@phdthesis{20362, author = {Babic, David}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana}}, doi = {10.15479/AT-ISTA-20362}, year = {2025}, } @phdthesis{20393, author = {Kishi, Kasumi}, issn = {2663-337X}, pages = {102}, publisher = {Institute of Science and Technology Austria}, title = {{Regulation of notochord and floor plate size during mouse development}}, doi = {10.15479/AT-ISTA-20393}, year = {2025}, } @phdthesis{20415, author = {Lee, Seungho}, issn = {2663-337X}, pages = {144}, publisher = {Institute of Science and Technology Austria}, title = {{Nanoparticle-based precursors toward advanced crystalline inorganic solids}}, doi = {10.15479/AT-ISTA-20415}, year = {2025}, } @article{20425, abstract = {Ultraviolet (UV) radiation from accreting black holes ionizes the intergalactic gas around early quasars, carving out highly ionized bubbles in their surroundings. Any changes in a quasar’s luminosity are therefore predicted to produce outward-propagating ionization gradients, affecting the Lyα absorption opacity near the quasar’s systemic redshift. This “proximity effect” is well-documented in rest-UV quasar spectra but only provides a one-dimensional probe along our line of sight. Here we present deep spectroscopic observations with the James Webb Space Telescope (JWST) of galaxies in the background of a superluminous quasar at zQSO ≈ 6.3, which reveal the quasar’s “light echo” with Lyα tomography in the transverse direction. This transverse proximity effect is detected for the first time toward multiple galaxy sightlines, allowing us to map the extent and geometry of the quasar’s ionization cone. We obtain constraints on the orientation and inclination of the cone, as well as an upper limit on the obscured solid angle fraction of fobsc < 91%. Additionally, we find a timescale of the quasar’s UV radiation of tqso = 10^5.6+0.1-0.3 yr, which is significantly shorter than would be required to build up the central supermassive black hole (SMBH) with conventional growth models, but is consistent with independent measurements of the quasars’ duty cycle. Our inferred obscured fraction disfavors a scenario where short quasar lifetimes can be explained exclusively by geometric obscuration, and instead supports the idea that radiatively inefficient accretion or growth in initially heavily enshrouded cocoons plays a pivotal role in early SMBH growth. Our results pave the way for novel studies of quasars’ ionizing geometries and radiative histories at early cosmic times.}, author = {Eilers, Anna Christina and Yue, Minghao and Matthee, Jorryt J and Hennawi, Joseph F. and Davies, Frederick B. and Simcoe, Robert A. and Teague, Richard and Bordoloi, Rongmon and Brammer, Gabriel and Kang, Yi and Kashino, Daichi and Mackenzie, Ruari and Naidu, Rohan P. and Navarrete, Benjamín}, issn = {2041-8213}, journal = {The Astrophysical Journal Letters}, number = {2}, publisher = {IOP Publishing}, title = {{The light echo of a high-redshift quasar mapped with Lyα tomography}}, doi = {10.3847/2041-8213/ae057a}, volume = {991}, year = {2025}, } @article{20454, abstract = {Context. γ Dor stars are ideal targets for studies of the innermost dynamical properties of stars, due to their rich asteroseismic spectrum of gravity modes. Integrating internal magnetism to the picture appears as the next milestone of detailed asteroseismic studies, for its prime importance on stellar evolution. The inertial dip in prograde dipole modes period-spacing pattern of γ Dors stands out as a unique window on the convective core structure and dynamics. Recent studies have highlighted the dependence of the dip structure on core density stratification, the contrast of the near-core Brunt-Väisälä frequency and rotation rate, as well as the core-to-near-core differential rotation. In addition, the effect of envelope magnetism has been derived on low-frequency magneto-gravito-inertial waves. Aims. We revisited the inertial dip formation including core and envelope magnetism, and explored the probing power of this feature on dynamo-generated core fields. Methods. We considered as a first step a toroidal magnetic field with a bi-layer (core and envelope) Alfvén frequency. This configuration allowed us to revisit the coupling problem using our knowledge on both core magneto-inertial modes and envelope magneto-gravito-inertial modes. Using this configuration, we were able to stay in an analytical framework to exhibit the magnetic effects on the inertial dip shape and location. This configuration allowed a laboratory to be set up that moves us towards the comprehension of magnetic effects on the dip structure. Results. We show a shift of the inertial dip towards lower spin parameter values and a thinner dip with increasing core magnetic field’s strength, quite similar to the signature of differential rotation. The magnetic effects become sizeable when the ratio of the magnetic to the Coriolis effects is high enough. We explored the potential degeneracy of the magnetic effects with differential rotation. We studied the detectability of core magnetism, considering both observational constraints on the periods of the modes and potential gravito-inertial mode suppression.}, author = {Barrault, Lucas and Bugnet, Lisa Annabelle and Mathis, S. and Mombarg, J. S.G.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{Exploring the probing power of γ Dor's inertial dip for core magnetism: The case of a toroidal field}}, doi = {10.1051/0004-6361/202555213}, volume = {701}, year = {2025}, } @phdthesis{20467, author = {Miteva, Florianne E}, issn = {2663-337X}, pages = {99}, publisher = {Institute of Science and Technology Austria}, title = {{The role of cyclooxygenase 1 on microglial response to inflammatory stressors}}, doi = {10.15479/AT-ISTA-20467}, year = {2025}, } @phdthesis{20485, author = {Misova, Michaela}, isbn = {978-3-99078-068-8}, issn = {2663-337X}, pages = {155}, publisher = {Institute of Science and Technology Austria}, title = {{Dissecting gap junction biology using the C. elegans nervous system}}, doi = {10.15479/AT-ISTA-20485}, year = {2025}, } @phdthesis{20551, abstract = {The space of codimension-2 shapes, such as curves in 3D and surfaces in 4D, is an infinite-dimensional manifold. This thesis explores geometric structures and dynamics on this space, with emphasis on their implications for physics, particularly hydrodynamics. Our investigation ranges from theoretical studies of infinite-dimensional symplectic and prequantum geometry to numerical computation of the time evolution of shapes. The thesis presents four main contributions. In the first part, we introduce implicit representations of codimension-2 shapes using a class of complex-valued functions, and prove that the space of these implicit representations forms a prequantum bundle over the codimension-2 shape space. This reveals a new geometric interpretation of the canonical symplectic structure on the codimension-2 shape space. In the second part, we use implicit representations to develop a simulation method for the dynamics of space curves. To handle chaotic systems such as vortex filaments in hydrodynamics, we exploit the infinite degrees of freedom, hidden in both the configuration and dynamics of implicit representations. In the third part, we introduce new symplectic structures on the space of space curves, which generalize the only previously known symplectic structure on this space, allowing for new Hamiltonian dynamics of space curves. In the fourth part, we apply a symplectic viewpoint to a differential geometric problem with practical applications. We derive a new area formula for spherical polygons via prequantization. }, author = {Ishida, Sadashige}, isbn = {978-3-99078-070-1}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{Symplectic-prequantum structures and dynamics on the codimension-2 shape space}}, doi = {10.15479/AT-ISTA-20551}, year = {2025}, } @phdthesis{20575, abstract = {This thesis deals with eigenvalue and eigenvector universality results for random matrix ensembles equipped with non-trivial spatial structure. We consider both mean-field models with a general variance profile (Wigner-type matrices) and correlation structure (correlated matrices) among the entries, as well as non-mean-field random band matrices with bandwidth W >> N^(1/2). To extract the universal properties of random matrix spectra and eigenvectors, we obtain concentration estimates for their resolvent, the local laws, which generalize the celebrated Wigner semicircle law for a broad class of random matrices to much finer spectral scales. The local laws hold for both a single resolvent as well as for products of multiple resolvents, known as resolvent chains, and express the remarkable approximately-deterministic behavior of these objects down to the microscopic scale. Our primary tool for establishing the local laws is the dynamical Zigzag strategy, which we develop in the setting of spatially-inhomogeneous random matrices. Our proof method systematically addresses the challenges arising from non-trivial spatial structures and is robust to all types of singularities in the spectrum, as we demonstrate in the correlated setting. Furthermore, we incorporate the analysis of the deterministic resolvent chain approximations into the dynamical framework of the Zigzag strategy, synthesizing a unified toolkit for establishing multi-resolvent local laws. Using these methods, we prove complete eigenvector delocalization, the Eigenstate Thermalization Hypothesis, and Wigner-Dyson universality in the bulk for random band matrices down to the optimal bandwidth W >> N^(1/2). For mean-field ensembles, we establish universality of local eigenvalue statistics at the cups for random matrices with correlated entries, and the Eigenstate Thermalization Hypothesis for Wigner-type matrices in the bulk of the spectrum. Finally, this thesis also contains other applications of the multi-resolvent local laws to spatially-inhomogeneous random matrices, obtained prior to the development of the Zigzag strategy. In particular, we provide a complete analysis of mesoscopic linear-eigenvalue statistics of Wigner-type matrices in all spectral regimes, including the novel cusps, and rigorously establish the prethermalization phenomenon for deformed Wigner matrices. The main body of this thesis consists of seven research papers (listed on page xi), each presented in a separate chapter with its own introduction and all relevant context, suitable to be read independently. We ask the reader’s indulgence for the repetitions in the historical overviews and other minor redundancies that remain among the chapters as a result. The overall Introduction, preceding the chapters, provides a condensed, informal summary of the main ideas and concepts at the core of these works. }, author = {Riabov, Volodymyr}, isbn = {978-3-99078-064-0}, issn = {2663-337X}, pages = {436}, publisher = {Institute of Science and Technology Austria}, title = {{Universality in random matrices with spatial structure}}, doi = {10.15479/AT-ISTA-20575}, year = {2025}, } @unpublished{20576, abstract = {We prove that a very general class of $N\times N$ Hermitian random band matrices is in the delocalized phase when the band width $W$ exceeds the critical threshold, $W\gg \sqrt{N}$. In this regime, we show that, in the bulk spectrum, the eigenfunctions are fully delocalized, the eigenvalues follow the universal Wigner-Dyson statistics, and quantum unique ergodicity holds for general diagonal observables with an optimal convergence rate. Our results are valid for general variance profiles, arbitrary single entry distributions, in both real-symmetric and complex-Hermitian symmetry classes. In particular, our work substantially generalizes the recent breakthrough result of Yau and Yin [arXiv:2501.01718], obtained for a specific complex Hermitian Gaussian block band matrix. The main technical input is the optimal multi-resolvent local laws -- both in the averaged and fully isotropic form. We also generalize the $\sqrtη$-rule from [arXiv:2012.13215] to exploit the additional effect of traceless observables. Our analysis is based on the zigzag strategy, complemented with a new global-scale estimate derived using the static version of the master inequalities, while the zig-step and the a priori estimates on the deterministic approximations are proven dynamically.}, author = {Erdös, László and Riabov, Volodymyr}, booktitle = {arXiv}, title = {{The zigzag strategy for random band matrices}}, doi = {10.48550/ARXIV.2506.06441}, year = {2025}, } @unpublished{20580, abstract = {This paper explores the geometry of the space of codimension-2 submanifolds. We implicitly represent these submanifolds by a class of complex-valued functions. This reveals a prequantum bundle structure over the space of submanifolds, equipped with the well-known Marsden-Weinstein symplectic structure. This bundle allows a new physical interpretation of the Marsden-Weinstein structure as the curvature of a connection form, which measures the average of volumes swept by the deformation of the S^1-family of hypersurfaces, defined as the phases of a complex function implicitly representing a submanifold.}, author = {Chern, Albert and Ishida, Sadashige}, booktitle = {arXiv}, title = {{Implicit representations of codimension-2 submanifolds and their prequantum structure}}, doi = {10.48550/ARXIV.2507.11727}, year = {2025}, } @article{20628, abstract = {The realistic simulation of sand, soil, powders, rubble piles, and large collections of rigid bodies is a common and important problem in the fields of computer graphics, computational physics, and engineering. Direct simulation of these individual bodies quickly becomes expensive, so we often approximate the entire group as a continuum material that can be more easily computed using tools for solving partial differential equations, like the material point method (MPM). In this paper, we present a method for automatically extracting continuum material properties from a collection of rigid bodies. We use numerical homogenization with periodic boundary conditions to simulate an effectively infinite number of rigid bodies in contact. We then record the effective stress-strain relationships from these simulations and convert them into elastic properties and yield criteria for the continuum simulations. Our experiments validate existing theoretical models like the Mohr-Coulomb yield surface by extracting material behaviors from a collection of spheres in contact. We further generalize these existing models to more exotic materials derived from diverse and non-convex shapes. We observe complicated jamming behaviors from non-convex grains, and we introduce a new material model for materials with extremely high levels of internal friction and cohesion. We simulate these new continuum models using MPM with an improved return mapping technique. The end result is a complete system for turning an input rigid body simulation into an efficient continuum simulation with the same effective mechanical properties.}, author = {Chen, Yi-Lu and Ly, Mickaël and Wojtan, Christopher J}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, location = {Hong Kong, China}, number = {6}, publisher = {Association for Computing Machinery}, title = {{Numerical homogenization of sand from grain-level simulations}}, doi = {10.1145/3763344}, volume = {44}, year = {2025}, } @article{20646, abstract = {Describing general quantum many-body dynamics is a challenging task due to the exponential growth of the Hilbert space with system size. The time-dependent variational principle (TDVP) provides a powerful tool to tackle this task by projecting quantum evolution onto a classical dynamical system within a variational manifold. In classical systems, periodic orbits play a crucial role in understanding the structure of the phase space and the long-term behavior of the system. However, finding periodic orbits is generally difficult, and their existence and properties in generic TDVP dynamics over matrix product states have remained largely unexplored. In this work, we develop an algorithm to systematically identify and characterize periodic orbits in TDVP dynamics. Applying our method to the periodically kicked Ising model, we uncover both stable and unstable periodic orbits. We characterize the Kolmogorov-Arnold-Moser tori in the vicinity of stable periodic orbits and track the change of the periodic orbits as we modify the Hamiltonian parameters. We observe that periodic orbits exist at any value of the coupling constant of the kicked Ising model between prethermal and fully thermalizing regimes, but their relevance to quantum dynamics and imprint on quantum eigenstates diminishes as the system leaves the prethermal regime. Our results demonstrate that periodic orbits provide valuable insights into the TDVP approximation of quantum many-body evolution and establish a closer connection between quantum and classical chaos.}, author = {Petrova, Elena and Ljubotina, Marko and Yalniz, Gökhan and Serbyn, Maksym}, issn = {2691-3399}, journal = {PRX Quantum}, number = {4}, publisher = {American Physical Society}, title = {{Finding periodic orbits in projected quantum many-body dynamics}}, doi = {10.1103/tldp-kvkd}, volume = {6}, year = {2025}, } @article{20664, abstract = {Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzing travel data from participants of 10 international conferences in the field of magnetic resonance, namely EUROMAR, ENC and ICMRBS. We find that attending a EUROMAR conference produces, on average, more than 1 t CO2 eq.. For the analyzed conferences outside Europe, the corresponding value is about 2–3 times higher, on average, with intercontinental trips amounting to up to 5 t. We compare these conference-related emissions to other activities associated with research and show that conference travel is a substantial portion of the total climate footprint of a researcher in magnetic resonance. We explore several strategies to reduce these emissions, including the impact of selecting conference venues more strategically and the possibility of decentralized conferences. Through a detailed comparison of train versus air travel – accounting for both direct and infrastructure-related emissions – we demonstrate that train travel offers considerable carbon savings. These data may provide a basis for strategic choices of future conferences in the field and for individuals deciding on their conference attendance.}, author = {Kapoor, Lucky and Ruzickova, Natalia and Zivadinovic, Predrag and Leitner, Valentin and Sisak, Maria A and Mweka, Cecelia N and Dobbelaere, Jeroen A and Katsaros, Georgios and Schanda, Paul}, issn = {2699-0016}, journal = {Magnetic Resonance}, number = {2}, pages = {243--256}, publisher = {Copernicus Publications}, title = {{Quantifying the carbon footprint of conference travel: The case of NMR meetings}}, doi = {10.5194/mr-6-243-2025}, volume = {6}, year = {2025}, } @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}, } @article{10045, abstract = {Given a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs. }, author = {Dvorak, Martin and Kolmogorov, Vladimir}, issn = {1436-4646}, journal = {Mathematical Programming}, keywords = {minimum 0-extension problem, metric labeling problem, discrete metric spaces, metric extensions, computational complexity, valued constraint satisfaction problems, discrete convex analysis, L-convex functions}, pages = {279--322}, publisher = {Springer Nature}, title = {{Generalized minimum 0-extension problem and discrete convexity}}, doi = {10.1007/s10107-024-02064-5}, volume = {209}, 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}, } @unpublished{21427, abstract = {While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.}, author = {Dunajova, Zuzana and Tasciyan, Saren and Majek, Juraj and Merrin, Jack and Sahai, Erik and Sixt, Michael K and Hannezo, Edouard B}, booktitle = {bioRxiv}, title = {{Substrate heterogeneity promotes cancer cell dissemination through interface roughening}}, doi = {10.1101/2025.05.20.655037}, year = {2025}, } @phdthesis{20364, author = {Giannini, Caterina}, issn = {2663-337X}, keywords = {Auxin Signaling, Plant Development}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}}, doi = {10.15479/AT-ISTA-20364}, year = {2025}, }