@phdthesis{20694, abstract = {Understanding the mechanisms underlying speciation is a central aim of evolutionary biology. A persistent challenge in the field is to identify loci that contribute to reproductive isolation, while disentangling signals of selection from demography, linkage and intrinsic genomic features. Traditional population genomic approaches that rely on site-based statistics in arbitrary fixed windows face inherent limitations, as they conflate historical and contemporary processes of divergence and overlook haplotype structure. Recent advances in whole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now offer the opportunity to study genealogical relationships explicitly, revealing how lineages coalesce and recombine through time. By directly analysing haplotype clustering by species or phenotype and their patterns of coalescence, ARG-based methods show promise for diagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene flow, and tracing their evolutionary history. In this thesis, I explore the utility of genealogical approaches for studying species divergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks through the structure of the ARG, using simulations and empirical data to highlight how genealogical processes generate rich and often overlooked haplotypic patterns. In chapter 3, I examine the genomic basis of a key evolutionary innovation in marine snails Littorina. These snails offer a unique opportunity to study an innovation because they include a very recent transition from egg-laying to live bearing, yet snails with the different reproductive modes are not reciprocally monophyletic. I exploited this by using topology clustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or haplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying to live-bearing involves multiple, live-bearer-specific sweeps. Chapter 4 establishes a population-scale, phased genomic resource for Antirrhinum majus, using cost-effective haplotagging, then optimizes imputation from low-coverage data against high-accuracy KASP sequencing to maximize sequence completeness with modest accuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing strategy combines molecular phasing with statistical phasing to generate phased whole genome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing costs. In chapter 5, I analyse hybridising populations from two replicate hybrid zones to find a parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape driven by variation in demographic history. While outlier genome scans of FST failed to dissect the causes of differentiation, ARG-based topology clustering revealed a reuse of colour associated haplotypes across hybrid zones. In addition to the biological insight, this chapter also presents a comparison of the latest ARG inference tools, showing that signals of Abstract viii topological clustering qualitatively agree between methods, despite differences in the tree sequences. Next, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I integrated genome-wide association studies of floral pigmentation with genealogical inference, to test for additional colour loci, and confirm the effect of previously described loci. This work demonstrates that flower colour variation is driven by a small number of large effect loci, while also hinting at the presence of a new candidate regulatory factor. Finally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of speciation around Rosea/Eluta to understand its evolutionary origins. My results show that it consists of 5 highly divergent loci, each of which is associated with flower colour. Using patterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps and a persistent localized barrier to gene flow within an otherwise permeable genome. Together, these chapters add to the increasing pool of studies using genealogical approaches to complement and extend site-based statistics to use haplotype structures in speciation research. By tracking haplotypes directly and connecting genealogical clustering to population processes, ARG-based inference promises to provide new insights into how local selective pressures, demographic history, and long-term barriers interact to shape the genomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about the benefits of using genealogical inference to learn more than what site-based statistics could tell us.}, author = {Pal, Arka}, issn = {2663-337X}, pages = {268}, publisher = {Institute of Science and Technology Austria}, title = {{Using genealogies to study the genomic basis of species divergence}}, doi = {10.15479/AT-ISTA-20694}, year = {2025}, } @article{20190, abstract = {A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.}, author = {Pal, Arka and Shipilina, Daria and Le Moan, Alan and Mcnairn, Adrian J. and Grenier, Jennifer K. and Kucka, Marek and Coop, Graham and Chan, Yingguang Frank and Barton, Nicholas H and Field, David and Stankowski, Sean}, issn = {1365-294X}, journal = {Molecular Ecology}, number = {22}, publisher = {Wiley}, title = {{Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum}}, doi = {10.1111/mec.70067}, volume = {34}, year = {2025}, } @phdthesis{19993, abstract = {Ants are frequently challenged by different pathogens, which they counter with individual and collective responses. Usually, the pathogens like fungi or viruses are solitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These entomopathogenic nematodes are active parasites with an own behavior and chasing pray. In the first chapter, we investigated the basic biology of the host-pathogen relationship. We tested different ant life stages and found that adult ants display defense behaviors and are generally resistant to nematode infection, whereas brood is highly susceptible. In the case of worker pupae, we found a slight protective effect of the cocoon. When larvae are accompanied by adults, meaning a queen or a group of workers, survival is significantly enhanced. Moreover, we found that nematodes can transmit from infected cadavers to healthy worker larvae, confirming a transmissible disease in ants. Again, worker presence significantly reduces transmission risk. In the end, we were also able to disentangle the pathogen system and investigate the pathogenic effect of the bacterial and nematode components. In the second chapter, we studied the effect of multiple infections in adult queens and queen larvae. By multiple exposures in the mode of coinfection and superinfections, we wanted to assess the detrimental effect of combined fungal and nematode exposure to better understand how the pathogens interact with each other in an ant host. We found instances where combined exposure lead to higher mortality in a given time frame in both, adult queens and queen larvae. Overall entomopathogenic nematodes are a promising model to study worm infections in ants which extend our knowledge on collective disease defense.}, author = {Strahodinsky, Florian}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Social immunity in a tri-partite host-pathogen relationship}}, doi = {10.15479/AT-ISTA-19993}, year = {2025}, } @phdthesis{20470, abstract = {Systems design has classically relied on composable systems, in which individual subsystems have defined inputs, outputs, and interactions with each other; however, attempts at designing complex systems in synthetic biology has often run in to issues of crosstalk and interference, given that these systems must function within the context of the host. In nature, mobile genetic elements are systems that have evolved to travel between hosts, and thus appear to be a good candidate with which to evaluate composability. Selecting temperate phages as a model system, I used mathematical modelling to identify sources of information that temperate phages should respond to. I found that essential proteins of temperate phages can interfere with potential hosts, indicating limitations to composability. I also designed a lysogeny reporter construct and characterize its behavior across various laboratory and environmental strains, finding differences in phage lambda lysogens, and potential interference from prophages that already exist within the environmental strains. Although the information gathered is not conclusive, it suggests that composability is not a key property of temperate phages, implying that biological systems may not be composable, and that other system design principles should be considered when designing synthetic systems.}, author = {Wu, Bryan}, issn = {2663-337X}, pages = {102}, publisher = {Institute of Science and Technology Austria}, title = {{An examination on phages as a naturally composable system}}, doi = {10.15479/AT-ISTA-20470}, year = {2025}, } @article{19735, abstract = {The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.}, author = {Bett, Vincent K and Trejo Arellano, Minerva S and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, number = {5}, publisher = {Oxford University Press}, title = {{Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana}}, doi = {10.1093/molbev/msaf085}, volume = {42}, year = {2025}, } @phdthesis{20777, abstract = {A major challenge in neuroscience is deciphering how the brain orchestrates behavior in response to changes in environmental conditions. This process is characterized by several processing stages, from perception to the storage of important information. Information storage is performed by a memory system implemented through complex networks of highly interconnected neurons. The collective operational principles of neuronal networks that support formation and storage are the main topics of this thesis. To investigate the collective dynamics of the hippocampus from the perspective of the brain criticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches ¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures derived from neuronal avalanches suggested that during wakefulness the hippocampus operated further away from criticality than during sleep/rest. In addition, neural activity propagated differently in these two brain states, as indicated by different collapses of the avalanche shapes. Next, the Phenomenological Renormalization Group approach also indicated conceptually similar differences, through the scaling exponent of activity variance α, which was higher during sleep/rest than during awake. These results confirmed that the activity of the hippocampus exhibits signatures of criticality and that these signatures change with the state of the brain. Next, I found that memory retention was predicted by the scaling exponent of activity variance α. The exponent α measured during the sleep/rest session that followed learning correlated with memory retention during the subsequent unrewarded testing session. Moreover, α predicted performance even when controlled for reactivation that occurs in parallel. Second, α measured in the sleep/rest phase that preceded learning was correlated with the learning speed. I analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day variability of these distributions, during sleep/rest that followed learning, correlated with the scaling exponent of activity variance α, as well as with memory retention. These findings confirmed that variance scaling and functional heterogeneity provide behaviorally meaningful perspectives on hippocampal activity, as they are directly related to memory consolidation. I further investigated the process of memory acquisition and consolidation between the hippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards the goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals during sleep/rest that followed learning. This shift during sleep/rest was supported by the reactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and independently of the hippocampal SWRs. Both types of reactivation predicted subsequent memory retention, as well as the amount of goal-related remapping. Again, the day-to-day variability of the distribution of the cell timescales correlated with the goal-related remapping, in CA1 during the learning session and in mEC during sleep/rest. These results suggest that in spatial navigation tasks, the functional responsibilities of CA1 and mEC change between learning and sleep/rest and that their function benefits from increased functional heterogeneity among cells. }, author = {Zivadinovic, Predrag}, issn = {2663-337X}, pages = {104}, publisher = {Institute of Science and Technology Austria}, title = {{Scale-free activity as a basis for spatial learning and memory in the brain}}, doi = {10.15479/AT-ISTA-20777}, year = {2025}, } @article{19424, abstract = {Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime is strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors.}, author = {Saez Mollejo, Jaime and Jirovec, Daniel and Schell, Yona A and Kukucka, Josip and Calcaterra, Stefano and Chrastina, Daniel and Isella, Giovanni and Rimbach-Russ, Maximilian and Bosco, Stefano and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Exchange anisotropies in microwave-driven singlet-triplet qubits}}, doi = {10.1038/s41467-025-58969-y}, volume = {16}, year = {2025}, } @phdthesis{19836, abstract = {Over the past century, researchers have been fascinated by the quantum nature of the physical world, initially striving to understand its fundamental principles and consequences, and eventually progressing toward engineering systems that can control and manipulate quantum properties. Today, we stand at the dawn of the quantum technology era. While some quantum technologies follow well-defined roadmaps, others are still in the exciting and uncertain early stages of development. In the fields of quantum computing and quantum simulation, research is being conducted across a wide variety of platforms. Each of these demonstrates control over quantum properties but also faces challenges in scaling up to the level of a mature technology. This thesis explores some of the fundamental properties of hole spin qubits in planar germanium. Semiconductor spin qubits are considered strong candidates for the realization of quantum processors, owing to their long relaxation and coherence times, as well as their compatibility with existing semiconductor industry infrastructure. Among these, hole spin qubits in planar germanium are particularly promising. Their advantages include a large effective mass, which eases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit interaction, which enables fast and purely electrical control. However, spin-orbit coupling also introduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip tunneling, which might cause that the quantization axes are not aligned. In this thesis, we investigate the tilt between the quantization axes of two hole spins hosted in a double quantum dot as a function of both the magnetic field direction and various electrostatic configurations, demonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove to be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the physics governing spin qubit behavior. }, author = {Saez Mollejo, Jaime}, issn = {2663-337X}, pages = {175}, publisher = {Institute of Science and Technology Austria}, title = {{Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning }}, doi = {10.15479/AT-ISTA-19836}, year = {2025}, } @phdthesis{20563, abstract = {The theory of optimal transport provides an elegant and powerful description of many evolution equations as gradient flows. The primary objective of this thesis is to adapt and extend the theory to deal with important equations that are not covered by the classical framework, specifically boundary value problems and kinetic equations. Additionally, we establish new results in periodic homogenization for discrete dynamical optimal transport and in quantization of measures. Section 1.1 serves as an invitation to the classical theory of optimal transport, including the main definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the main results of this thesis, outline the motivations, and review the current state of the art. In Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet boundary conditions. We construct a time-discrete scheme involving a modification of the Wasserstein distance and, under weak assumptions, prove its convergence to a solution of this boundary value problem. In dimension 1, we show that this solution is a gradient flow in a suitable space of measures. Chapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory of optimal transport to describe and study particle systems at the mesoscopic scale. We prove adapted versions of some fundamental theorems, including the Benamou–Brenier formula and the identification of absolutely continuous curves of measures. Chapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical transportation functionals on periodic graphs in the large-scale limit when the cost functional is asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge to 1-Wasserstein distances constructed from crystalline norms on R d . Chapter 5 concerns optimal empirical quantization: the problem of approximating a measure by the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein distance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for the minimal error as n tends to infinity. }, author = {Quattrocchi, Filippo}, issn = {2663-337X}, keywords = {optimal transport, kinetic equations, boundary value problems, quantization, gradient flows, homogenization}, pages = {240}, publisher = {Institute of Science and Technology Austria}, title = {{Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures}}, doi = {10.15479/AT-ISTA-20563}, year = {2025}, } @unpublished{20569, abstract = {This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.}, author = {Brigati, Giovanni and Maas, Jan and Quattrocchi, Filippo}, booktitle = {arXiv}, keywords = {optimal transport, kinetic theory, second-order discrepancy, Vlasov equation, Wasserstein splines.}, title = {{Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures}}, doi = {10.48550/arXiv.2502.15665}, year = {2025}, } @phdthesis{19906, abstract = {Flows of ordinary fluids such as water or air transition from laminar to turbulent motion as the velocity increases. This simple dependence of the flow state solely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here various different instabilities and turbulent states can arise at low and even vanishing inertia, while high inertia turbulence counterintuitively is suppressed and its drag strongly reduced. We here show in experiments of a viscoelastic model fluid that the phenomena observed at low and high inertia have a common origin and that the same dynamical state, elasto-inertial turbulence, persists across four orders of magnitude in Reynolds number, ranging from very low inertia, all the way to high inertia Maximum drag reduction (MDR) asymptote. We also explore the transitions from Newtonian turbulence to MDR, and specific cases of flow at high polymer concentrations, exploring the relationship between flow at these wide range of control parameters. }, author = {Suresh, Sarath S}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote}}, doi = {10.15479/AT-ISTA-19906}, year = {2025}, } @phdthesis{19533, abstract = {This thesis explores advancements in quantum remote sensing and non-equilibrium phase transitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing. In the first project, I experimentally studied photon blockade breakdown as a dissipative phase transition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic limit, we demonstrated that the observed bistability is a genuine signature of a first-order phase transition in this system. This work provides insight into non-equilibrium quantum dynamics and phase transitions in driven-dissipative open quantum systems. The second project focuses on the experimental realization of a phase-conjugate receiver for quantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy environments using entangled light. While an ideal spontaneous parametric down-conversion (SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical illumination, no such ideal receiver exists. Instead, we explore an experimental realization of a phase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a Josephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled signal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate key experimental limitations that constrain practical QI performance, contributing to the development of quantum-enhanced sensing. Additionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These methods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been essential in data acquisition, noise filtering, and correlation analysis across multiple research projects. Although not real-time, these DSP techniques significantly enhance the accuracy of quantum measurements. Overall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic limit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver for QI. These findings contribute to quantum metrology, particularly for weak signal detection and remote sensing in noisy environments. }, author = {Sett, Riya}, issn = {2663-337X}, keywords = {phase transition, open quantum system, phase diagram, cavity quantum electrodynamics, superconducting qubits, semiclassical physics, quantum optics, josephson junction, parametric converter, phase conjugation, quantum radar, quantum entanglement, correlation, quantum sensing}, pages = {109}, publisher = {Institute of Science and Technology Austria}, title = {{Quantum remote sensing and non-equilibrium phase transitions in the microwave regime}}, doi = {10.15479/AT-ISTA-19533}, year = {2025}, } @article{19280, abstract = {Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics.}, author = {Redchenko, Elena and Zens, M. and Zemlicka, Martin and Peruzzo, Matilda and Hassani, Farid and Sett, Riya and Zielinski, Przemyslaw D and Dhar, H. S. and Krimer, D. O. and Rotter, S. and Fink, Johannes M}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {6}, publisher = {American Physical Society}, title = {{Observation of collapse and revival in a superconducting atomic frequency comb}}, doi = {10.1103/PhysRevLett.134.063601}, volume = {134}, year = {2025}, } @article{12178, abstract = {In this paper we consider the stochastic primitive equation for geophysical flows subject to transport noise and turbulent pressure. Admitting very rough noise terms, the global existence and uniqueness of solutions to this stochastic partial differential equation are proven using stochastic maximal L² regularity, the theory of critical spaces for stochastic evolution equations, and global a priori bounds. Compared to other results in this direction, we do not need any smallness assumption on the transport noise which acts directly on the velocity field and we also allow rougher noise terms. The adaptation to Stratonovich type noise and, more generally, to variable viscosity and/or conductivity are discussed as well.}, author = {Agresti, Antonio and Hieber, Matthias and Hussein, Amru and Saal, Martin}, issn = {2194-041X}, journal = {Stochastics and Partial Differential Equations: Analysis and Computations}, keywords = {Applied Mathematics, Modeling and Simulation, Statistics and Probability}, pages = {53--133}, publisher = {Springer Nature}, title = {{The stochastic primitive equations with transport noise and turbulent pressure}}, doi = {10.1007/s40072-022-00277-3}, volume = {12}, year = {2024}, } @article{12485, abstract = {In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation.}, author = {Agresti, Antonio and Veraar, Mark}, issn = {1432-2064}, journal = {Probability Theory and Related Fields}, pages = {957--1015}, publisher = {Springer Nature}, title = {{The critical variational setting for stochastic evolution equations}}, doi = {10.1007/s00440-023-01249-x}, volume = {188}, year = {2024}, } @article{12486, abstract = {This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas.}, author = {Agresti, Antonio}, issn = {2194-041X}, journal = {Stochastics and Partial Differential Equations: Analysis and Computations}, pages = {1907--1981}, publisher = {Springer Nature}, title = {{Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations}}, doi = {10.1007/s40072-023-00319-4}, volume = {12}, year = {2024}, } @article{12738, abstract = {We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies.}, author = {Chatterjee, Krishnendu and Katoen, Joost P and Mohr, Stefanie and Weininger, Maximilian and Winkler, Tobias}, issn = {1572-8102}, journal = {Formal Methods in System Design}, pages = {40--80}, publisher = {Springer Nature}, title = {{Stochastic games with lexicographic objectives}}, doi = {10.1007/s10703-023-00411-4}, volume = {63}, year = {2024}, } @article{12846, abstract = {We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.}, author = {Chern, Albert and Ishida, Sadashige}, issn = {2470-6566}, journal = {SIAM Journal on Applied Algebra and Geometry}, number = {3}, pages = {782--796}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Area formula for spherical polygons via prequantization}}, doi = {10.1137/23M1565255}, volume = {8}, year = {2024}, } @article{12875, abstract = {The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.}, author = {Cheung, Giselle T and Pauler, Florian and Koppensteiner, Peter and Krausgruber, Thomas and Streicher, Carmen and Schrammel, Martin and Özgen, Natalie Y and Ivec, Alexis and Bock, Christoph and Shigemoto, Ryuichi and Hippenmeyer, Simon}, issn = {0896-6273}, journal = {Neuron}, number = {2}, pages = {230--246.e11}, publisher = {Elsevier}, title = {{Multipotent progenitors instruct ontogeny of the superior colliculus}}, doi = {10.1016/j.neuron.2023.11.009}, volume = {112}, year = {2024}, } @article{13093, abstract = {The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated.}, author = {Nan, Bingfei and Li, Mengyao and Zhang, Yu and Xiao, Ke and Lim, Khak Ho and Chang, Cheng and Han, Xu and Zuo, Yong and Li, Junshan and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {2637-6113}, journal = {ACS Applied Electronic Materials}, number = {5}, pages = {2807--215}, publisher = {American Chemical Society}, title = {{Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature}}, doi = {10.1021/acsaelm.3c00055}, volume = {6}, year = {2024}, }