Physical review. E最新文献

{"title":"Selection principle for the screening parameters in the mechanical response of amorphous solids.","authors":"Pawandeep Kaur, Itamar Procaccia, Tuhin Samanta","doi":"10.1103/PhysRevE.111.015506","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.015506","url":null,"abstract":"<p><p>The mechanical response of amorphous solids to external strains is riddled with plastic events that create topological charges in the resulting displacement field. It was recently shown that the latter lead to screening phenomena that are accompanied by the breaking of both translational and Chiral symmetries. The screening effects are quantified by two screening parameters κ_{e} and κ_{o}, which are inverse characteristic lengths that do not exist in classical elasticity. The screening parameters (and the associated lengths) are emergent, and it is important to understand how they are selected. This Letter explores the mechanism of selection of these characteristic lengths in two examples of strain protocols that allow analytic scrutiny.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-2","pages":"015506"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integer traffic assignment problem: Algorithms and insights on random graphs.","authors":"Rayan Harfouche, Giovanni Piccioli, Lenka Zdeborová","doi":"10.1103/PhysRevE.111.014316","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014316","url":null,"abstract":"<p><p>Path optimization is a fundamental concern across various real-world scenarios, ranging from traffic congestion issues to efficient data routing over the Internet. The traffic assignment problem (TAP) is a classic continuous optimization problem in this field. This study considers the integer traffic assignment problem (ITAP), a discrete variant of TAP. ITAP involves determining optimal routes for commuters in a city represented by a graph, aiming to minimize congestion while adhering to integer flow constraints on paths. This restriction makes ITAP an NP-hard problem. While conventional TAP prioritizes repulsive interactions to minimize congestion, this work also explores the case of attractive interactions, related to minimizing the number of occupied edges. We present and evaluate multiple algorithms to address ITAP, including a message passing algorithm, a greedy approach, simulated annealing, and relaxation of ITAP to TAP, including the message passing algorithm in Yeung, Saad, and Wong [Proc. Natl. Acad. Sci. USA 110, 13717 (2013)0027-842410.1073/pnas.1301111110], a greedy approach, simulated annealing, and relaxation of ITAP to TAP. Inspired by studies of random ensembles in the large-size limit in statistical physics, comparisons between these algorithms are conducted on large sparse random regular graphs with a random set of origin-destination pairs. Our results indicate that while the simplest greedy algorithm performs competitively in the repulsive scenario, in the attractive case the message-passing-based algorithm and simulated annealing demonstrate superiority. We then investigate the relationship between TAP and ITAP in the repulsive case. We find that, as the number of paths increases, the solution of TAP converges toward that of ITAP, and we investigate the speed of this convergence. Depending on the number of paths, our analysis leads us to identify two scaling regimes: In one the average flow per edge is of order one, and in another, the number of paths scales quadratically with the size of the graph, in which case the continuous relaxation solves the integer problem closely.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014316"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kaleidoscopic reorganization of network communities across different scales.","authors":"Wonhee Jeong, Daekyung Lee, Heetae Kim, Sang Hoon Lee","doi":"10.1103/PhysRevE.111.014312","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014312","url":null,"abstract":"<p><p>The notion of structural heterogeneity is pervasive in real networks, and their community organization is no exception. Still, a vast majority of community detection methods assume neatly hierarchically organized communities of a characteristic scale for a given hierarchical level. In this work, we demonstrate that the reality of scale-dependent community reorganization is convoluted with simultaneous processes of community splitting and merging, challenging the conventional understanding of community-scale adjustment. We provide a mathematical argument concerning the modularity function, the results from real-network analysis, and a simple network model for a comprehensive understanding of the nontrivial community reorganization process. The reorganization is characterized by a local drop in the number of communities as the resolution parameter varies. This study suggests a need for a paradigm shift in the study of network communities, which emphasizes the importance of considering scale-dependent reorganization to better understand the genuine structural organization of networks.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014312"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Classical scattering and fragmentation of clusters of ions in helical confinement.","authors":"Ansgar Siemens, Peter Schmelcher","doi":"10.1103/PhysRevE.111.014140","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014140","url":null,"abstract":"<p><p>We explore the scattering dynamics of classical Coulomb-interacting clusters of ions confined to a helical geometry. Ion clusters of equally charged particles constrained to a helix can form many-body bound states; i.e., they exhibit stable motion of Coulomb-interacting identical ions. We analyze the scattering and fragmentation behavior of two ion clusters, thereby understanding the rich phenomenology of their dynamics. The scattering dynamics is complex in the sense that it exhibits cascades of decay processes involving strongly varying cluster sizes. These processes are governed by the internal energy flow and the underlying oscillatory many-body potential. We specifically focus on the impact of the collision energy on the dynamics of individual ions during and immediately after the collision of two clusters and on the internal dynamics of ion clusters that are excited during a cluster collision.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014140"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Weighted-ensemble network simulations of the susceptible-infected-susceptible model of epidemics.","authors":"Elad Korngut, Ohad Vilk, Michael Assaf","doi":"10.1103/PhysRevE.111.014146","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014146","url":null,"abstract":"<p><p>The presence of erratic or unstable paths in standard kinetic Monte Carlo simulations significantly undermines the accurate simulation and sampling of transition pathways. While typically reliable methods, such as the Gillespie algorithm, are employed to simulate such paths, they encounter challenges in efficiently identifying rare events due to their sequential nature and reliance on exact Monte Carlo sampling. In contrast, the weighted-ensemble method effectively samples rare events and accelerates the exploration of complex reaction pathways by distributing computational resources among multiple replicas, where each replica is assigned a weight reflecting its importance, and evolves independently from the others. Here, we implement the highly efficient and robust weighted-ensemble method to model susceptible-infected-susceptible dynamics on large heterogeneous population networks, and explore the interplay between stochasticity and contact heterogeneity, which ultimately gives rise to disease clearance. Studying a wide variety of networks characterized by fat-tailed asymmetric degree distributions, we are able to compute the mean time to extinction and quasistationary distribution around it in previously inaccessible parameter regimes.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014146"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maintaining an autocatalytic reaction system in a protocell: Nonenzymatic RNA templating and the link between replication and metabolism.","authors":"Quentin C C Sanders, Alex Verbeem, Paul G Higgs","doi":"10.1103/PhysRevE.111.014424","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014424","url":null,"abstract":"<p><p>The first protocells must have been driven by a reaction system in which autocatalysis is maintained inside the cell while food molecules outside the cell are unreactive. We show that if there is a second-order autocatalytic mechanism, then an active state can be stable inside the cell with a high catalyst concentration while the environment remains stable in an unreactive state with no catalyst. Addition of a small amount of catalyst to the environment does not cause the initiation of the autocatalytic cycle outside the cell. In contrast, for a first-order mechanism, addition of a small amount of catalyst initiates the reaction outside the cell unless there is continual removal of the catalyst from the environment. Hence, a second-order reaction mechanism maintains the difference between the inside and outside of a protocell much better than a first-order mechanism. The formose reaction, although a prebiotically plausible autocatalytic system, is first order and therefore is unlikely as a means of support for the first protocells. We give other theoretical examples of first- and second-order reaction networks but note there are few known real-world chemical systems that fit these schemes. However, we show that nonenzymatic RNA templating constitutes a second-order autocatalytic system with the necessary properties to support a protocell. Templating is maintained inside the cell but is not initiated outside the cell. If the reaction is driven by an external supply of activated nucleotides, then templating is itself a metabolic cycle. It is not necessary to have an additional separate metabolic cycle before templating reactions can occur. In this view, templating reactions, which are usually considered as the origin of replication and heredity, are also the origin of metabolism.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014424"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multistable states of light in two coupled silica microresonators with dominating thermo-optical nonlinearity.","authors":"Maria P Marisova, Alexey V Andrianov, Alexey V Yulin, Elena A Anashkina","doi":"10.1103/PhysRevE.111.014203","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014203","url":null,"abstract":"<p><p>We present a comprehensive theoretical analysis of thermo-optical multistability in two coupled silica microresonators with identical and slightly different partial eigenfrequencies. We consider a unidirectionally pumped system with a relatively low total Q-factor, where thermo-optical nonlinearity dominates. To analyze the system behavior, we employ a dynamical system approach that takes into account the hierarchy of the timescales associated with optical and thermal processes. We show that up to nine stationary states are possible for the same system parameters and that no more than four of them can be stable. Additionally, self-oscillation regimes are observed within specific parameter ranges. Bifurcations are discussed and nontrivial hysteretic switchings between light states under smooth pump frequency sweeping for different pump powers are demonstrated. It is also shown that even small intermode detuning can affect the dynamics of the system dramatically. This intriguing phenomenon is of fundamental interest and may potentially be used in the development of ultrasensitive sensors when operating near a bifurcation point, which is also discussed.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014203"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating ion dynamics through Coulomb and Yukawa interaction potentials in one-component strongly coupled plasmas.","authors":"Swati Swagatika Mishra, Sudeep Bhattacharjee, Pascal Brault","doi":"10.1103/PhysRevE.111.015208","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.015208","url":null,"abstract":"<p><p>Atmospheric pressure helium plasmas are investigated through molecular dynamics simulations at room temperature (300 K) for various ionization fractions (χ_{i}=10^{-1}-10^{-5}) in the strongly coupled regime (ion coupling parameter, Γ_{i}∼1-10) employing Coulomb and Yukawa interaction potentials. The role of electron screening in ion dynamics and energetics is examined through ion and gas temperatures, mean squared displacement of ions, ion coupling parameter, and radial distribution function of the system. It is found that electron screening in the Yukawa potential significantly limits the disorder-induced heating (DIH) mechanism for strongly ionized plasmas (χ_{i}≥10^{-3}). Whereas, ions show a prominent subdiffusive behavior associated with the DIH during the nonequilibrium phase for the Coulomb potential. The DIH mechanism is explained using a model based upon the conservation of energy. However, for weakly ionized plasmas (χ_{i}≤10^{-4}), the maximum ion temperatures are almost similar for both potentials. Furthermore, electron screening affects the separation distance and arrangement of the ion-neutral pairs for all the values of χ_{i}. In general, Yukawa potential results in a lower mean potential energy of the interacting particles, which is energetically favorable for the stability of the system.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-2","pages":"015208"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Josephson-Anderson relation as diagnostic of turbulent drag reduction by polymers.","authors":"Samvit Kumar, Simon Toedtli, Tamer A Zaki, Gregory L Eyink","doi":"10.1103/PhysRevE.111.015105","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.015105","url":null,"abstract":"<p><p>The detailed Josephson-Anderson relation, which equates instantaneously the volume-integrated vorticity flux and the work by pressure drop, has been the key to drag reduction in superconductors and superfluids. We employ a classical version of this relation to investigate the dynamics of polymer drag-reduced channel flows, particularly in the high-extent drag reduction (HDR) regime which is known to exhibit strong space-time intermittency. We show that high drag is not created instantaneously by near-wall coherent vortex structures as assumed in prior works. These predominantly spanwise near-wall vortex structures can produce a net \"up-gradient\" flux of vorticity toward the wall, which instead reduces instantaneous drag. Increase of wall vorticity and skin friction due to this up-gradient flux occurs after an apparent lag of several advection times, increasing with the Weissenberg number. This increasing lag appears to be due to polymer damping of up-gradient nonlinear vorticity transport that arises from large-scale eddies in the logarithmic layer. The relatively greater polymer damping of down-gradient transport due to small-scale eddies results in lower net vorticity flux and hence lower drag. The Josephson-Anderson relation thus provides an exact tool to diagnose the mechanism of polymer drag reduction in terms of vorticity dynamics and it explains also prior puzzling observations on transient drag reduction, as for centerline-release experiments in pipe flow.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-2","pages":"015105"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of microscale and nanoscale systems in the weak-memory regime: A mathematical framework beyond the Markov approximation.","authors":"Kay Brandner","doi":"10.1103/PhysRevE.111.014137","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014137","url":null,"abstract":"<p><p>The visible dynamics of small-scale systems are strongly affected by unobservable degrees of freedom, which can belong to either external environments or internal subsystems and almost inevitably induce memory effects. Formally, such inaccessible degrees of freedom can be systematically eliminated from essentially any microscopic model through projection operator techniques, which result in nonlocal time evolution equations. This article investigates how and under what conditions locality in time can be rigorously restored beyond the standard Markov approximation, which generally requires the characteristic timescales of accessible and inaccessible degrees of freedom to be sharply separated. Specifically, we consider nonlocal time evolution equations that are autonomous and linear in the variables of interest. For this class of models, we prove a mathematical theorem that establishes a well-defined weak-memory regime, where faithful local approximations exist, even if the relevant timescales are of comparable order of magnitude. The generators of these local approximations, which become exact in the long-time limit, are time independent and can be determined to arbitrary accuracy through a convergent perturbation theory in the memory strength, where the Markov generator is recovered in first order. For illustration, we work out three simple, yet instructive, examples covering coarse-grained Markov jump networks, semi-Markov jump processes, and generalized Langevin equations.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014137"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}