@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}, } @article{12349, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.}, author = {Gupta, Divyansh and Mlynarski, Wiktor F and Sumser, Anton L and Symonova, Olga and Svaton, Jan and Jösch, Maximilian A}, issn = {1546-1726}, journal = {Nature Neuroscience}, pages = {606--614}, publisher = {Springer Nature}, title = {{Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.1038/s41593-023-01280-0}, volume = {26}, year = {2023}, } @misc{12370, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. }, author = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.15479/AT:ISTA:12370}, year = {2023}, } @article{12829, abstract = {The deployment of direct formate fuel cells (DFFCs) relies on the development of active and stable catalysts for the formate oxidation reaction (FOR). Palladium, providing effective full oxidation of formate to CO2, has been widely used as FOR catalyst, but it suffers from low stability, moderate activity, and high cost. Herein, we detail a colloidal synthesis route for the incorporation of P on Pd2Sn nanoparticles. These nanoparticles are dispersed on carbon black and the obtained composite is used as electrocatalytic material for the FOR. The Pd2Sn0.8P-based electrodes present outstanding catalytic activities with record mass current densities up to 10.0 A mgPd-1, well above those of Pd1.6Sn/C reference electrode. These high current densities are further enhanced by increasing the temperature from 25 °C to 40 °C. The Pd2Sn0.8P electrode also allows for slowing down the rapid current decay that generally happens during operation and can be rapidly re-activated through potential cycling. The excellent catalytic performance obtained is rationalized using density functional theory (DFT) calculations.}, author = {Montaña-Mora, Guillem and Qi, Xueqiang and Wang, Xiang and Chacón-Borrero, Jesus and Martinez-Alanis, Paulina R. and Yu, Xiaoting and Li, Junshan and Xue, Qian and Arbiol, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {1572-6657}, journal = {Journal of Electroanalytical Chemistry}, publisher = {Elsevier}, title = {{Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction}}, doi = {10.1016/j.jelechem.2023.117369}, volume = {936}, year = {2023}, } @article{12764, abstract = {We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique.}, author = {Kourimska, Hana}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {123--153}, publisher = {Springer Nature}, title = {{Discrete yamabe problem for polyhedral surfaces}}, doi = {10.1007/s00454-023-00484-2}, volume = {70}, year = {2023}, } @phdthesis{13331, abstract = {The extension of extremal combinatorics to the setting of exterior algebra is a work in progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms. }, author = {Köse, Seyda}, issn = {2791-4585}, pages = {26}, publisher = {Institute of Science and Technology Austria}, title = {{Exterior algebra and combinatorics}}, doi = {10.15479/at:ista:13331}, year = {2023}, } @article{12765, abstract = {Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection. Because they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group. Here, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals. We discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies. Finally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.}, author = {Stockmaier, Sebastian and Ulrich, Yuko and Albery, Gregory F. and Cremer, Sylvia and Lopes, Patricia C.}, issn = {1365-2435}, journal = {Functional Ecology}, number = {4}, pages = {809--820}, publisher = {British Ecological Society}, title = {{Behavioural defences against parasites across host social structures}}, doi = {10.1111/1365-2435.14310}, volume = {37}, year = {2023}, } @article{12680, abstract = {The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.}, author = {Ivanov, Grigory and Köse, Seyda}, issn = {0012-365X}, journal = {Discrete Mathematics}, number = {6}, publisher = {Elsevier}, title = {{Erdős-Ko-Rado and Hilton-Milner theorems for two-forms}}, doi = {10.1016/j.disc.2023.113363}, volume = {346}, year = {2023}, } @article{12792, abstract = {In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {1665--1700}, publisher = {Springer Nature}, title = {{On the spectral form factor for random matrices}}, doi = {10.1007/s00220-023-04692-y}, volume = {401}, year = {2023}, } @article{12709, abstract = {Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.}, author = {Corbet, René and Kerber, Michael and Lesnick, Michael and Osang, Georg F}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {376--405}, publisher = {Springer Nature}, title = {{Computing the multicover bifiltration}}, doi = {10.1007/s00454-022-00476-8}, volume = {70}, year = {2023}, } @article{12763, abstract = {Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.}, author = {Boissonnat, Jean Daniel and Wintraecken, Mathijs}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, pages = {619--641}, publisher = {Springer Nature}, title = {{The reach of subsets of manifolds}}, doi = {10.1007/s41468-023-00116-x}, volume = {7}, year = {2023}, } @inproceedings{13221, abstract = {The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications.}, author = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {34th International Conference on Concurrency Theory}, isbn = {9783959772990}, issn = {1868-8969}, location = {Antwerp, Belgium}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Safety and liveness of quantitative automata}}, doi = {10.4230/LIPIcs.CONCUR.2023.17}, volume = {279}, year = {2023}, } @article{14406, abstract = {Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model ( NL σ M ) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the NL σ M for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization.}, author = {Babkin, Serafim and Karcher, Jonas F. and Burmistrov, Igor S. and Mirlin, Alexander D.}, issn = {2469-9969}, journal = {Physical Review B}, number = {10}, publisher = {American Physical Society}, title = {{Generalized surface multifractality in two-dimensional disordered systems}}, doi = {10.1103/PhysRevB.108.104205}, volume = {108}, year = {2023}, } @inproceedings{14410, abstract = {This paper focuses on the implementation details of the baseline methods and a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming data under class-prior shift. LIMES achieves superior performance over the baseline methods, especially concerning the minimum-across-day accuracy, which is important for the users of the system. In this work, the key measures to facilitate reproducibility and enhance the credibility of the results are described.}, author = {Tomaszewska, Paulina and Lampert, Christoph}, booktitle = {International Workshop on Reproducible Research in Pattern Recognition}, isbn = {9783031407727}, issn = {1611-3349}, location = {Montreal, Canada}, pages = {67--73}, publisher = {Springer Nature}, title = {{On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift}}, doi = {10.1007/978-3-031-40773-4_6}, volume = {14068}, year = {2023}, } @inproceedings{14405, abstract = {We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.}, author = {Bartocci, Ezio and Henzinger, Thomas A and Nickovic, Dejan and Oliveira da Costa, Ana}, booktitle = {34th International Conference on Concurrency Theory}, isbn = {9783959772990}, issn = {18688969}, location = {Antwerp, Belgium}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Hypernode automata}}, doi = {10.4230/LIPIcs.CONCUR.2023.21}, volume = {279}, year = {2023}, } @article{14408, abstract = {We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 01+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.}, author = {Dubach, Guillaume and Erdös, László}, issn = {1083-589X}, journal = {Electronic Communications in Probability}, pages = {1--13}, publisher = {Institute of Mathematical Statistics}, title = {{Dynamics of a rank-one perturbation of a Hermitian matrix}}, doi = {10.1214/23-ECP516}, volume = {28}, year = {2023}, } @article{12761, abstract = {We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine the fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent multiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1050-5164}, journal = {Annals of Applied Probability}, number = {1}, pages = {447--489}, publisher = {Institute of Mathematical Statistics}, title = {{Functional central limit theorems for Wigner matrices}}, doi = {10.1214/22-AAP1820}, volume = {33}, year = {2023}, } @article{8682, abstract = {It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.}, author = {Browning, Timothy D and Boudec, Pierre Le and Sawin, Will}, issn = {0003-486X}, journal = {Annals of Mathematics}, number = {3}, pages = {1115--1203}, publisher = {Princeton University}, title = {{The Hasse principle for random Fano hypersurfaces}}, doi = {10.4007/annals.2023.197.3.3}, volume = {197}, year = {2023}, } @article{12706, abstract = {Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.}, author = {Mckerral, Jody C. and Kleshnina, Maria and Ejov, Vladimir and Bartle, Louise and Mitchell, James G. and Filar, Jerzy A.}, issn = {1932-6203}, journal = {PLoS One}, number = {2}, pages = {e0279838}, publisher = {Public Library of Science}, title = {{Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations}}, doi = {10.1371/journal.pone.0279838}, volume = {18}, year = {2023}, } @article{13202, abstract = {Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons.}, author = {Eguchi, Kohgaku and Le Monnier, Elodie and Shigemoto, Ryuichi}, issn = {1529-2401}, journal = {The Journal of Neuroscience}, number = {23}, pages = {4197--4216}, publisher = {Society for Neuroscience}, title = {{Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons}}, doi = {10.1523/JNEUROSCI.1514-22.2023}, volume = {43}, year = {2023}, } @article{12916, abstract = {We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface. }, author = {Bonolis, Dante and Browning, Timothy D}, issn = {2036-2145}, journal = {Annali della Scuola Normale Superiore di Pisa - Classe di Scienze}, number = {1}, pages = {173--204}, publisher = {Scuola Normale Superiore - Edizioni della Normale}, title = {{Uniform bounds for rational points on hyperelliptic fibrations}}, doi = {10.2422/2036-2145.202010_018}, volume = {24}, year = {2023}, } @phdthesis{14422, abstract = {Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of changes in the brain throughout adulthood, regrouped under the term "plasticity". Some cells in the brain —neurons— and specifically changes in the connections between neurons, the synapses, were shown to be crucial for the formation, selection, and consolidation of memories from past experiences. These ongoing changes of synapses across time are called synaptic plasticity. Understanding how a myriad of biochemical processes operating at individual synapses can somehow work in concert to give rise to meaningful changes in behavior is a fascinating problem and an active area of research. However, the experimental search for the precise plasticity mechanisms at play in the brain is daunting, as it is difficult to control and observe synapses during learning. Theoretical approaches have thus been the default method to probe the plasticity-behavior connection. Such studies attempt to extract unifying principles across synapses and model all observed synaptic changes using plasticity rules: equations that govern the evolution of synaptic strengths across time in neuronal network models. These rules can use many relevant quantities to determine the magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic action potentials, the recent neuronal activity levels, the state of neighboring synapses, etc. However, analytical studies rely heavily on human intuition and are forced to make simplifying assumptions about plasticity rules. In this thesis, we aim to assist and augment human intuition in this search for plasticity rules. We explore whether a numerical approach could automatically discover the plasticity rules that elicit desired behaviors in large networks of interconnected neurons. This approach is dubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make neuronal networks learn how to solve a desired task. We first write all the potential plasticity mechanisms to consider using a single expression with adjustable parameters. We then optimize these plasticity parameters using evolutionary strategies or Bayesian inference on tasks known to involve synaptic plasticity, such as familiarity detection and network stabilization. We show that these automated approaches are powerful tools, able to complement established analytical methods. By comprehensively screening plasticity rules at all synapse types in realistic, spiking neuronal network models, we discover entire sets of degenerate plausible plasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more robust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity rules, and provide fresh insights on synaptic plasticity in spiking network models. }, author = {Confavreux, Basile J}, issn = {2663 - 337X}, pages = {148}, publisher = {Institute of Science and Technology Austria}, title = {{Synapseek: Meta-learning synaptic plasticity rules}}, doi = {10.15479/at:ista:14422}, year = {2023}, } @phdthesis{14374, abstract = {Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary. BCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries. For Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary. Second, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality. In the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.}, author = {Roos, Barbara}, issn = {2663 - 337X}, pages = {206}, publisher = {Institute of Science and Technology Austria}, title = {{Boundary superconductivity in BCS theory}}, doi = {10.15479/at:ista:14374}, year = {2023}, } @article{13207, abstract = {We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity.}, author = {Hainzl, Christian and Roos, Barbara and Seiringer, Robert}, issn = {1664-0403}, journal = {Journal of Spectral Theory}, number = {4}, pages = {1507–1540}, publisher = {EMS Press}, title = {{Boundary superconductivity in the BCS model}}, doi = {10.4171/JST/439}, volume = {12}, year = {2023}, } @article{14452, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√⁠. We illustrate our results with some numerical examples.}, author = {Barton, Nicholas H and Etheridge, Alison M. and Véber, Amandine}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Oxford Academic}, title = {{The infinitesimal model with dominance}}, doi = {10.1093/genetics/iyad133}, volume = {225}, year = {2023}, } @misc{12949, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, } @inproceedings{14461, abstract = {Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.}, author = {Markov, Ilia and Vladu, Adrian and Guo, Qi and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {24020--24044}, publisher = {ML Research Press}, title = {{Quantized distributed training of large models with convergence guarantees}}, volume = {202}, year = {2023}, } @inproceedings{14462, abstract = {We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount . Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error.}, author = {Fichtenberger, Hendrik and Henzinger, Monika H and Upadhyay, Jalaj}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {10072--10092}, publisher = {ML Research Press}, title = {{Constant matters: Fine-grained error bound on differentially private continual observation}}, volume = {202}, year = {2023}, } @inproceedings{14459, abstract = {Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.}, author = {Shevchenko, Aleksandr and Kögler, Kevin and Hassani, Hamed and Mondelli, Marco}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {31151--31209}, publisher = {ML Research Press}, title = {{Fundamental limits of two-layer autoencoders, and achieving them with gradient methods}}, volume = {202}, year = {2023}, } @inproceedings{14460, abstract = {We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware.}, author = {Nikdan, Mahdi and Pegolotti, Tommaso and Iofinova, Eugenia B and Kurtic, Eldar and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {26215--26227}, publisher = {ML Research Press}, title = {{SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge}}, volume = {202}, year = {2023}, } @inproceedings{14457, abstract = {Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n). In this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise. }, author = {Hoffmann, Charlotte and Simkin, Mark}, booktitle = {8th International Conference on Cryptology and Information Security in Latin America}, isbn = {9783031444685}, issn = {1611-3349}, location = {Quito, Ecuador}, pages = {215--228}, publisher = {Springer Nature}, title = {{Stronger lower bounds for leakage-resilient secret sharing}}, doi = {10.1007/978-3-031-44469-2_11}, volume = {14168}, year = {2023}, } @inproceedings{14458, abstract = {We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.}, author = {Frantar, Elias and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {10323--10337}, publisher = {ML Research Press}, title = {{SparseGPT: Massive language models can be accurately pruned in one-shot}}, volume = {202}, year = {2023}, } @article{14451, abstract = {We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.}, author = {Cornalba, Federico and Disselkamp, Constantin and Scassola, Davide and Helf, Christopher}, issn = {1433-3058}, journal = {Neural Computing and Applications}, publisher = {Springer Nature}, title = {{Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading}}, doi = {10.1007/s00521-023-09033-7}, year = {2023}, } @article{14442, abstract = {In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter.}, author = {Rojas Vega, Mauricio Nicolas and De Castro, Pablo and Soto, Rodrigo}, issn = {1292-895X}, journal = {The European Physical Journal E}, number = {10}, publisher = {Springer Nature}, title = {{Mixtures of self-propelled particles interacting with asymmetric obstacles}}, doi = {10.1140/epje/s10189-023-00354-y}, volume = {46}, year = {2023}, } @article{14444, abstract = {We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare) is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN , where N is the number of intercalates in a uniformly random order- n Latin square. In fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2)) and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)). Finally, as an application of some new general tools for studying substructures in random Latin squares, we show that in almost all order- n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices with the same arrangement of symbols) is of order n4, which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring ``how associative'' the quasigroup associated with the Latin square is.}, author = {Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab and Simkin, Michael}, issn = {1565-8511}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {363--416}, publisher = {Springer Nature}, title = {{Substructures in Latin squares}}, doi = {10.1007/s11856-023-2513-9}, volume = {256}, year = {2023}, } @inproceedings{14454, abstract = {As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples.}, author = {Henzinger, Thomas A and Kueffner, Konstantin and Mallik, Kaushik}, booktitle = {23rd International Conference on Runtime Verification}, isbn = {9783031442667}, issn = {1611-3349}, location = {Thessaloniki, Greece}, pages = {291--311}, publisher = {Springer Nature}, title = {{Monitoring algorithmic fairness under partial observations}}, doi = {10.1007/978-3-031-44267-4_15}, volume = {14245}, year = {2023}, } @article{14446, abstract = {Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal.}, author = {Jakubík, Jozef and Bui Thi Mai, Phuong and Chvosteková, Martina and Krakovská, Anna}, issn = {1335-8871}, journal = {Measurement Science Review}, number = {4}, pages = {175--183}, publisher = {Sciendo}, title = {{Against the flow of time with multi-output models}}, doi = {10.2478/msr-2023-0023}, volume = {23}, year = {2023}, } @article{14443, abstract = {Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known. Observations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse. Conclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness.}, author = {Schumann, Gunter and Andreassen, Ole A. and Banaschewski, Tobias and Calhoun, Vince D. and Clinton, Nicholas and Desrivieres, Sylvane and Brandlistuen, Ragnhild Eek and Feng, Jianfeng and Hese, Soeren and Hitchen, Esther and Hoffmann, Per and Jia, Tianye and Jirsa, Viktor and Marquand, Andre F. and Nees, Frauke and Nöthen, Markus M. and Novarino, Gaia and Polemiti, Elli and Ralser, Markus and Rapp, Michael and Schepanski, Kerstin and Schikowski, Tamara and Slater, Mel and Sommer, Peter and Stahl, Bernd Carsten and Thompson, Paul M. and Twardziok, Sven and Van Der Meer, Dennis and Walter, Henrik and Westlye, Lars}, issn = {2168-6238}, journal = {JAMA Psychiatry}, number = {10}, pages = {1066--1074}, publisher = {American Medical Association}, title = {{Addressing global environmental challenges to mental health using population neuroscience: A review}}, doi = {10.1001/jamapsychiatry.2023.2996}, volume = {80}, year = {2023}, } @article{14441, abstract = {We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation.}, author = {Brooks, Morris and Seiringer, Robert}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {287--337}, publisher = {Springer Nature}, title = {{The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy}}, doi = {10.1007/s00220-023-04841-3}, volume = {404}, year = {2023}, } @inproceedings{14448, abstract = {We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.}, author = {Kolmogorov, Vladimir}, booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, isbn = {9798350301298}, issn = {1063-6919}, location = {Vancouver, Canada}, pages = {11980--11989}, publisher = {IEEE}, title = {{Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions}}, doi = {10.1109/CVPR52729.2023.01153}, volume = {2023}, year = {2023}, } @article{12672, abstract = {Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.}, author = {Lyons, David B. and Briffa, Amy and He, Shengbo and Choi, Jaemyung and Hollwey, Elizabeth and Colicchio, Jack and Anderson, Ian and Feng, Xiaoqi and Howard, Martin and Zilberman, Daniel}, issn = {2211-1247}, journal = {Cell Reports}, number = {3}, publisher = {Elsevier}, title = {{Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons}}, doi = {10.1016/j.celrep.2023.112132}, volume = {42}, year = {2023}, } @article{13178, abstract = {We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.}, author = {Mitrouskas, David Johannes and Mysliwy, Krzysztof and Seiringer, Robert}, issn = {2050-5094}, journal = {Forum of Mathematics}, pages = {1--52}, publisher = {Cambridge University Press}, title = {{Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron}}, doi = {10.1017/fms.2023.45}, volume = {11}, year = {2023}, } @article{14484, abstract = {Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling.}, author = {Kicheva, Anna and Briscoe, James}, issn = {1530-8995}, journal = {Annual Review of Cell and Developmental Biology}, pages = {91--121}, publisher = {Annual Reviews}, title = {{Control of tissue development by morphogens}}, doi = {10.1146/annurev-cellbio-020823-011522}, volume = {39}, year = {2023}, } @article{14488, abstract = {Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.}, author = {Rao, Pramod and Mallikarjun, B. R. and Fox, Gereon and Weyrich, Tim and Bickel, Bernd and Pfister, Hanspeter and Matusik, Wojciech and Zhan, Fangneng and Tewari, Ayush and Theobalt, Christian and Elgharib, Mohamed}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, publisher = {Springer Nature}, title = {{A deeper analysis of volumetric relightiable faces}}, doi = {10.1007/s11263-023-01899-3}, year = {2023}, } @article{14487, abstract = {High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified.}, author = {Buri, Pascal and Fatichi, Simone and Shaw, Thomas and Miles, Evan S. 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}, issn = {1944-7973}, journal = {Water Resources Research}, number = {10}, publisher = {Wiley}, title = {{Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment}}, doi = {10.1029/2022WR033841}, volume = {59}, year = {2023}, } @inproceedings{14485, abstract = {Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching. In this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct "data" and "index" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is "close" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.}, author = {Aksenov, Vitaly and Anoprenko, Michael and Fedorov, Alexander and Spear, Michael}, booktitle = {37th International Symposium on Distributed Computing}, isbn = {9783959773010}, issn = {1868-8969}, location = {L'Aquila, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Brief announcement: BatchBoost: Universal batching for concurrent data structures}}, doi = {10.4230/LIPIcs.DISC.2023.35}, volume = {281}, year = {2023}, } @article{14486, abstract = {We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites.}, author = {Koutentakis, Georgios and Ghazaryan, Areg and Lemeshko, Mikhail}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Rotor lattice model of ferroelectric large polarons}}, doi = {10.1103/PhysRevResearch.5.043016}, volume = {5}, year = {2023}, } @article{14313, abstract = {To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.}, author = {Fiedler, Lukas and Friml, Jiří}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, number = {10}, publisher = {Elsevier}, title = {{Rapid auxin signaling: Unknowns old and new}}, doi = {10.1016/j.pbi.2023.102443}, volume = {75}, year = {2023}, } @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}, } @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}, } @misc{12869, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. }, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for: A stochastic cellular automaton model of culture formation}}, doi = {10.15479/AT:ISTA:12869}, year = {2023}, } @article{12890, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.}, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, issn = {2470-0053}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Stochastic cellular automaton model of culture formation}}, doi = {10.1103/PhysRevE.108.054307}, volume = {108}, 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}, } @article{14517, abstract = {State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. }, author = {Zemlicka, Martin and Redchenko, Elena and Peruzzo, Matilda and Hassani, Farid and Trioni, Andrea and Barzanjeh, Shabir and Fink, Johannes M}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {4}, publisher = {American Physical Society}, title = {{Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses}}, doi = {10.1103/PhysRevApplied.20.044054}, volume = {20}, 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}, } @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}, } @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}, } @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}, } @article{13096, abstract = {Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.}, author = {Degen, Morris and Santos, José Carlos and Pluhackova, Kristyna and Cebrero, Gonzalo and Ramos, Saray and Jankevicius, Gytis and Hartenian, Ella and Guillerm, Undina and Mari, Stefania A. and Kohl, Bastian and Müller, Daniel J. and Schanda, Paul and Maier, Timm and Perez, Camilo and Sieben, Christian and Broz, Petr and Hiller, Sebastian}, issn = {1476-4687}, journal = {Nature}, pages = {1065--1071}, publisher = {Springer Nature}, title = {{Structural basis of NINJ1-mediated plasma membrane rupture in cell death}}, doi = {10.1038/s41586-023-05991-z}, volume = {618}, year = {2023}, } @article{13041, abstract = {A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance.}, author = {Farag, Nadia L. and Jethwa, Rajesh B and Beardmore, Alice E. and Insinna, Teresa and O'Keefe, Christopher A. and Klusener, Peter A.A. and Grey, Clare P. and Wright, Dominic S.}, issn = {1864-564X}, journal = {ChemSusChem}, number = {13}, publisher = {Wiley}, title = {{Triarylamines as catholytes in aqueous organic redox flow batteries}}, doi = {10.1002/cssc.202300128}, volume = {16}, year = {2023}, } @article{13118, abstract = {Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers.}, author = {Hernandez, J.-A. and Bethkenhagen, Mandy and Ninet, S. and French, M. and Benuzzi-Mounaix, A. and Datchi, F. and Guarguaglini, M. and Lefevre, F. and Occelli, F. and Redmer, R. and Vinci, T. and Ravasio, A.}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1280--1285}, publisher = {Springer Nature}, title = {{Melting curve of superionic ammonia at planetary interior conditions}}, doi = {10.1038/s41567-023-02074-8}, volume = {19}, year = {2023}, } @article{13119, abstract = {A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.}, author = {Helson, Victor and Zwettler, Timo and Mivehvar, Farokh and Colella, Elvia and Roux, Kevin Etienne Robert and Konishi, Hideki and Ritsch, Helmut and Brantut, Jean Philippe}, issn = {1476-4687}, journal = {Nature}, pages = {716--720}, publisher = {Springer Nature}, title = {{Density-wave ordering in a unitary Fermi gas with photon-mediated interactions}}, doi = {10.1038/s41586-023-06018-3}, volume = {618}, year = {2023}, } @article{12911, abstract = {This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.}, author = {Feliciangeli, Dario and Gerolin, Augusto and Portinale, Lorenzo}, issn = {1096-0783}, journal = {Journal of Functional Analysis}, number = {4}, publisher = {Elsevier}, title = {{A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature}}, doi = {10.1016/j.jfa.2023.109963}, volume = {285}, year = {2023}, } @article{13177, abstract = {In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.}, author = {Hua, Bobo and Keller, Matthias and Schwarz, Michael and Wirth, Melchior}, issn = {1088-6826}, journal = {Proceedings of the American Mathematical Society}, number = {8}, pages = {3401--3414}, publisher = {American Mathematical Society}, title = {{Sobolev-type inequalities and eigenvalue growth on graphs with finite measure}}, doi = {10.1090/proc/14361}, volume = {151}, 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}, } @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{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}, publisher = {Wiley}, title = {{How chromosomal inversions reorient the evolutionary process}}, doi = {10.1111/jeb.14242}, 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{14543, abstract = {The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.}, author = {Kaiyrzhanov, Rauan and Rad, Aboulfazl and Lin, Sheng-Jia and Bertoli-Avella, Aida and Kallemeijn, Wouter W and Godwin, Annie and Zaki, Maha S and Huang, Kevin and Lau, Tracy and Petree, Cassidy and Efthymiou, Stephanie and Ghayoor Karimiani, Ehsan and Hempel, Maja and Normand, Elizabeth A and Rudnik-Schöneborn, Sabine and Schatz, Ulrich A and Baggelaar, Marc P and Ilyas, Muhammad and Sultan, Tipu and Alvi, Javeria Raza and Ganieva, Manizha and Fowler, Ben and Aanicai, Ruxandra and Akay Tayfun, Gulsen and Al Saman, Abdulaziz and Alswaid, Abdulrahman and Amiri, Nafise and Asilova, Nilufar and Shotelersuk, Vorasuk and Yeetong, Patra and Azam, Matloob and Babaei, Meisam and Bahrami Monajemi, Gholamreza and Mohammadi, Pouria and Samie, Saeed and Banu, Selina Husna and Basto, Jorge Pinto and Kortüm, Fanny and Bauer, Mislen and Bauer, Peter and Beetz, Christian and Garshasbi, Masoud and Hameed Issa, Awatif and Eyaid, Wafaa and Ahmed, Hind and Hashemi, Narges and Hassanpour, Kazem and Herman, Isabella and Ibrohimov, Sherozjon and Abdul-Majeed, Ban A and Imdad, Maria and Isrofilov, Maksudjon and Kaiyal, Qassem and Khan, Suliman and Kirmse, Brian and Koster, Janet and Lourenço, Charles Marques and Mitani, Tadahiro and Moldovan, Oana and Murphy, David and Najafi, Maryam and Pehlivan, Davut and Rocha, Maria Eugenia and Salpietro, Vincenzo and Schmidts, Miriam and Shalata, Adel and Mahroum, Mohammad and Talbeya, Jawabreh Kassem and Taylor, Robert W and Vazquez, Dayana and Vetro, Annalisa and Waterham, Hans R and Zaman, Mashaya and Schrader, Tina A and Chung, Wendy K and Guerrini, Renzo and Lupski, James R and Gleeson, Joseph and Suri, Mohnish and Jamshidi, Yalda and Bhatia, Kailash P and Vona, Barbara and Schrader, Michael and Severino, Mariasavina and Guille, Matthew and Tate, Edward W and Varshney, Gaurav K and Houlden, Henry and Maroofian, Reza}, issn = {1460-2156}, journal = {Brain}, keywords = {Neurology (clinical)}, publisher = {Oxford University Press}, title = {{Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders}}, doi = {10.1093/brain/awad380}, year = {2023}, } @article{14542, abstract = {It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.}, author = {Henheik, Sven Joscha and Lauritsen, Asbjørn Bækgaard and Roos, Barbara}, issn = {1793-6659}, journal = {Reviews in Mathematical Physics}, publisher = {World Scientific Publishing}, title = {{Universality in low-dimensional BCS theory}}, doi = {10.1142/s0129055x2360005x}, 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{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{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{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}, } @misc{14579, abstract = {This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science. }, author = {Wetzel, William}, publisher = {Zenodo}, title = {{HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0}}, doi = {10.5281/ZENODO.8133117}, year = {2023}, } @article{12334, 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 = {Fäßler, Florian and Javoor, Manjunath and Datler, Julia and Döring, Hermann and Hofer, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Faix, Jan and Rottner, Klemens and Schur, Florian KM}, issn = {2375-2548}, journal = {Science Advances}, keywords = {Multidisciplinary}, number = {3}, publisher = {American Association for the Advancement of Science}, title = {{ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning}}, doi = {10.1126/sciadv.add6495}, volume = {9}, 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}, } @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{13342, abstract = {Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.}, author = {Kroll, Janina and Hauschild, Robert and Kuznetcov, Arthur and Stefanowski, Kasia and Hermann, Monika D. and Merrin, Jack and Shafeek, Lubuna B and Müller-Taubenberger, Annette and Renkawitz, Jörg}, issn = {1460-2075}, journal = {EMBO Journal}, publisher = {Embo Press}, title = {{Adaptive pathfinding by nucleokinesis during amoeboid migration}}, doi = {10.15252/embj.2023114557}, year = {2023}, } @article{14610, abstract = {AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.}, author = {Bussi, Claudio and Mangiarotti, Agustín and Vanhille-Campos, Christian Eduardo and Aylan, Beren and Pellegrino, Enrica and Athanasiadi, Natalia and Fearns, Antony and Rodgers, Angela and Franzmann, Titus M. and Šarić, Anđela and Dimova, Rumiana and Gutierrez, Maximiliano G.}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, publisher = {Springer Nature}, title = {{Stress granules plug and stabilize damaged endolysosomal membranes}}, doi = {10.1038/s41586-023-06726-w}, year = {2023}, } @misc{14472, abstract = {Data related to the following paper: "Stress granules plug and stabilize damaged endolysosomal membranes" (https://doi.org/10.1038/s41586-023-06726-w) Abstract: Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.}, author = {Vanhille-Campos, Christian Eduardo and Šarić, Anđela}, publisher = {Institute of Science and Technology Austria}, title = {{Stress granules plug and stabilize damaged endolysosomal membranes}}, doi = {10.15479/AT:ISTA:14472}, year = {2023}, }