@misc{14494, abstract = {We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023). Buri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841}, author = {Buri, Pascal and Fatichi, Simone and Shaw, Thomas and Miles, Evan and McCarthy, Michael and Fyffe, Catriona Louise and Fugger, Stefan and Ren, Shaoting and Kneib, Marin and Jouberton, Achille and Steiner, Jakob and Fujita, Koji and Pellicciotti, Francesca}, publisher = {Zenodo}, title = {{Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"}}, doi = {10.5281/ZENODO.8402426}, year = {2023}, } @article{14499, abstract = {An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables. The proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes.}, author = {Kwan, Matthew Alan and Sah, Ashwin and Sauermann, Lisa and Sawhney, Mehtaab}, issn = {2050-5086}, journal = {Forum of Mathematics, Pi}, keywords = {Discrete Mathematics and Combinatorics, Geometry and Topology, Mathematical Physics, Statistics and Probability, Algebra and Number Theory, Analysis}, publisher = {Cambridge University Press}, title = {{Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture}}, doi = {10.1017/fmp.2023.17}, volume = {11}, year = {2023}, } @misc{14502, abstract = {A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.}, author = {Dimchev, Georgi A and Amiri, Behnam and Fäßler, Florian and Falcke, Martin and Schur, Florian KM}, keywords = {cryo-electron tomography, actin cytoskeleton, toolbox}, publisher = {Institute of Science and Technology Austria}, title = {{Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data}}, doi = {10.15479/AT:ISTA:14502}, year = {2023}, } @article{14513, abstract = {Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems.}, author = {Mistakidis, S. I. and Volosniev, Artem and Barfknecht, R. E. and Fogarty, T. and Busch, Th and Foerster, A. and Schmelcher, P. and Zinner, N. T.}, issn = {0370-1573}, journal = {Physics Reports}, pages = {1--108}, publisher = {Elsevier}, title = {{Few-body Bose gases in low dimensions - A laboratory for quantum dynamics}}, doi = {10.1016/j.physrep.2023.10.004}, volume = {1042}, year = {2023}, } @article{14514, abstract = {The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta V. and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James E. and Souslov, Anton}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Modeling Leidenfrost levitation of soft elastic solids}}, doi = {10.1103/PhysRevLett.131.168201}, volume = {131}, year = {2023}, } @article{14515, abstract = {Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.}, author = {Reinhardt, Manuel and Tkačik, Gašper and Ten Wolde, Pieter Rein}, issn = {2160-3308}, journal = {Physical Review X}, number = {4}, publisher = {American Physical Society}, title = {{Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories}}, doi = {10.1103/PhysRevX.13.041017}, volume = {13}, year = {2023}, } @inproceedings{14516, abstract = {We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.}, author = {Beaver, Donald and Kelkar, Mahimna and Lewi, Kevin and Nikolaenko, Valeria and Sonnino, Alberto and Chalkias, Konstantinos and Kokoris Kogias, Eleftherios and Naurois, Ladi De and Roy, Arnab}, booktitle = {5th Conference on Advances in Financial Technologies}, isbn = {9783959773034}, issn = {1868-8969}, location = {Princeton, NJ, United States}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{STROBE: Streaming Threshold Random Beacons}}, doi = {10.4230/LIPIcs.AFT.2023.7}, volume = {282}, year = {2023}, } @inproceedings{14518, abstract = {We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.}, author = {Avni, Guy and Meggendorfer, Tobias and Sadhukhan, Suman and Tkadlec, Josef and Zikelic, Dorde}, booktitle = {Frontiers in Artificial Intelligence and Applications}, isbn = {9781643684369}, issn = {0922-6389}, location = {Krakow, Poland}, pages = {141--148}, publisher = {IOS Press}, title = {{Reachability poorman discrete-bidding games}}, doi = {10.3233/FAIA230264}, volume = {372}, year = {2023}, } @misc{14523, abstract = {see Readme file}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James and Souslov, Anton}, publisher = {Zenodo}, title = {{SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1}}, doi = {10.5281/ZENODO.8329143}, year = {2023}, } @article{14551, abstract = {Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.}, author = {Briffa, Amy and Hollwey, Elizabeth and Shahzad, Zaigham and Moore, Jonathan D. and Lyons, David B. and Howard, Martin and Zilberman, Daniel}, issn = {2405-4720}, journal = {Cell Systems}, number = {11}, pages = {953--967}, publisher = {Elsevier}, title = {{Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations}}, doi = {10.1016/j.cels.2023.10.007}, volume = {14}, year = {2023}, } @article{14552, abstract = {Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.}, author = {Robinson, M. L. and Hahn, P. G. and Inouye, B. D. and Underwood, N. and Whitehead, S. R. and Abbott, K. C. and Bruna, E. M. and Cacho, N. I. and Dyer, L. A. and Abdala-Roberts, L. and Allen, W. J. and Andrade, J. F. and Angulo, D. F. and Anjos, D. and Anstett, D. N. and Bagchi, R. and Bagchi, S. and Barbosa, M. and Barrett, S. and Baskett, Carina and Ben-Simchon, E. and Bloodworth, K. J. and Bronstein, J. L. and Buckley, Y. M. and Burghardt, K. T. and Bustos-Segura, C. and Calixto, E. S. and Carvalho, R. L. and Castagneyrol, B. and Chiuffo, M. C. and Cinoğlu, D. and Cinto Mejía, E. and Cock, M. C. and Cogni, R. and Cope, O. L. and Cornelissen, T. and Cortez, D. R. and Crowder, D. W. and Dallstream, C. and Dáttilo, W. and Davis, J. K. and Dimarco, R. D. and Dole, H. E. and Egbon, I. N. and Eisenring, M. and Ejomah, A. and Elderd, B. D. and Endara, M. J. and Eubanks, M. D. and Everingham, S. E. and Farah, K. N. and Farias, R. P. and Fernandes, A. P. and Fernandes, G. W. and Ferrante, M. and Finn, A. and Florjancic, G. A. and Forister, M. L. and Fox, Q. N. and Frago, E. and França, F. M. and Getman-Pickering, A. S. and Getman-Pickering, Z. and Gianoli, E. and Gooden, B. and Gossner, M. M. and Greig, K. A. and Gripenberg, S. and Groenteman, R. and Grof-Tisza, P. and Haack, N. and Hahn, L. and Haq, S. M. and Helms, A. M. and Hennecke, J. and Hermann, S. L. and Holeski, L. M. and Holm, S. and Hutchinson, M. C. and Jackson, E. E. and Kagiya, S. and Kalske, A. and Kalwajtys, M. and Karban, R. and Kariyat, R. and Keasar, T. and Kersch-Becker, M. F. and Kharouba, H. M. and Kim, T. N. and Kimuyu, D. M. and Kluse, J. and Koerner, S. E. and Komatsu, K. J. and Krishnan, S. and Laihonen, M. and Lamelas-López, L. and Lascaleia, M. C. and Lecomte, N. and Lehn, C. R. and Li, X. and Lindroth, R. L. and Lopresti, E. F. and Losada, M. and Louthan, A. M. and Luizzi, V. J. and Lynch, S. C. and Lynn, J. S. and Lyon, N. J. and Maia, L. F. and Maia, R. A. and Mannall, T. L. and Martin, B. S. and Massad, T. J. and Mccall, A. C. and Mcgurrin, K. and Merwin, A. C. and Mijango-Ramos, Z. and Mills, C. H. and Moles, A. T. and Moore, C. M. and Moreira, X. and Morrison, C. R. and Moshobane, M. C. and Muola, A. and Nakadai, R. and Nakajima, K. and Novais, S. and Ogbebor, C. O. and Ohsaki, H. and Pan, V. S. and Pardikes, N. A. and Pareja, M. and Parthasarathy, N. and Pawar, R. R. and Paynter, Q. and Pearse, I. S. and Penczykowski, R. M. and Pepi, A. A. and Pereira, C. C. and Phartyal, S. S. and Piper, F. I. and Poveda, K. and Pringle, E. G. and Puy, J. and Quijano, T. and Quintero, C. and Rasmann, S. and Rosche, C. and Rosenheim, L. Y. and Rosenheim, J. A. and Runyon, J. B. and Sadeh, A. and Sakata, Y. and Salcido, D. M. and Salgado-Luarte, C. and Santos, B. A. and Sapir, Y. and Sasal, Y. and Sato, Y. and Sawant, M. and Schroeder, H. and Schumann, I. and Segoli, M. and Segre, H. and Shelef, O. and Shinohara, N. and Singh, R. P. and Smith, D. S. and Sobral, M. and Stotz, G. C. and Tack, A. J.M. and Tayal, M. and Tooker, J. F. and Torrico-Bazoberry, D. and Tougeron, K. and Trowbridge, A. M. and Utsumi, S. and Uyi, O. and Vaca-Uribe, J. L. and Valtonen, A. and Van Dijk, L. J.A. and Vandvik, V. and Villellas, J. and Waller, L. P. and Weber, M. G. and Yamawo, A. and Yim, S. and Zarnetske, P. L. and Zehr, L. N. and Zhong, Z. and Wetzel, W. C.}, issn = {1095-9203}, journal = {Science}, number = {6671}, pages = {679--683}, publisher = {AAAS}, title = {{Plant size, latitude, and phylogeny explain within-population variability in herbivory}}, doi = {10.1126/science.adh8830}, volume = {382}, year = {2023}, } @article{14553, abstract = {Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.}, author = {Fedotova, Ekaterina and Kuznetsov, Nikolai and Tiunov, Egor and Ulanov, A. E. and Lvovsky, A. I.}, issn = {2469-9934}, journal = {Physical Review A}, number = {4}, publisher = {American Physical Society}, title = {{Continuous-variable quantum tomography of high-amplitude states}}, doi = {10.1103/PhysRevA.108.042430}, volume = {108}, year = {2023}, } @article{14554, abstract = {The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format.}, author = {Cornalba, Federico and Shardlow, Tony}, issn = {2804-7214}, journal = {ESAIM: Mathematical Modelling and Numerical Analysis}, number = {5}, pages = {3061--3090}, publisher = {EDP Sciences}, title = {{The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime}}, doi = {10.1051/m2an/2023077}, volume = {57}, year = {2023}, } @article{14555, abstract = {The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems.}, author = {Riedl, Michael and Sixt, Michael K}, issn = {2296-634X}, journal = {Frontiers in Cell and Developmental Biology}, publisher = {Frontiers}, title = {{The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction}}, doi = {10.3389/fcell.2023.1287420}, volume = {11}, year = {2023}, } @article{14556, abstract = {Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.}, author = {Berdan, Emma L. and Barton, Nicholas H and Butlin, Roger and Charlesworth, Brian and Faria, Rui and Fragata, Inês and Gilbert, Kimberly J. and Jay, Paul and Kapun, Martin and Lotterhos, Katie E. and Mérot, Claire and Durmaz Mitchell, Esra and Pascual, Marta and Peichel, Catherine L. and Rafajlović, Marina and Westram, Anja M and Schaeffer, Stephen W. and Johannesson, Kerstin and Flatt, Thomas}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {12}, publisher = {Wiley}, title = {{How chromosomal inversions reorient the evolutionary process}}, doi = {10.1111/jeb.14242}, volume = {36}, year = {2023}, } @article{14557, abstract = {Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem.}, author = {Dikranjan, D. and Giordano Bruno, A. and Zava, Nicolò}, issn = {1727-933X}, journal = {Quaestiones Mathematicae}, number = {S1}, pages = {191--221}, publisher = {Taylor & Francis}, title = {{Epimorphisms and closure operators of categories of semilattices}}, doi = {10.2989/16073606.2023.2247731}, volume = {46}, year = {2023}, } @article{14558, abstract = {n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2 and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon and Wu, Xiaowei}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {5}, pages = {1132--1192}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Deterministic near-optimal approximation algorithms for dynamic set cover}}, doi = {10.1137/21M1428649}, volume = {52}, year = {2023}, } @inproceedings{14559, abstract = {We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.}, author = {Ansaripour, Matin and Chatterjee, Krishnendu and Henzinger, Thomas A and Lechner, Mathias and Zikelic, Dorde}, booktitle = {21st International Symposium on Automated Technology for Verification and Analysis}, isbn = {9783031453281}, issn = {1611-3349}, location = {Singapore, Singapore}, pages = {357--379}, publisher = {Springer Nature}, title = {{Learning provably stabilizing neural controllers for discrete-time stochastic systems}}, doi = {10.1007/978-3-031-45329-8_17}, volume = {14215}, year = {2023}, } @misc{14562, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. }, author = {Schur, Florian KM}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning"}}, doi = {10.15479/AT:ISTA:14562}, year = {2023}, } @article{14564, abstract = {Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.}, author = {Khouider, B. and GOSWAMI, BIDYUT B and Phani, R. and Majda, A. J.}, issn = {1942-2466}, journal = {Journal of Advances in Modeling Earth Systems}, keywords = {General Earth and Planetary Sciences, Environmental Chemistry, Global and Planetary Change}, number = {11}, publisher = {American Geophysical Union}, title = {{A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model}}, doi = {10.1029/2022ms003391}, volume = {15}, year = {2023}, }