesia and Gallei, Michelle C and Zou, Minxia and Smejkal, Michael and Cervenova, Ema and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}},
  doi          = {10.1101/2025.02.28.640727},
  year         = {2025},
}

@phdthesis{19684,
  abstract     = {The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. 

Initially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.

In more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.

In larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.

Finally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.},
  author       = {Yalniz, Gökhan},
  issn         = {2663-337X},
  pages        = {155},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transition to turbulence: Data-, solution-, and pattern-driven approaches}},
  doi          = {10.15479/AT-ISTA-19684},
  year         = {2025},
}