@inproceedings{14105, abstract = {Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks: object detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. }, author = {Sinha, Samarth and Gehler, Peter and Locatello, Francesco and Schiele, Bernt}, booktitle = {2023 IEEE/CVF Winter Conference on Applications of Computer Vision}, isbn = {9781665493475}, issn = {2642-9381}, location = {Waikoloa, HI, United States}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{TeST: Test-time Self-Training under distribution shift}}, doi = {10.1109/wacv56688.2023.00278}, year = {2023}, } @article{14256, abstract = {Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes. Aims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields. Methods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies. Results. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies. Conclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.}, author = {Mathis, S. and Bugnet, Lisa Annabelle}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields}}, doi = {10.1051/0004-6361/202346832}, volume = {676}, year = {2023}, } @article{14261, abstract = {In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing.}, author = {Gamper, Jakob and Kluibenschedl, Florian and Weiss, Alexander K.H. and Hofer, Thomas S.}, issn = {1948-7185}, journal = {Journal of Physical Chemistry Letters}, number = {33}, pages = {7395--7403}, publisher = {American Chemical Society}, title = {{Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems}}, doi = {10.1021/acs.jpclett.3c01707}, volume = {14}, year = {2023}, } @inproceedings{14208, abstract = {This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory.}, author = {Zhu, Zhenyu and Liu, Fanghui and Chrysos, Grigorios G and Locatello, Francesco and Cevher, Volkan}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, location = {Honolulu, Hawaii, United States}, pages = {43105--43128}, publisher = {ML Research Press}, title = {{Benign overfitting in deep neural networks under lazy training}}, volume = {202}, year = {2023}, } @unpublished{14209, abstract = {Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks.}, author = {Burg, Max F. and Wenzel, Florian and Zietlow, Dominik and Horn, Max and Makansi, Osama and Locatello, Francesco and Russell, Chris}, booktitle = {arXiv}, title = {{A data augmentation perspective on diffusion models and retrieval}}, doi = {10.48550/arXiv.2304.10253}, year = {2023}, } @inproceedings{14211, abstract = {Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data.}, author = {Montagna, Francesco and Noceti, Nicoletta and Rosasco, Lorenzo and Zhang, Kun and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Causal discovery with score matching on additive models with arbitrary noise}}, year = {2023}, } @inproceedings{14212, abstract = {This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar.}, author = {Montagna, Francesco and Noceti, Nicoletta and Rosasco, Lorenzo and Zhang, Kun and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Scalable causal discovery with score matching}}, year = {2023}, } @inproceedings{14214, abstract = {Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work.}, author = {Liu, Yuejiang and Alahi, Alexandre and Russell, Chris and Horn, Max and Zietlow, Dominik and Schölkopf, Bernhard and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Causal triplet: An open challenge for intervention-centric causal representation learning}}, year = {2023}, } @inproceedings{14217, abstract = {Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).}, author = {Moschella, Luca and Maiorca, Valentino and Fumero, Marco and Norelli, Antonio and Locatello, Francesco and Rodolà, Emanuele}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Relative representations enable zero-shot latent space communication}}, year = {2023}, } @inproceedings{14222, abstract = {Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional "dead leaves" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set.}, author = {Tangemann, Matthias and Schneider, Steffen and Kügelgen, Julius von and Locatello, Francesco and Gehler, Peter and Brox, Thomas and Kümmerer, Matthias and Bethge, Matthias and Schölkopf, Bernhard}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Unsupervised object learning via common fate}}, year = {2023}, } @inproceedings{14218, abstract = {Humans naturally decompose their environment into entities at the appropriate level of abstraction to act in the world. Allowing machine learning algorithms to derive this decomposition in an unsupervised way has become an important line of research. However, current methods are restricted to simulated data or require additional information in the form of motion or depth in order to successfully discover objects. In this work, we overcome this limitation by showing that reconstructing features from models trained in a self-supervised manner is a sufficient training signal for object-centric representations to arise in a fully unsupervised way. Our approach, DINOSAUR, significantly out-performs existing image-based object-centric learning models on simulated data and is the first unsupervised object-centric model that scales to real-world datasets such as COCO and PASCAL VOC. DINOSAUR is conceptually simple and shows competitive performance compared to more involved pipelines from the computer vision literature.}, author = {Seitzer, Maximilian and Horn, Max and Zadaianchuk, Andrii and Zietlow, Dominik and Xiao, Tianjun and Carl-Johann Simon-Gabriel, Carl-Johann Simon-Gabriel and He, Tong and Zhang, Zheng and Schölkopf, Bernhard and Brox, Thomas and Locatello, Francesco}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Bridging the gap to real-world object-centric learning}}, year = {2023}, } @inproceedings{14219, abstract = {In this paper, we show that recent advances in self-supervised feature learning enable unsupervised object discovery and semantic segmentation with a performance that matches the state of the field on supervised semantic segmentation 10 years ago. We propose a methodology based on unsupervised saliency masks and self-supervised feature clustering to kickstart object discovery followed by training a semantic segmentation network on pseudo-labels to bootstrap the system on images with multiple objects. We present results on PASCAL VOC that go far beyond the current state of the art (50.0 mIoU), and we report for the first time results on MS COCO for the whole set of 81 classes: our method discovers 34 categories with more than $20\%$ IoU, while obtaining an average IoU of 19.6 for all 81 categories.}, author = {Zadaianchuk, Andrii and Kleindessner, Matthaeus and Zhu, Yi and Locatello, Francesco and Brox, Thomas}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Unsupervised semantic segmentation with self-supervised object-centric representations}}, year = {2023}, } @unpublished{14333, abstract = {As causal ground truth is incredibly rare, causal discovery algorithms are commonly only evaluated on simulated data. This is concerning, given that simulations reflect common preconceptions about generating processes regarding noise distributions, model classes, and more. In this work, we propose a novel method for falsifying the output of a causal discovery algorithm in the absence of ground truth. Our key insight is that while statistical learning seeks stability across subsets of data points, causal learning should seek stability across subsets of variables. Motivated by this insight, our method relies on a notion of compatibility between causal graphs learned on different subsets of variables. We prove that detecting incompatibilities can falsify wrongly inferred causal relations due to violation of assumptions or errors from finite sample effects. Although passing such compatibility tests is only a necessary criterion for good performance, we argue that it provides strong evidence for the causal models whenever compatibility entails strong implications for the joint distribution. We also demonstrate experimentally that detection of incompatibilities can aid in causal model selection.}, author = {Faller, Philipp M. and Vankadara, Leena Chennuru and Mastakouri, Atalanti A. and Locatello, Francesco and Janzing, Dominik}, booktitle = {arXiv}, title = {{Self-compatibility: Evaluating causal discovery without ground truth}}, doi = {10.48550/arXiv.2307.09552}, year = {2023}, } @article{14277, abstract = {Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.}, author = {Boocock, Daniel R and Hirashima, Tsuyoshi and Hannezo, Edouard B}, issn = {2835-8279}, journal = {PRX Life}, number = {1}, publisher = {American Physical Society}, title = {{Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers}}, doi = {10.1103/prxlife.1.013001}, volume = {1}, year = {2023}, } @article{14314, abstract = {The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.}, author = {Nardin, Michele and Käfer, Karola and Stella, Federico and Csicsvari, Jozsef L}, issn = {2211-1247}, journal = {Cell Reports}, number = {9}, publisher = {Elsevier}, title = {{Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions}}, doi = {10.1016/j.celrep.2023.113015}, volume = {42}, year = {2023}, } @article{14315, abstract = {During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.}, author = {Cho, Ukrae H. and Hetzer, Martin W}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress}}, doi = {10.7554/eLife.89066}, volume = {12}, year = {2023}, } @article{14319, abstract = {We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We also make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour multiplicities.}, author = {Anastos, Michael and Fabian, David and Müyesser, Alp and Szabó, Tibor}, issn = {1077-8926}, journal = {Electronic Journal of Combinatorics}, number = {3}, publisher = {Electronic Journal of Combinatorics}, title = {{Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets}}, doi = {10.37236/11714}, volume = {30}, year = {2023}, } @inproceedings{14318, abstract = {Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis. In this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.}, author = {Sun, Yican and Fu, Hongfei and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar}, booktitle = {Computer Aided Verification}, isbn = {9783031377082}, issn = {1611-3349}, location = {Paris, France}, pages = {16--39}, publisher = {Springer Nature}, title = {{Automated tail bound analysis for probabilistic recurrence relations}}, doi = {10.1007/978-3-031-37709-9_2}, volume = {13966}, year = {2023}, } @inproceedings{14317, abstract = {Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization. In light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples.}, author = {Akshay, S. and Chatterjee, Krishnendu and Meggendorfer, Tobias and Zikelic, Dorde}, booktitle = {International Conference on Computer Aided Verification}, isbn = {9783031377082}, issn = {1611-3349}, location = {Paris, France}, pages = {86--112}, publisher = {Springer Nature}, title = {{MDPs as distribution transformers: Affine invariant synthesis for safety objectives}}, doi = {10.1007/978-3-031-37709-9_5}, volume = {13966}, year = {2023}, } @article{14316, abstract = {Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.}, author = {Nagano, Makoto and Aoshima, Kaito and Shimamura, Hiroki and Siekhaus, Daria E and Toshima, Junko Y. and Toshima, Jiro}, issn = {1477-9137}, journal = {Journal of Cell Science}, number = {17}, publisher = {The Company of Biologists}, title = {{Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway}}, doi = {10.1242/jcs.261448}, volume = {136}, year = {2023}, } @article{14320, abstract = {The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.}, author = {Henderson, Paul M and Ghazaryan, Areg and Zibrov, Alexander A. and Young, Andrea F. and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {12}, publisher = {American Physical Society}, title = {{Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene}}, doi = {10.1103/physrevb.108.125411}, volume = {108}, year = {2023}, } @phdthesis{12732, abstract = {Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices. Going beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium. In this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models. In particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models. Using tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods. In this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges. Inspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect. In the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model. The system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping. We show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon. We further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes. The study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times. This work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies. Next, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density. This feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies. The time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities. Our results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument. To support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied. In the last Chapter of this Thesis, we address the topic of many-body localization proximity effect. We study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons. The interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques. Our simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong. We furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory. Finally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.}, author = {Brighi, Pietro}, issn = {2663-337X}, pages = {158}, publisher = {Institute of Science and Technology Austria}, title = {{Ergodicity breaking in disordered and kinetically constrained quantum many-body systems}}, doi = {10.15479/at:ista:12732}, year = {2023}, } @article{14334, abstract = {Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.}, author = {Brighi, Pietro and Ljubotina, Marko and Serbyn, Maksym}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {SciPost Foundation}, title = {{Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models}}, doi = {10.21468/scipostphys.15.3.093}, volume = {15}, year = {2023}, } @article{14321, abstract = {We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.}, author = {Al Hyder, Ragheed and Cappellaro, Alberto and Lemeshko, Mikhail and Volosniev, Artem}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {10}, publisher = {AIP Publishing}, title = {{Achiral dipoles on a ferromagnet can affect its magnetization direction}}, doi = {10.1063/5.0165806}, volume = {159}, year = {2023}, } @article{14342, abstract = {We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.}, author = {Lorenc, Dusan and Alpichshev, Zhanybek}, issn = {0003-6951}, journal = {Applied Physics Letters}, number = {9}, publisher = {AIP Publishing}, title = {{Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam}}, doi = {10.1063/5.0161713}, volume = {123}, year = {2023}, } @article{14341, abstract = {Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines.}, author = {Scarselli, Davide and Lopez Alonso, Jose M and Varshney, Atul and Hof, Björn}, issn = {1476-4687}, journal = {Nature}, number = {7977}, pages = {71--74}, publisher = {Springer Nature}, title = {{Turbulence suppression by cardiac-cycle-inspired driving of pipe flow}}, doi = {10.1038/s41586-023-06399-5}, volume = {621}, year = {2023}, } @article{14368, abstract = {Purpose: Biallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants. Methods: Exome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model. Results: We report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model. Conclusion: We define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity.}, author = {Accogli, Andrea and Lin, Sheng-Jia and Severino, Mariasavina and Kim, Sung-Hoon and Huang, Kevin and Rocca, Clarissa and Landsverk, Megan and Zaki, Maha S. and Al-Maawali, Almundher and Srinivasan, Varunvenkat M. and Al-Thihli, Khalid and Schaefer, G. Bradly and Davis, Monica and Tonduti, Davide and Doneda, Chiara and Marten, Lara M. and Mühlhausen, Chris and Gomez, Maria and Lamantea, Eleonora and Mena, Rafael and Nizon, Mathilde and Procaccio, Vincent and Begtrup, Amber and Telegrafi, Aida and Cui, Hong and Schulz, Heidi L. and Mohr, Julia and Biskup, Saskia and Loos, Mariana Amina and Aráoz, Hilda Verónica and Salpietro, Vincenzo and Keppen, Laura Davis and Chitre, Manali and Petree, Cassidy and Raymond, Lucy and Vogt, Julie and Sawyer, Lindsey B. and Basinger, Alice A. and Pedersen, Signe Vandal and Pearson, Toni S. and Grange, Dorothy K. and Lingappa, Lokesh and McDunnah, Paige and Horvath, Rita and Cognè, Benjamin and Isidor, Bertrand and Hahn, Andreas and Gripp, Karen W. and Jafarnejad, Seyed Mehdi and Østergaard, Elsebet and Prada, Carlos E. and Ghezzi, Daniele and Gowda, Vykuntaraju K. and Taylor, Robert W. and Sonenberg, Nahum and Houlden, Henry and Sissler, Marie and Varshney, Gaurav K. and Maroofian, Reza}, issn = {1098-3600}, journal = {Genetics in Medicine}, keywords = {Genetics (clinical)}, number = {11}, publisher = {Elsevier}, title = {{Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder}}, doi = {10.1016/j.gim.2023.100938}, volume = {25}, year = {2023}, } @inproceedings{13120, abstract = {We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.}, author = {Dvorak, Martin and Blanchette, Jasmin}, booktitle = {14th International Conference on Interactive Theorem Proving}, isbn = {9783959772846}, issn = {1868-8969}, location = {Bialystok, Poland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Closure properties of general grammars - formally verified}}, doi = {10.4230/LIPIcs.ITP.2023.15}, volume = {268}, year = {2023}, } @article{13969, abstract = {Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider good drawings, i.e., we require that any two edges have at most one common point which can be a common vertex or a crossing. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of a good drawing with no toothed hole. In general the number of toothed holes has to be added to the 8-approximation. In the special case of circular drawings the approximation factor is 8, this improves upon the 10-approximation of Fink et al. [14]. Our approach also works with the same approximation factor for families of pseudosegments, i.e., curves intersecting at most once. We also show how to compute a 9/2-approximation when the intersection graph of the pseudosegments is bipartite and has no toothed hole.}, author = {Arroyo Guevara, Alan M and Felsner, Stefan}, issn = {1526-1719}, journal = {Journal of Graph Algorithms and Applications}, number = {6}, pages = {433--457}, publisher = {Brown University}, title = {{Approximating the bundled crossing number}}, doi = {10.7155/jgaa.00629}, volume = {27}, year = {2023}, } @inproceedings{14344, abstract = {We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively, each being best possible in its own setting.}, author = {Anastos, Michael}, booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9781611977554}, location = {Florence, Italy}, pages = {2286--2323}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Fast algorithms for solving the Hamilton cycle problem with high probability}}, doi = {10.1137/1.9781611977554.ch88}, volume = {2023}, year = {2023}, } @article{12710, abstract = {Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.}, author = {Schamberger, Barbara and Ziege, Ricardo and Anselme, Karine and Ben Amar, Martine and Bykowski, Michał and Castro, André P.G. and Cipitria, Amaia and Coles, Rhoslyn A. and Dimova, Rumiana and Eder, Michaela and Ehrig, Sebastian and Escudero, Luis M. and Evans, Myfanwy E. and Fernandes, Paulo R. and Fratzl, Peter and Geris, Liesbet and Gierlinger, Notburga and Hannezo, Edouard B and Iglič, Aleš and Kirkensgaard, Jacob J.K. and Kollmannsberger, Philip and Kowalewska, Łucja and Kurniawan, Nicholas A. and Papantoniou, Ioannis and Pieuchot, Laurent and Pires, Tiago H.V. and Renner, Lars D. and Sageman-Furnas, Andrew O. and Schröder-Turk, Gerd E. and Sengupta, Anupam and Sharma, Vikas R. and Tagua, Antonio and Tomba, Caterina and Trepat, Xavier and Waters, Sarah L. and Yeo, Edwina F. and Roschger, Andreas and Bidan, Cécile M. and Dunlop, John W.C.}, issn = {1521-4095}, journal = {Advanced Materials}, number = {13}, publisher = {Wiley}, title = {{Curvature in biological systems: Its quantification, emergence, and implications across the scales}}, doi = {10.1002/adma.202206110}, volume = {35}, year = {2023}, } @article{14377, abstract = {Coherent flows of self-propelled particles are characterized by vortices and jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal a crossover between defect-free active turbulence and active turbulence laden with topological defects. Interestingly, we show that concurrent to the crossover from defect-free to defect-laden active turbulence is the restoration of the previously broken SO(2) symmetry signaled by the fast decay of the two-point correlations. By stability analyses of the topological charge density field, we provide theoretical insights on the criterion for the crossover to the defect-laden active turbulent state. Despite the distinct symmetry features between these two active turbulence regimes, the flow fluctuations exhibit universal statistical scaling behaviors at large scales, while the spectrum of polarity fluctuations decays exponentially at small length scales compared to the active energy injection length. These findings reveal a dynamical crossover between distinct spatiotemporal organization patterns in polar active matter.}, author = {Andersen, Benjamin H. and Renaud, Julian B and Rønning, Jonas and Angheluta, Luiza and Doostmohammadi, Amin}, issn = {2469-990X}, journal = {Physical Review Fluids}, keywords = {Fluid Flow and Transfer Processes, Modeling and Simulation, Computational Mechanics}, number = {6}, publisher = {American Physical Society}, title = {{Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter}}, doi = {10.1103/physrevfluids.8.063101}, volume = {8}, year = {2023}, } @article{13340, abstract = {Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.}, author = {Gemen, Julius and Church, Jonathan R. and Ruoko, Tero-Petri and Durandin, Nikita and Białek, Michał J. and Weissenfels, Maren and Feller, Moran and Kazes, Miri and Borin, Veniamin A. and Odaybat, Magdalena and Kalepu, Rishir and Diskin-Posner, Yael and Oron, Dan and Fuchter, Matthew J. and Priimagi, Arri and Schapiro, Igor and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, number = {6664}, pages = {1357--1363}, publisher = {American Association for the Advancement of Science}, title = {{Disequilibrating azoarenes by visible-light sensitization under confinement}}, doi = {10.1126/science.adh9059}, volume = {381}, year = {2023}, } @article{12705, abstract = {The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.}, author = {Sorichetti, Valerio and Ninarello, Andrea and Ruiz-Franco, José and Hugouvieux, Virginie and Zaccarelli, Emanuela and Micheletti, Cristian and Kob, Walter and Rovigatti, Lorenzo}, issn = {1089-7690}, journal = {Journal of Chemical Physics}, number = {7}, publisher = {American Institute of Physics}, title = {{Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks}}, doi = {10.1063/5.0134271}, volume = {158}, year = {2023}, } @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}, publisher = {Springer Nature}, title = {{Stochastic games with lexicographic objectives}}, doi = {10.1007/s10703-023-00411-4}, year = {2023}, } @misc{14279, abstract = {The zip file includes source data used in the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript. A sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.}, author = {Ucar, Mehmet C}, publisher = {Zenodo}, title = {{Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration"}}, doi = {10.5281/ZENODO.8133960}, year = {2023}, } @article{10405, abstract = {We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. }, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1097-0312}, journal = {Communications on Pure and Applied Mathematics}, number = {5}, pages = {946--1034}, publisher = {Wiley}, title = {{Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices}}, doi = {10.1002/cpa.22028}, volume = {76}, year = {2023}, } @article{10770, abstract = {Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings.}, author = {Graham, Thomas and Kleshnina, Maria and Filar, Jerzy A.}, issn = {2153-0793}, journal = {Dynamic Games and Applications}, pages = {231--264}, publisher = {Springer Nature}, title = {{Where do mistakes lead? A survey of games with incompetent players}}, doi = {10.1007/s13235-022-00425-3}, volume = {13}, year = {2023}, } @article{10145, abstract = {We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.}, author = {Dello Schiavo, Lorenzo}, issn = {1572-929X}, journal = {Potential Analysis}, pages = {573--615}, publisher = {Springer Nature}, title = {{Ergodic decomposition of Dirichlet forms via direct integrals and applications}}, doi = {10.1007/s11118-021-09951-y}, volume = {58}, year = {2023}, } @article{12669, abstract = {The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.}, author = {Manavella, Pablo A and Godoy Herz, Micaela A and Kornblihtt, Alberto R and Sorenson, Reed and Sieburth, Leslie E and Nakaminami, Kentaro and Seki, Motoaki and Ding, Yiliang and Sun, Qianwen and Kang, Hunseung and Ariel, Federico D and Crespi, Martin and Giudicatti, Axel J and Cai, Qiang and Jin, Hailing and Feng, Xiaoqi and Qi, Yijun and Pikaard, Craig S}, issn = {1532-298X}, journal = {The Plant Cell}, keywords = {Cell Biology, Plant Science}, number = {6}, publisher = {Oxford University Press}, title = {{Beyond transcription: compelling open questions in plant RNA biology}}, doi = {10.1093/plcell/koac346}, volume = {35}, year = {2023}, } @article{11706, abstract = {We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. }, author = {Liebenau, Anita and Mattos, Letícia and Mendonca Dos Santos, Walner and Skokan, Jozef}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {1035--1055}, publisher = {Wiley}, title = {{Asymmetric Ramsey properties of random graphs involving cliques and cycles}}, doi = {10.1002/rsa.21106}, volume = {62}, year = {2023}, } @article{12707, abstract = {We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.}, author = {Erdös, László and Xu, Yuanyuan}, issn = {1350-7265}, journal = {Bernoulli}, number = {2}, pages = {1063--1079}, publisher = {Bernoulli Society for Mathematical Statistics and Probability}, title = {{Small deviation estimates for the largest eigenvalue of Wigner matrices}}, doi = {10.3150/22-BEJ1490}, volume = {29}, year = {2023}, } @article{12837, abstract = {As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.}, author = {Bocanegra, Laura and Singh, Amrita and Hannezo, Edouard B and Zagórski, Marcin P and Kicheva, Anna}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1050--1058}, publisher = {Springer Nature}, title = {{Cell cycle dynamics control fluidity of the developing mouse neuroepithelium}}, doi = {10.1038/s41567-023-01977-w}, volume = {19}, year = {2023}, } @phdthesis{13081, abstract = {During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.}, author = {Bocanegra, Laura}, issn = {2663 - 337X}, pages = {93}, publisher = {Institute of Science and Technology Austria}, title = {{Epithelial dynamics during mouse neural tube development}}, doi = {10.15479/at:ista:13081}, year = {2023}, } @article{12863, abstract = {In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.}, author = {Filipović Marijić, Vlatka and Krasnici, Nesrete and Valić, Damir and Kapetanović, Damir and Vardić Smrzlić, Irena and Jordanova, Maja and Rebok, Katerina and Ramani, Sheriban and Kostov, Vasil and Nastova, Rodne and Dragun, Zrinka}, issn = {1614-7499}, journal = {Environmental Science and Pollution Research}, pages = {63510--63521}, publisher = {Springer Nature}, title = {{Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish}}, doi = {10.1007/s11356-023-26844-2}, volume = {30}, year = {2023}, } @article{12836, abstract = {Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.}, author = {Khatoniar, Mandeep and Yama, Nicholas and Ghazaryan, Areg and Guddala, Sriram and Ghaemi, Pouyan and Majumdar, Kausik and Menon, Vinod}, issn = {2195-1071}, journal = {Advanced Optical Materials}, number = {13}, publisher = {Wiley}, title = {{Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities}}, doi = {10.1002/adom.202202631}, volume = {11}, year = {2023}, } @article{12959, abstract = {This paper deals with the large-scale behaviour of dynamical optimal transport on Zd -periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ -convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs.}, author = {Gladbach, Peter and Kopfer, Eva and Maas, Jan and Portinale, Lorenzo}, issn = {1432-0835}, journal = {Calculus of Variations and Partial Differential Equations}, number = {5}, publisher = {Springer Nature}, title = {{Homogenisation of dynamical optimal transport on periodic graphs}}, doi = {10.1007/s00526-023-02472-z}, volume = {62}, year = {2023}, } @article{12915, abstract = {Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K.}, author = {Xing, Congcong and Zhang, Yu and Xiao, Ke and Han, Xu and Liu, Yu and Nan, Bingfei and Ramon, Maria Garcia and Lim, Khak Ho and Li, Junshan and Arbiol, Jordi and Poudel, Bed and Nozariasbmarz, Amin and Li, Wenjie and Ibáñez, Maria and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, number = {9}, pages = {8442--8452}, publisher = {American Chemical Society}, title = {{Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites}}, doi = {10.1021/acsnano.3c00495}, volume = {17}, year = {2023}, } @article{12961, abstract = {Two notes separated by a doubling in frequency sound similar to humans. This “octave equivalence” is critical to perception and production of music and speech and occurs early in human development. Because it also occurs cross-culturally, a biological basis of octave equivalence has been hypothesized. Members of our team previousy suggested four human traits are at the root of this phenomenon: (1) vocal learning, (2) clear octave information in vocal harmonics, (3) differing vocal ranges, and (4) vocalizing together. Using cross-species studies, we can test how relevant these respective traits are, while controlling for enculturation effects and addressing questions of phylogeny. Common marmosets possess forms of three of the four traits, lacking differing vocal ranges. We tested 11 common marmosets by adapting an established head-turning paradigm, creating a parallel test to an important infant study. Unlike human infants, marmosets responded similarly to tones shifted by an octave or other intervals. Because previous studies with the same head-turning paradigm produced differential results to discernable acoustic stimuli in common marmosets, our results suggest that marmosets do not perceive octave equivalence. Our work suggests differing vocal ranges between adults and children and men and women and the way they are used in singing together may be critical to the development of octave equivalence.}, author = {Wagner, Bernhard and Šlipogor, Vedrana and Oh, Jinook and Varga, Marion and Hoeschele, Marisa}, issn = {1467-7687}, journal = {Developmental Science}, number = {5}, publisher = {Wiley}, title = {{A comparison between common marmosets (Callithrix jacchus) and human infants sheds light on traits proposed to be at the root of human octave equivalence}}, doi = {10.1111/desc.13395}, volume = {26}, year = {2023}, } @article{12877, abstract = {We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.}, author = {De Simoi, Jacopo and Kaloshin, Vadim and Leguil, Martin}, issn = {1432-1297}, journal = {Inventiones Mathematicae}, pages = {829--901}, publisher = {Springer Nature}, title = {{Marked Length Spectral determination of analytic chaotic billiards with axial symmetries}}, doi = {10.1007/s00222-023-01191-8}, volume = {233}, year = {2023}, }