TY - JOUR AB - Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. Results: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. Conclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis. AU - Zhao, Long AU - Yang, Yiman AU - Chen, Jinchao AU - Lin, Xuelei AU - Zhang, Hao AU - Wang, Hao AU - Wang, Hongzhe AU - Bie, Xiaomin AU - Jiang, Jiafu AU - Feng, Xiaoqi AU - Fu, Xiangdong AU - Zhang, Xiansheng AU - Du, Zhuo AU - Xiao, Jun ID - 12668 JF - Genome Biology SN - 1474-760X TI - Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat VL - 24 ER - TY - CONF AB - In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis. AU - Lieutier, André AU - Wintraecken, Mathijs ID - 13048 SN - 9781450399135 T2 - Proceedings of the 55th Annual ACM Symposium on Theory of Computing TI - Hausdorff and Gromov-Hausdorff stable subsets of the medial axis ER - TY - CONF AB - Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL . AU - Peste, Elena-Alexandra AU - Vladu, Adrian AU - Kurtic, Eldar AU - Lampert, Christoph AU - Alistarh, Dan-Adrian ID - 13053 T2 - 11th International Conference on Learning Representations TI - CrAM: A Compression-Aware Minimizer ER - TY - CONF AB - GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime. In this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic. Our approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality. AU - Hoffmann, Charlotte AU - Hubáček, Pavel AU - Kamath, Chethan AU - Pietrzak, Krzysztof Z ID - 13143 SN - 0302-9743 T2 - Public-Key Cryptography - PKC 2023 TI - Certifying giant nonprimes VL - 13940 ER - TY - CONF AB - Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A AU - Lechner, Mathias AU - Zikelic, Dorde ID - 13142 SN - 0302-9743 T2 - Tools and Algorithms for the Construction and Analysis of Systems TI - A learner-verifier framework for neural network controllers and certificates of stochastic systems VL - 13993 ER - TY - CONF AB - We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness). For parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω -regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive. AU - Anand, Ashwani AU - Mallik, Kaushik AU - Nayak, Satya Prakash AU - Schmuck, Anne Kathrin ID - 13141 SN - 0302-9743 T2 - TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems TI - Computing adequately permissive assumptions for synthesis VL - 13994 ER - TY - THES AB - During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. Firstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations. Secondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns. Taken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster. AU - Pokusaeva, Victoria ID - 12826 SN - 2663 - 337X TI - Neural control of optic flow-based navigation in Drosophila melanogaster ER - TY - JOUR AB - We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets. AU - Edelsbrunner, Herbert AU - Osang, Georg F ID - 12086 JF - Algorithmica SN - 0178-4617 TI - A simple algorithm for higher-order Delaunay mosaics and alpha shapes VL - 85 ER - TY - JOUR AB - We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces. AU - Dello Schiavo, Lorenzo AU - Wirth, Melchior ID - 12104 IS - 1 JF - Journal of Evolution Equations SN - 1424-3199 TI - Ergodic decompositions of Dirichlet forms under order isomorphisms VL - 23 ER - TY - JOUR AB - The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall. AU - Goswami, Bidyut B ID - 11434 JF - Climate Dynamics SN - 0930-7575 TI - Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend VL - 60 ER - TY - CONF AB - Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states. AU - Henzinger, Thomas A AU - Mazzocchi, Nicolas Adrien AU - Sarac, Naci E ID - 12467 SN - 0302-9743 T2 - 26th International Conference Foundations of Software Science and Computation Structures TI - Quantitative safety and liveness VL - 13992 ER - TY - JOUR AB - Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads. This paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives. AU - Koval, Nikita AU - Khalanskiy, Dmitry AU - Alistarh, Dan-Adrian ID - 13179 JF - Proceedings of the ACM on Programming Languages TI - CQS: A formally-verified framework for fair and abortable synchronization VL - 7 ER - TY - JOUR AB - We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface AU - Browning, Timothy D AU - Lyczak, Julian AU - Sarapin, Roman ID - 13180 IS - 2 JF - Involve SN - 1944-4176 TI - Local solubility for a family of quadrics over a split quadric surface VL - 16 ER - TY - CONF AB - We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges. AU - Zheng, Da Wei AU - Henzinger, Monika H ID - 13236 SN - 0302-9743 T2 - International Conference on Integer Programming and Combinatorial Optimization TI - Multiplicative auction algorithm for approximate maximum weight bipartite matching VL - 13904 ER - TY - GEN AU - Elefante, Stefano AU - Stadlbauer, Stephan AU - Alexander, Michael F AU - Schlögl, Alois ID - 13162 T2 - ASHPC23 - Austrian-Slovenian HPC Meeting 2023 TI - Cryo-EM software packages: A sys-admins point of view ER - TY - GEN AU - Schlögl, Alois AU - Elefante, Stefano AU - Hodirnau, Victor-Valentin ID - 13161 T2 - ASHPC23 - Austrian-Slovenian HPC Meeting 2023 TI - Running Windows-applications on a Linux HPC cluster using WINE ER - TY - JOUR AB - A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy. AU - Wei, Yujing AU - Volosniev, Artem AU - Lorenc, Dusan AU - Zhumekenov, Ayan A. AU - Bakr, Osman M. AU - Lemeshko, Mikhail AU - Alpichshev, Zhanybek ID - 13251 IS - 27 JF - The Journal of Physical Chemistry Letters KW - General Materials Science KW - Physical and Theoretical Chemistry TI - Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites VL - 14 ER - TY - CONF AB - The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time. AU - Henzinger, Thomas A AU - Kebis, Pavol AU - Mazzocchi, Nicolas Adrien AU - Sarac, Naci E ID - 13292 SN - 9783959772785 T2 - 50th International Colloquium on Automata, Languages, and Programming TI - Regular methods for operator precedence languages VL - 261 ER - TY - JOUR AB - Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results. AU - Tucci, Gennaro AU - De Nicola, Stefano AU - Wald, Sascha AU - Gambassi, Andrea ID - 13277 IS - 2 JF - SciPost Physics Core KW - Statistical and Nonlinear Physics KW - Atomic and Molecular Physics KW - and Optics KW - Nuclear and High Energy Physics KW - Condensed Matter Physics SN - 2666-9366 TI - Stochastic representation of the quantum quartic oscillator VL - 6 ER - TY - JOUR AB - We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost. AU - Rammelmüller, Lukas AU - Huber, David AU - Volosniev, Artem ID - 13276 JF - SciPost Physics Codebases SN - 2949-804X TI - A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D ER - TY - GEN AB - We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost. AU - Rammelmüller, Lukas AU - Huber, David AU - Volosniev, Artem ID - 13275 TI - Codebase release 1.0 for FermiFCI ER - TY - CONF AB - Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited. AU - Fedorov, Alexander AU - Hashemi, Diba AU - Nadiradze, Giorgi AU - Alistarh, Dan-Adrian ID - 13262 SN - 9781450395458 T2 - Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures TI - Provably-efficient and internally-deterministic parallel Union-Find ER - TY - JOUR AB - Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results. AU - De Jode, Aurélien AU - Le Moan, Alan AU - Johannesson, Kerstin AU - Faria, Rui AU - Stankowski, Sean AU - Westram, Anja M AU - Butlin, Roger K. AU - Rafajlović, Marina AU - Fraisse, Christelle ID - 11479 IS - 2 JF - Evolutionary Applications TI - Ten years of demographic modelling of divergence and speciation in the sea VL - 16 ER - TY - JOUR AB - In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection. AU - Gómez, Arturo AU - Oliveira, Goncalo ID - 12329 JF - Scientific Reports TI - New approaches to epidemic modeling on networks VL - 13 ER - TY - JOUR AB - We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors. AU - Wilsch, Florian Alexander ID - 9034 IS - 8 JF - International Mathematics Research Notices SN - 1073-7928 TI - Integral points of bounded height on a log Fano threefold VL - 2023 ER - TY - JOUR AB - Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management. AU - Viljakainen, Lumi AU - Fürst, Matthias AU - Grasse, Anna V AU - Jurvansuu, Jaana AU - Oh, Jinook AU - Tolonen, Lassi AU - Eder, Thomas AU - Rattei, Thomas AU - Cremer, Sylvia ID - 12469 JF - Frontiers in Microbiology TI - Antiviral immune response reveals host-specific virus infections in natural ant populations VL - 14 ER - TY - JOUR AB - We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use. AU - Boissonnat, Jean-Daniel AU - Dyer, Ramsay AU - Ghosh, Arijit AU - Wintraecken, Mathijs ID - 12287 JF - Discrete & Computational Geometry KW - Computational Theory and Mathematics KW - Discrete Mathematics and Combinatorics KW - Geometry and Topology KW - Theoretical Computer Science SN - 0179-5376 TI - Local criteria for triangulating general manifolds VL - 69 ER - TY - JOUR AB - It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective. AU - Hof, Björn ID - 12165 JF - Nature Reviews Physics KW - General Physics and Astronomy TI - Directed percolation and the transition to turbulence VL - 5 ER - TY - JOUR AB - The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions. AU - Fäßler, Florian AU - Javoor, Manjunath AU - Schur, Florian KM ID - 12421 IS - 1 JF - Biochemical Society Transactions KW - Biochemistry SN - 0300-5127 TI - Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM VL - 51 ER - TY - JOUR AB - Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion. AU - Marensi, Elena AU - Yalniz, Gökhan AU - Hof, Björn AU - Budanur, Nazmi B ID - 12105 JF - Journal of Fluid Mechanics SN - 0022-1120 TI - Symmetry-reduced dynamic mode decomposition of near-wall turbulence VL - 954 ER - TY - JOUR AB - The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model. AU - Bolnick, Daniel I. AU - Hund, Amanda K. AU - Nosil, Patrik AU - Peng, Foen AU - Ravinet, Mark AU - Stankowski, Sean AU - Subramanian, Swapna AU - Wolf, Jochen B.W. AU - Yukilevich, Roman ID - 12514 IS - 1 JF - Evolution: International journal of organic evolution TI - A multivariate view of the speciation continuum VL - 77 ER - TY - CONF AB - The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts. AU - Forghani, Mohammad AU - Claramunt, Christophe AU - Karimipour, Farid AU - Heiler, Georg ID - 12548 T2 - 2022 IEEE International Conference on Data Mining Workshops TI - Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic ER - TY - JOUR AB - he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems. AU - Krokhin, Andrei AU - Opršal, Jakub AU - Wrochna, Marcin AU - Živný, Stanislav ID - 12563 IS - 1 JF - SIAM Journal on Computing KW - General Mathematics KW - General Computer Science SN - 0097-5397 TI - Topology and adjunction in promise constraint satisfaction VL - 52 ER - TY - JOUR AB - We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front. AU - Rojas Vega, Mauricio Nicolas AU - De Castro, Pablo AU - Soto, Rodrigo ID - 12545 IS - 1 JF - Physical Review E SN - 2470-0045 TI - Wetting dynamics by mixtures of fast and slow self-propelled particles VL - 107 ER - TY - JOUR AB - Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent. AU - Balestrieri, Francesca ID - 12427 IS - 3 JF - Proceedings of the American Mathematical Society SN - 0002-9939 TI - Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups VL - 151 ER - TY - JOUR AB - In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo. AU - Villalba Requena, Ana AU - Hippenmeyer, Simon ID - 12542 IS - 3 JF - Neuron TI - Going back in time with TEMPO VL - 111 ER - TY - JOUR AB - Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations. AU - Mrestani, Achmed AU - Lichter, Katharina AU - Sirén, Anna Leena AU - Heckmann, Manfred AU - Paul, Mila M. AU - Pauli, Martin ID - 12567 IS - 3 JF - International Journal of Molecular Sciences TI - Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation VL - 24 ER - TY - JOUR AB - Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that – all the outputs are within distance 1 of one another, and – each output value lies on a shortest path between two input values. From prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018). In this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs. AU - Alistarh, Dan-Adrian AU - Ellen, Faith AU - Rybicki, Joel ID - 12566 IS - 2 JF - Theoretical Computer Science SN - 0304-3975 TI - Wait-free approximate agreement on graphs VL - 948 ER - TY - JOUR AB - The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT. AU - Dubief, Yves AU - Terrapon, Vincent E. AU - Hof, Björn ID - 12681 IS - 1 JF - Annual Review of Fluid Mechanics SN - 0066-4189 TI - Elasto-inertial turbulence VL - 55 ER - TY - JOUR AB - Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed. AU - Avila, Marc AU - Barkley, Dwight AU - Hof, Björn ID - 12682 JF - Annual Review of Fluid Mechanics SN - 0066-4189 TI - Transition to turbulence in pipe flow VL - 55 ER - TY - JOUR AB - Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter. AU - Araújo, Nuno A.M. AU - Janssen, Liesbeth M.C. AU - Barois, Thomas AU - Boffetta, Guido AU - Cohen, Itai AU - Corbetta, Alessandro AU - Dauchot, Olivier AU - Dijkstra, Marjolein AU - Durham, William M. AU - Dussutour, Audrey AU - Garnier, Simon AU - Gelderblom, Hanneke AU - Golestanian, Ramin AU - Isa, Lucio AU - Koenderink, Gijsje H. AU - Löwen, Hartmut AU - Metzler, Ralf AU - Polin, Marco AU - Royall, C. Patrick AU - Šarić, Anđela AU - Sengupta, Anupam AU - Sykes, Cécile AU - Trianni, Vito AU - Tuval, Idan AU - Vogel, Nicolas AU - Yeomans, Julia M. AU - Zuriguel, Iker AU - Marin, Alvaro AU - Volpe, Giorgio ID - 12708 JF - Soft Matter SN - 1744-683X TI - Steering self-organisation through confinement VL - 19 ER - TY - JOUR AB - Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution. AU - Cheng, Bingqing AU - Hamel, Sebastien AU - Bethkenhagen, Mandy ID - 12702 JF - Nature Communications TI - Thermodynamics of diamond formation from hydrocarbon mixtures in planets VL - 14 ER - TY - JOUR AB - Background Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture. Methods First, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study). Results Through the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations. Conclusions The integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age. AU - Bernabeu, Elena AU - Mccartney, Daniel L. AU - Gadd, Danni A. AU - Hillary, Robert F. AU - Lu, Ake T. AU - Murphy, Lee AU - Wrobel, Nicola AU - Campbell, Archie AU - Harris, Sarah E. AU - Liewald, David AU - Hayward, Caroline AU - Sudlow, Cathie AU - Cox, Simon R. AU - Evans, Kathryn L. AU - Horvath, Steve AU - Mcintosh, Andrew M. AU - Robinson, Matthew Richard AU - Vallejos, Catalina A. AU - Marioni, Riccardo E. ID - 12719 JF - Genome Medicine TI - Refining epigenetic prediction of chronological and biological age VL - 15 ER - TY - JOUR AB - Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice. AU - Lechner, Mathias AU - Amini, Alexander AU - Rus, Daniela AU - Henzinger, Thomas A ID - 12704 IS - 3 JF - IEEE Robotics and Automation Letters TI - Revisiting the adversarial robustness-accuracy tradeoff in robot learning VL - 8 ER - TY - JOUR AB - The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed. AU - García-Romero, Álvaro AU - Waters, Jessica E. AU - Jethwa, Rajesh B AU - Bond, Andrew D. AU - Colebatch, Annie L. AU - García-Rodríguez, Raúl AU - Wright, Dominic S. ID - 12737 IS - 11 JF - Inorganic Chemistry SN - 0020-1669 TI - Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals VL - 62 ER - TY - JOUR AB - Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order. AU - Volosniev, Artem AU - Shiva Kumar, Abhishek AU - Lorenc, Dusan AU - Ashourishokri, Younes AU - Zhumekenov, Ayan A. AU - Bakr, Osman M. AU - Lemeshko, Mikhail AU - Alpichshev, Zhanybek ID - 12723 IS - 10 JF - Physical Review Letters KW - General Physics and Astronomy SN - 0031-9007 TI - Spin-electric coupling in lead halide perovskites VL - 130 ER - TY - JOUR AB - We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation. AU - Volosniev, Artem AU - Shiva Kumar, Abhishek AU - Lorenc, Dusan AU - Ashourishokri, Younes AU - Zhumekenov, Ayan AU - Bakr, Osman M. AU - Lemeshko, Mikhail AU - Alpichshev, Zhanybek ID - 12724 IS - 12 JF - Physical Review B SN - 2469-9950 TI - Effective model for studying optical properties of lead halide perovskites VL - 107 ER - TY - JOUR AB - Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density. AU - Rothman, Jason Seth AU - Borges Merjane, Carolina AU - Holderith, Noemi AU - Jonas, Peter M AU - Angus Silver, R. ID - 12759 IS - 3 March JF - PLoS ONE TI - Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy VL - 18 ER - TY - JOUR AB - ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling. AU - Hurtig, Fredrik AU - Burgers, Thomas C.Q. AU - Cezanne, Alice AU - Jiang, Xiuyun AU - Mol, Frank N. AU - Traparić, Jovan AU - Pulschen, Andre Arashiro AU - Nierhaus, Tim AU - Tarrason-Risa, Gabriel AU - Harker-Kirschneck, Lena AU - Löwe, Jan AU - Šarić, Anđela AU - Vlijm, Rifka AU - Baum, Buzz ID - 12756 IS - 11 JF - Science Advances TI - The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division VL - 9 ER - TY - JOUR AB - AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding. AU - Pak, Marina A. AU - Markhieva, Karina A. AU - Novikova, Mariia S. AU - Petrov, Dmitry S. AU - Vorobyev, Ilya S. AU - Maksimova, Ekaterina AU - Kondrashov, Fyodor AU - Ivankov, Dmitry N. ID - 12758 IS - 3 JF - PLoS ONE TI - Using AlphaFold to predict the impact of single mutations on protein stability and function VL - 18 ER - TY - JOUR AB - My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues. AU - Sazanov, Leonid A ID - 12757 IS - 5 JF - The Biochemical Journal SN - 0264-6021 TI - From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I VL - 480 ER - TY - JOUR AB - Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results. AU - Svoboda, Jakub AU - Tkadlec, Josef AU - Kaveh, Kamran AU - Chatterjee, Krishnendu ID - 12787 IS - 2271 JF - Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences SN - 1364-5021 TI - Coexistence times in the Moran process with environmental heterogeneity VL - 479 ER - TY - JOUR AB - We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants. AU - Karle, Volker AU - Ghazaryan, Areg AU - Lemeshko, Mikhail ID - 12788 IS - 10 JF - Physical Review Letters SN - 0031-9007 TI - Topological charges of periodically kicked molecules VL - 130 ER - TY - JOUR AB - Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity. AU - Ghazaryan, Areg AU - Holder, Tobias AU - Berg, Erez AU - Serbyn, Maksym ID - 12790 IS - 10 JF - Physical Review B SN - 2469-9950 TI - Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity VL - 107 ER - TY - JOUR AB - We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra. AU - Clark Di Leoni, Patricio AU - Agasthya, Lokahith N AU - Buzzicotti, Michele AU - Biferale, Luca ID - 12791 IS - 3 JF - The European Physical Journal E SN - 1292-8941 TI - Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks VL - 46 ER - TY - JOUR AB - Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization. AU - Huljev, Karla AU - Shamipour, Shayan AU - Nunes Pinheiro, Diana C AU - Preusser, Friedrich AU - Steccari, Irene AU - Sommer, Christoph M AU - Naik, Suyash AU - Heisenberg, Carl-Philipp J ID - 12830 IS - 7 JF - Developmental Cell SN - 1534-5807 TI - A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish VL - 58 ER - TY - JOUR AB - The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions. AU - Zeng, Zhongda AU - Yakaboylu, Enderalp AU - Lemeshko, Mikhail AU - Shi, Tao AU - Schmidt, Richard ID - 12831 IS - 13 JF - The Journal of Chemical Physics TI - Variational theory of angulons and their rotational spectroscopy VL - 158 ER - TY - JOUR AB - Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport. AU - Ljubotina, Marko AU - Desaules, Jean Yves AU - Serbyn, Maksym AU - Papić, Zlatko ID - 12839 IS - 1 JF - Physical Review X TI - Superdiffusive energy transport in kinetically constrained models VL - 13 ER - TY - JOUR AB - The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2. AU - He, Ren AU - Yang, Linlin AU - Zhang, Yu AU - Wang, Xiang AU - Lee, Seungho AU - Zhang, Ting AU - Li, Lingxiao AU - Liang, Zhifu AU - Chen, Jingwei AU - Li, Junshan AU - Ostovari Moghaddam, Ahmad AU - Llorca, Jordi AU - Ibáñez, Maria AU - Arbiol, Jordi AU - Xu, Ying AU - Cabot, Andreu ID - 12832 IS - 4 JF - Energy Storage Materials TI - A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance VL - 58 ER - TY - JOUR AB - Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter. AU - Martinet, Quentin AU - Aubret, Antoine AU - Palacci, Jérémie A ID - 12822 IS - 1 JF - Advanced Intelligent Systems SN - 2640-4567 TI - Rotation control, interlocking, and self‐positioning of active cogwheels VL - 5 ER - TY - JOUR AB - The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues. AU - Brandstätter, Tom AU - Brückner, David AU - Han, Yu Long AU - Alert, Ricard AU - Guo, Ming AU - Broedersz, Chase P. ID - 12818 JF - Nature Communications TI - Curvature induces active velocity waves in rotating spherical tissues VL - 14 ER - TY - JOUR AB - Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds. AU - Sokolova, Alesya AU - Kalacheva, D. A. AU - Fedorov, G. P. AU - Astafiev, O. V. ID - 12819 IS - 3 JF - Physical Review A SN - 2469-9926 TI - Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling VL - 107 ER - TY - JOUR AB - The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight," have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations. AU - Schmid, Laura AU - Ekbatani, Farbod AU - Hilbe, Christian AU - Chatterjee, Krishnendu ID - 12861 JF - Nature Communications TI - Quantitative assessment can stabilize indirect reciprocity under imperfect information VL - 14 ER - TY - JOUR AB - Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings. AU - Safavi, Shervin AU - Panagiotaropoulos, Theofanis I. AU - Kapoor, Vishal AU - Ramirez Villegas, Juan F AU - Logothetis, Nikos K. AU - Besserve, Michel ID - 12862 IS - 4 JF - PLoS Computational Biology TI - Uncovering the organization of neural circuits with Generalized Phase Locking Analysis VL - 19 ER - TY - JOUR AB - Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations. AU - Chen, Ke AU - Kunkel, Christian AU - Cheng, Bingqing AU - Reuter, Karsten AU - Margraf, Johannes T. ID - 12879 JF - Chemical Science SN - 2041-6520 TI - Physics-inspired machine learning of localized intensive properties ER - TY - JOUR AB - Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components. AU - Jiang, Lihui AU - Yao, Baolin AU - Zhang, Xiaoyan AU - Wu, Lixia AU - Fu, Qijing AU - Zhao, Yiting AU - Cao, Yuxin AU - Zhu, Ruomeng AU - Lu, Xinqi AU - Huang, Wuying AU - Zhao, Jianping AU - Li, Kuixiu AU - Zhao, Shuanglu AU - Han, Li AU - Zhou, Xuan AU - Luo, Chongyu AU - Zhu, Haiyan AU - Yang, Jing AU - Huang, Huichuan AU - Zhu, Zhengge AU - He, Xiahong AU - Friml, Jiří AU - Zhang, Zhongkai AU - Liu, Changning AU - Du, Yunlong ID - 12878 IS - 1 JF - Plant Journal SN - 0960-7412 TI - Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth VL - 115 ER - TY - JOUR AB - Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only. Results: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data. AU - Beneš, Nikola AU - Brim, Luboš AU - Huvar, Ondřej AU - Pastva, Samuel AU - Šafránek, David ID - 12876 IS - 4 JF - Bioinformatics TI - Boolean network sketches: A unifying framework for logical model inference VL - 39 ER - TY - JOUR AB - Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1. AU - Kaneshiro, Jeanae M. AU - Capitanio, Juliana S. AU - Hetzer, Martin W ID - 12880 IS - 1 JF - Nucleus SN - 1949-1034 TI - Lamin B1 overexpression alters chromatin organization and gene expression VL - 14 ER - TY - JOUR AB - We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier. AU - Suzuki, Fumika AU - Unruh, William G. ID - 12914 IS - 4 JF - Physical Review A SN - 2469-9926 TI - Numerical quantum clock simulations for measuring tunneling times VL - 107 ER - TY - JOUR AB - The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices. AU - Díez-Mérida, J. AU - Díez-Carlón, A. AU - Yang, S. Y. AU - Xie, Y. M. AU - Gao, X. J. AU - Senior, Jorden L AU - Watanabe, K. AU - Taniguchi, T. AU - Lu, X. AU - Higginbotham, Andrew P AU - Law, K. T. AU - Efetov, Dmitri K. ID - 12913 JF - Nature Communications TI - Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene VL - 14 ER - TY - JOUR AB - The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter. AU - Fellner, Klemens AU - Fischer, Julian L AU - Kniely, Michael AU - Tang, Bao Quoc ID - 10550 JF - Journal of Nonlinear Science SN - 0938-8974 TI - Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion VL - 33 ER - TY - JOUR AB - We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions. AU - Hensel, Sebastian AU - Laux, Tim ID - 13043 IS - 1 JF - Interfaces and Free Boundaries SN - 1463-9963 TI - Weak-strong uniqueness for the mean curvature flow of double bubbles VL - 25 ER - TY - JOUR AB - The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes. AU - Schmid, Rochus AU - Cheng, Bingqing ID - 12912 IS - 16 JF - The Journal of Chemical Physics TI - Computing chemical potentials of adsorbed or confined fluids VL - 158 ER - TY - JOUR AB - Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths. AU - Liu, Zhenyuan AU - Piovarci, Michael AU - Hafner, Christian AU - Charrondiere, Raphael AU - Bickel, Bernd ID - 12972 IS - 2 JF - Computer Graphics Forum KW - embroidery KW - design KW - directionality KW - density KW - image SN - 1467-8659 TI - Directionality-aware design of embroidery patterns VL - 42 ER - TY - JOUR AB - Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases. AU - Zavadakova, Anna AU - Vistejnova, Lucie AU - Belinova, Tereza AU - Tichanek, Filip AU - Bilikova, Dagmar AU - Mouton, Peter R. ID - 13033 IS - 1 JF - Scientific Reports KW - Multidisciplinary SN - 2045-2322 TI - Novel stereological method for estimation of cell counts in 3D collagen scaffolds VL - 13 ER - TY - JOUR AB - Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts. AU - Troussicot, Laura AU - Vallet, Alicia AU - Molin, Mikael AU - Burmann, Björn M. AU - Schanda, Paul ID - 13095 IS - 19 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR VL - 145 ER - TY - JOUR AB - Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞. AU - Anastos, Michael ID - 13042 IS - 2 JF - Electronic Journal of Combinatorics TI - A note on long cycles in sparse random graphs VL - 30 ER - TY - DATA AB - Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. This data repository contains NMR data presented in the associated manuscript AU - Schanda, Paul ID - 12820 TI - Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR" ER - TY - JOUR AB - We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression. AU - French, Martin AU - Bethkenhagen, Mandy AU - Ravasio, Alessandra AU - Hernandez, Jean Alexis ID - 13039 IS - 13 JF - Physical Review B SN - 2469-9950 TI - Ab initio calculation of the reflectivity of molecular fluids under shock compression VL - 107 ER - TY - JOUR AB - There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe. AU - Nan, Bingfei AU - Song, Xuan AU - Chang, Cheng AU - Xiao, Ke AU - Zhang, Yu AU - Yang, Linlin AU - Horta, Sharona AU - Li, Junshan AU - Lim, Khak Ho AU - Ibáñez, Maria AU - Cabot, Andreu ID - 13092 IS - 19 JF - ACS Applied Materials and Interfaces SN - 1944-8244 TI - Bottom-up synthesis of SnTe-based thermoelectric composites VL - 15 ER - TY - JOUR AB - Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states. AU - Azadbakht, Ali AU - Meadowcroft, Billie AU - Varkevisser, Thijs AU - Šarić, Anđela AU - Kraft, Daniela J. ID - 13094 IS - 10 JF - Nano Letters SN - 1530-6984 TI - Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles VL - 23 ER - TY - JOUR AB - The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated. AU - Nan, Bingfei AU - Li, Mengyao AU - Zhang, Yu AU - Xiao, Ke AU - Lim, Khak Ho AU - Chang, Cheng AU - Han, Xu AU - Zuo, Yong AU - Li, Junshan AU - Arbiol, Jordi AU - Llorca, Jordi AU - Ibáñez, Maria AU - Cabot, Andreu ID - 13093 JF - ACS Applied Electronic Materials TI - Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature ER - TY - JOUR AB - We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle. AU - Browning, Timothy D AU - Sawin, Will ID - 13091 IS - 3 JF - Algebra and Number Theory SN - 1937-0652 TI - Free rational curves on low degree hypersurfaces and the circle method VL - 17 ER - TY - JOUR AB - The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality. AU - Redchenko, Elena AU - Poshakinskiy, Alexander V. AU - Sett, Riya AU - Zemlicka, Martin AU - Poddubny, Alexander N. AU - Fink, Johannes M ID - 13117 JF - Nature Communications TI - Tunable directional photon scattering from a pair of superconducting qubits VL - 14 ER - TY - JOUR AB - Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification. AU - Sahu, Rishabh AU - Qiu, Liu AU - Hease, William J AU - Arnold, Georg M AU - Minoguchi, Y. AU - Rabl, P. AU - Fink, Johannes M ID - 13106 IS - 6646 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Entangling microwaves with light VL - 380 ER - TY - JOUR AB - We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩ , we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩ of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function. AU - Clozeau, Nicolas AU - Josien, Marc AU - Otto, Felix AU - Xu, Qiang ID - 13129 JF - Foundations of Computational Mathematics SN - 1615-3375 TI - Bias in the representative volume element method: Periodize the ensemble instead of its realizations ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request. AU - Redchenko, Elena AU - Poshakinskiy, Alexander AU - Sett, Riya AU - Zemlicka, Martin AU - Poddubny, Alexander AU - Fink, Johannes M ID - 13124 TI - Tunable directional photon scattering from a pair of superconducting qubits ER - TY - GEN AB - Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1 AU - Sahu, Rishabh ID - 13122 TI - Entangling microwaves with light ER - TY - JOUR AB - Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans. AU - Vetrova, Alexandra A. AU - Kupaeva, Daria M. AU - Kizenko, Alena AU - Lebedeva, Tatiana S. AU - Walentek, Peter AU - Tsikolia, Nikoloz AU - Kremnyov, Stanislav V. ID - 13166 JF - Scientific Reports TI - The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization VL - 13 ER - TY - JOUR AB - We consider the spin- 1 2 Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain. AU - Orlov, Pavel AU - Tiutiakina, Anastasiia AU - Sharipov, Rustem AU - Petrova, Elena AU - Gritsev, Vladimir AU - Kurlov, Denis V. ID - 13138 IS - 18 JF - Physical Review B SN - 2469-9950 TI - Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain VL - 107 ER - TY - JOUR AB - The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth. AU - Chen, C AU - Zhang, Y AU - Cai, J AU - Qiu, Y AU - Li, L AU - Gao, C AU - Gao, Y AU - Ke, M AU - Wu, S AU - Wei, C AU - Chen, J AU - Xu, T AU - Friml, Jiří AU - Wang, J AU - Li, R AU - Chao, D AU - Zhang, B AU - Chen, X AU - Gao, Z ID - 13213 IS - 3 JF - Plant Physiology SN - 0032-0889 TI - Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots VL - 192 ER - TY - JOUR AB - In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype. AU - Guet, Calin C AU - Bruneaux, L AU - Oikonomou, P AU - Aldana, M AU - Cluzel, P ID - 12478 JF - Frontiers in Microbiology TI - Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression VL - 14 ER - TY - JOUR AB - The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases. AU - Michaels, Thomas C.T. AU - Qian, Daoyuan AU - Šarić, Anđela AU - Vendruscolo, Michele AU - Linse, Sara AU - Knowles, Tuomas P.J. ID - 13237 JF - Nature Reviews Physics TI - Amyloid formation as a protein phase transition VL - 5 ER - TY - JOUR AB - Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation. AU - Shamipour, Shayan AU - Hofmann, Laura AU - Steccari, Irene AU - Kardos, Roland AU - Heisenberg, Carl-Philipp J ID - 13229 IS - 6 JF - PLoS Biology TI - Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes VL - 21 ER - TY - JOUR AB - Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop an analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally. AU - Grosjean, Galien M AU - Waitukaitis, Scott R ID - 13197 IS - 6 JF - Physical Review Materials KW - Physics and Astronomy (miscellaneous) KW - General Materials Science SN - 2475-9953 TI - Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts VL - 7 ER - TY - JOUR AB - To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals. AU - Charlton, Julie A. AU - Mlynarski, Wiktor F AU - Bai, Yoon H. AU - Hermundstad, Ann M. AU - Goris, Robbe L.T. ID - 13230 IS - 6 JF - PLoS Computational Biology TI - Environmental dynamics shape perceptual decision bias VL - 19 ER - TY - JOUR AB - The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study. AU - Dormeshkin, Dmitri AU - Katsin, Mikalai AU - Stegantseva, Maria AU - Golenchenko, Sergey AU - Shapira, Michail AU - Dubovik, Simon AU - Lutskovich, Dzmitry AU - Kavaleuski, Anton AU - Meleshko, Alexander ID - 13232 IS - 6 JF - Vaccines TI - Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein VL - 11 ER - TY - JOUR AB - AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications. AU - Liu, Yu AU - Li, Mingquan AU - Wan, Shanhong AU - Lim, Khak Ho AU - Zhang, Yu AU - Li, Mengyao AU - Li, Junshan AU - Ibáñez, Maria AU - Hong, Min AU - Cabot, Andreu ID - 13235 IS - 12 JF - ACS Nano SN - 1936-0851 TI - Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance VL - 17 ER - TY - JOUR AB - We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles. AU - Schörner, Maximilian AU - Bethkenhagen, Mandy AU - Döppner, Tilo AU - Kraus, Dominik AU - Fletcher, Luke B. AU - Glenzer, Siegfried H. AU - Redmer, Ronald ID - 13231 IS - 6 JF - Physical Review E SN - 2470-0045 TI - X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula VL - 107 ER - TY - JOUR AB - We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters. AU - Agafonova, Sofya AU - Lemeshko, Mikhail AU - Volosniev, Artem ID - 13233 IS - 6 JF - Physical Review A SN - 2469-9926 TI - Finite-range bias in fitting three-body loss to the zero-range model VL - 107 ER -