@phdthesis{20737,
  author       = {Casado Polanco, Raquel},
  isbn         = {978-3-99078-072-5},
  issn         = {2663-337X},
  keywords     = {NOTCH, radial glial progenitor, lineage progression, cortical development},
  pages        = {133},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Role of NOTCH signaling in radial glial progenitor lineage progression}},
  doi          = {10.15479/AT-ISTA-20737},
  year         = {2025},
}

@phdthesis{20741,
  abstract     = {Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. 

Firstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. 

Next, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. 

Finally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. },
  author       = {Kojic, Marko},
  isbn         = {978-3-99078-073-2},
  issn         = {2663-337X},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria}},
  doi          = {10.15479/AT-ISTA-20741},
  year         = {2025},
}

@inproceedings{22120,
  author       = {Muñoz Hermosilla, José M and Miles, Evan and McCarthy, Michael and Hardmeier, Florian and Melo Velasco, Juan Vicente and Jouvet, Guillaume and Pellicciotti, Francesca},
  booktitle    = {EGU General Assembly 2025},
  location     = {Vienna, Austria & Virtual},
  publisher    = {European Geosciences Union},
  title        = {{Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier}},
  doi          = {10.5194/egusphere-egu25-17446},
  year         = {2025},
}

@phdthesis{20441,
  abstract     = {Epithelial spreading plays a pivotal role in the development of organisms especially those
such as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the
substantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium
with cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the
cells show tissue-scale mechanosensation with mechanisms such as direct mechanical control
over the axis of cell division.
Cytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating
mechanical stability but also helping facilitate the mechanosensitive response of the cell.
Mechanosenstivity displayed by intermediate filaments is due not just to their interesting
physical properties but also to their interactions with other cytoskeletal elements such as actin
and microtubules. Keratin is the predominant intermediate filament expressed in the EVL.
It expresses concomitantly with the gastrulation movements of the developing embryo. Our
work focuses on understanding the role and dynamics of the keratin cytoskeletal network in
modulating the physical aspects of EVL spreading. We demonstrated with the combination of
physical characterisation and manipulations of the EVL, utilising a variety of biophysical tools
and microscopy, the mechanistic role of keratin in tissue spreading.
Generating novel genetic morphants and mutants, we probe the effect that the loss of the
keratin network has on the physiology of the epithelium and the developing embryo. We
show that the changing organisation of the keratin network is important for changing EVL
physical properties as the stress imposed on the EVL increases during epiboly. By modelling
the epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into
a mechanical loop to the maturation of the keratin network and hence affect the mechanics
of the epithelium. However, unlike what would be predicted by the effect of intermediate
filaments in acting as a security belt and increasing the resistance of the epithelium, we observe
that loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the
YSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation
in a keratin-dependent manner.
Furthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into
the mechanisms underlying the organisation and distribution of keratin. Interestingly, the
phenotype observed upon this loss of microtubules shows that keratins interact with the nucleus
through microtubular interactions. Together with these diverse observations, we describe
the mechanosensory feedback between resilience and that is critical for uniform and robust
spreading of the epithelium.},
  author       = {Naik, Suyash},
  isbn         = {978-3-99078-069-5},
  issn         = {2663-337X},
  pages        = {105},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Keratins act as global coordinators of tissue spreading through mechanosensitive feedback}},
  doi          = {10.15479/AT-ISTA-20441},
  year         = {2025},
}

@phdthesis{20920,
  abstract     = {Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.

The only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).
The iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \pi. Given \pi, the output of VDF can be verified in time much less than T.

We first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.

Secondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.

We then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).

Finally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.

Together, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications.},
  author       = {Hoffmann, Charlotte},
  issn         = {2663-337X},
  pages        = {116},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Theory and applications of verifiable delay functions}},
  doi          = {10.15479/AT-ISTA-20920},
  year         = {2025},
}

@phdthesis{20556,
  abstract     = {Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.

The only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).
The iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \pi. Given \pi, the output of VDF can be verified in time much less than T.

We first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.

Secondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.

We then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).

Finally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.

Together, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications.},
  author       = {Hoffmann, Charlotte},
  issn         = {2663-337X},
  pages        = {116},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Theory and applications of verifiable delay functions}},
  doi          = {10.15479/AT-ISTA-20556},
  year         = {2025},
}

@article{20101,
  abstract     = {Evading imminent threat from predators is critical for animal survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours remains poorly understood1,2,3,4. Here we find that two sister species of deer mice (genus Peromyscus)5 show different responses to the same looming stimulus: Peromyscus maniculatus, which occupies densely vegetated habitats, predominantly escapes, whereas the open field specialist, Peromyscus polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal grey (dPAG) in driving behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus, and their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain.},
  author       = {Baier, Felix and Reinhard, Katja and Nuttin, Bram and Sans-Dublanc, Arnau and Liu, Chen and Tong, Victoria and Murmann, Julie Stefanie and Wierda, Keimpe and Farrow, Karl and Hoekstra, Hopi E.},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {439--447},
  publisher    = {Springer Nature},
  title        = {{The neural basis of species-specific defensive behaviour in Peromyscus mice}},
  doi          = {10.1038/s41586-025-09241-2},
  volume       = {645},
  year         = {2025},
}

@misc{20883,
  abstract     = {Evading imminent predator threat is critical for survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours is still poorly understood. Here we find that two sister species of deer mice (genus Peromyscus) show different responses to the same looming stimulus: P. maniculatus, which occupies densely vegetated habitats, predominantly escapes, while the open field specialist, P. polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour differs. While dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not P. polionotus, while their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain.},
  author       = {Felix, Baier and Reinhard, Katja and Nuttin, Bram and Sans Dublanc, Arnau and Liu, Chen and Tong, Victoria and Murmann, Julie Stefanie and Wierda, Keimpe and Farrow, Karl and Hoekstra, Hopi},
  publisher    = {Dryad},
  title        = {{The neural basis of species-specific defensive behaviour in Peromyscus mice}},
  doi          = {10.5061/DRYAD.Q2BVQ83XC},
  year         = {2025},
}

@unpublished{21399,
  abstract     = {We report on the Equational Theories Project (ETP), an online collaborative pilot project to explore new ways to collaborate in mathematics with machine assistance. The project successfully determined all 22 028 942 edges of the implication graph between the 4694 simplest equational laws on magmas, by a combination of human-generated and automated proofs, all validated by the formal proof assistant language Lean. As a result of this project, several new constructions of magmas satisfying specific laws were discovered, and several auxiliary questions were also addressed, such as the effect of restricting attention to finite magmas.},
  author       = {Bolan, Matthew and Breitner, Joachim and Brox, Jose and Carlini, Nicholas and Carneiro, Mario and Doorn, Floris van and Dvorak, Martin and Goens, Andrés and Hill, Aaron and Husum, Harald and Mejia, Hernán Ibarra and Kocsis, Zoltan A. and Floch, Bruno Le and Bar-on, Amir and Luccioli, Lorenzo and McNeil, Douglas and Meiburg, Alex and Monticone, Pietro and Nielsen, Pace P. and Osazuwa, Emmanuel Osalotioman and Paolini, Giovanni and Petracci, Marco and Reinke, Bernhard and Renshaw, David and Rossel, Marcus and Roux, Cody and Scanvic, Jérémy and Srinivas, Shreyas and Tadipatri, Anand Rao and Tao, Terence and Tsyrklevich, Vlad and Vaquerizo-Villar, Fernando and Weber, Daniel and Zheng, Fan},
  booktitle    = {arXiv},
  title        = {{The equational theories project: Advancing collaborative mathematical research at scale}},
  doi          = {10.48550/arXiv.2512.07087},
  year         = {2025},
}

@unpublished{21858,
  abstract     = {The recent surge in high-quality open-source Generative AI text models (colloquially: LLMs), as well as efficient finetuning techniques, have opened the possibility of creating high-quality personalized models that generate text attuned to a specific individual’s needs and are capable of credibly imitating their writing style by refining an open-source model with that person’s own data. The technology to create such models is accessible to private individuals, and training and running such models can be done cheaply on consumer-grade hardware. While these advancements are a huge gain for usability and privacy, this position paper argues that the practical feasibility of impersonating specific individuals also introduces novel safety risks. For instance, this technology enables the creation of phishing emails
or fraudulent social media accounts, based on small amounts of publicly available text, or by the individuals themselves to escape AI text detection. We further argue that these risks are complementary to—and distinct from—the much-discussed risks of other impersonation attacks such as image, voice, or video deepfakes, and are not adequately addressed by the larger research community, or the current generation of open- and closed-source models.},
  author       = {Iofinova, Eugenia B and Jovanovic, Andrej and Alistarh, Dan-Adrian},
  booktitle    = {arXiv},
  title        = {{Position: It's time to act on the risk of efficient personalized text generation}},
  doi          = {10.48550/arXiv.2502.06560},
  year         = {2025},
}

@article{21144,
  abstract     = {This paper deals with the algorithmic aspects of solving feasibility problems of semidefinite programming (SDP), aka linear matrix inequalities (LMIs). Since in some SDP instances all feasible solutions have irrational entries, numerical solvers that work with rational numbers can only find an approximate solution. We study the following question: Is it possible to certify feasibility of a given SDP using an approximate solution that is sufficiently close to some exact solution? Existing approaches make the assumption that there exist rational feasible solutions (and use techniques such as rounding and lattice reduction algorithms). We propose an alternative approach that does not need this assumption. More specifically, we show how to construct a system of polynomial equations whose set of real solutions is guaranteed to have an isolated correct solution (assuming that the target exact solution is maximum-rank). This allows, in particular, for us to use algorithms from real algebraic geometry for solving systems of polynomial equations, yielding a hybrid (or symbolic-numerical) method for SDPs. We experimentally compare it with a pure symbolic method in [D. Henrion, S. Naldi, and M. Safey El Din, SIAM J. Optim., 26 (2016), pp. 2512–2539]; the hybrid method was able to certify feasibility of many SDP instances on which the aforementioned paper failed. Our approach may have further applications, such as refining an approximate solution using methods of numerical algebraic geometry for systems of polynomial equations.},
  author       = {Kolmogorov, Vladimir and Naldi, Simone and Zapata, Jeferson},
  issn         = {1095-7189},
  journal      = {SIAM Journal on Optimization},
  number       = {3},
  pages        = {1630--1654},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Certifying solutions of degenerate semidefinite programs}},
  doi          = {10.1137/24m1664691},
  volume       = {35},
  year         = {2025},
}

@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{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},
}

@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},
}

@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},
}