@article{13251, abstract = {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.}, author = {Wei, Yujing and Volosniev, Artem and Lorenc, Dusan and Zhumekenov, Ayan A. and Bakr, Osman M. and Lemeshko, Mikhail and Alpichshev, Zhanybek}, issn = {1948-7185}, journal = {The Journal of Physical Chemistry Letters}, keywords = {General Materials Science, Physical and Theoretical Chemistry}, number = {27}, pages = {6309--6314}, publisher = {American Chemical Society}, title = {{Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites}}, doi = {10.1021/acs.jpclett.3c01158}, volume = {14}, year = {2023}, } @inproceedings{13292, abstract = {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.}, author = {Henzinger, Thomas A and Kebis, Pavol and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {1868-8969}, location = {Paderborn, Germany}, pages = {129:1----129:20}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Regular methods for operator precedence languages}}, doi = {10.4230/LIPIcs.ICALP.2023.129}, volume = {261}, year = {2023}, } @article{13277, abstract = {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.}, author = {Tucci, Gennaro and De Nicola, Stefano and Wald, Sascha and Gambassi, Andrea}, issn = {2666-9366}, journal = {SciPost Physics Core}, keywords = {Statistical and Nonlinear Physics, Atomic and Molecular Physics, and Optics, Nuclear and High Energy Physics, Condensed Matter Physics}, number = {2}, publisher = {SciPost Foundation}, title = {{Stochastic representation of the quantum quartic oscillator}}, doi = {10.21468/scipostphyscore.6.2.029}, volume = {6}, year = {2023}, } @article{13276, abstract = {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.}, author = {Rammelmüller, Lukas and Huber, David and Volosniev, Artem}, issn = {2949-804X}, journal = {SciPost Physics Codebases}, publisher = {SciPost Foundation}, title = {{A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D}}, doi = {10.21468/scipostphyscodeb.12}, year = {2023}, } @misc{13275, abstract = {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.}, author = {Rammelmüller, Lukas and Huber, David and Volosniev, Artem}, publisher = {SciPost Foundation}, title = {{Codebase release 1.0 for FermiFCI}}, doi = {10.21468/scipostphyscodeb.12-r1.0}, year = {2023}, } @inproceedings{13262, abstract = {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.}, author = {Fedorov, Alexander and Hashemi, Diba and Nadiradze, Giorgi and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures}, isbn = {9781450395458}, location = {Orlando, FL, United States}, pages = {261--271}, publisher = {Association for Computing Machinery}, title = {{Provably-efficient and internally-deterministic parallel Union-Find}}, doi = {10.1145/3558481.3591082}, year = {2023}, } @article{11479, abstract = {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.}, author = {De Jode, Aurélien and Le Moan, Alan and Johannesson, Kerstin and Faria, Rui and Stankowski, Sean and Westram, Anja M and Butlin, Roger K. and Rafajlović, Marina and Fraisse, Christelle}, issn = {1752-4571}, journal = {Evolutionary Applications}, number = {2}, pages = {542--559}, publisher = {Wiley}, title = {{Ten years of demographic modelling of divergence and speciation in the sea}}, doi = {10.1111/eva.13428}, volume = {16}, year = {2023}, } @article{12329, abstract = {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.}, author = {Gómez, Arturo and Oliveira, Goncalo}, issn = {2045-2322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{New approaches to epidemic modeling on networks}}, doi = {10.1038/s41598-022-19827-9}, volume = {13}, year = {2023}, } @article{9034, abstract = {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.}, author = {Wilsch, Florian Alexander}, issn = {1687-0247}, journal = {International Mathematics Research Notices}, number = {8}, pages = {6780--6808}, publisher = {Oxford Academic}, title = {{Integral points of bounded height on a log Fano threefold}}, doi = {10.1093/imrn/rnac048}, volume = {2023}, year = {2023}, } @article{12469, abstract = {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.}, author = {Viljakainen, Lumi and Fürst, Matthias and Grasse, Anna V and Jurvansuu, Jaana and Oh, Jinook and Tolonen, Lassi and Eder, Thomas and Rattei, Thomas and Cremer, Sylvia}, issn = {1664-302X}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, title = {{Antiviral immune response reveals host-specific virus infections in natural ant populations}}, doi = {10.3389/fmicb.2023.1119002}, volume = {14}, year = {2023}, }