Physical review. E最新文献

{"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":"Ergodicity breaking and restoration in models of heat transport with microscopic reversibility.","authors":"Piero Olla","doi":"10.1103/PhysRevE.111.014155","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014155","url":null,"abstract":"<p><p>The behavior of lattice models in which time reversibility is enforced at the level of trajectories (microscopic reversibility) is studied analytically. Conditions for ergodicity breaking are explored, and a few examples of systems characterized by an additional conserved quantity besides energy are presented. All the systems are characterized by ergodicity restoration when put in contact with a thermal bath, except for specific choices of the interactions between the atoms in the system and the bath. The study shows that the additional conserved quantities return to play a role in nonequilibrium conditions. The similarities with the behavior of some mesoscale systems, in which the transition rates satisfy detailed balance but not microscopic reversibility, are discussed.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014155"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458531","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":"Quantum channel learning.","authors":"Mikhail Gennadievich Belov, Victor Victorovich Dubov, Alexey Vladimirovich Filimonov, Vladislav Gennadievich Malyshkin","doi":"10.1103/PhysRevE.111.015302","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.015302","url":null,"abstract":"<p><p>The problem of an optimal mapping between Hilbert spaces IN and OUT, based on a series of density matrix mapping measurements ρ^{(l)}→ϱ^{(l)}, l=1⋯M, is formulated as an optimization problem maximizing the total fidelity F=∑_{l=1}^{M}ω^{(l)}F(ϱ^{(l)},∑_{s}B_{s}ρ^{(l)}B_{s}^{†}) subject to probability preservation constraints on Kraus operators B_{s}. For F(ϱ,σ) in the form that total fidelity can be represented as a quadratic form with superoperator F=∑_{s}〈B_{s}|S|B_{s}〉 (either exactly or as an approximation) an iterative algorithm is developed. The work introduces two important generalizations of unitary learning: (1) IN/OUT states are represented as density matrices; (2) the mapping itself is formulated as a mixed unitary quantum channel A^{OUT}=∑_{s}|w_{s}|^{2}U_{s}A^{IN}U_{s}^{†} (no general quantum channel yet). This marks a crucial advancement from the commonly studied unitary mapping of pure states ϕ_{l}=Uψ_{l} to a quantum channel, which allows us to distinguish probabilistic mixture of states and their superposition. An application of the approach is demonstrated on unitary learning of density matrix mapping ϱ^{(l)}=Uρ^{(l)}U^{†}, in this case a quadratic on U fidelity can be constructed by considering sqrt[ρ^{(l)}]→sqrt[ϱ^{(l)}] mapping, and on a quantum channel, where quadratic on B_{s} fidelity is an approximation-a quantum channel is then obtained as a hierarchy of unitary mappings, a mixed unitary channel. The approach can be applied to studying quantum inverse problems, variational quantum algorithms, quantum tomography, and more. A software product implementing the algorithm is available from the authors.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-2","pages":"015302"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458876","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":"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":"Quasiphase transition of a single-file water chain influenced by atomic charges in a water model using orientational-biased replica exchange Monte Carlo simulations.","authors":"Liang Zhao, Junqing Ni, Zhi Zhu, Yusong Tu, Chunlei Wang","doi":"10.1103/PhysRevE.111.015419","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.015419","url":null,"abstract":"<p><p>The recently observed temperature-dependent quasiphase transition of the single-file water chain confined within a carbon nanotube in experiments has been validated by the simple lattice theory and molecular dynamics simulations. It has been pointed out that the atomic charges in water models are important, yet how the values will affect the structural details and thermodynamic properties of the quasiphase transition has not been fully revealed. In this work we perform orientational-biased replica exchange Monte Carlo simulations in the canonical ensemble to explore the effect of atomic charges in the SPC/E water model on the quasiphase transition of a single-file water chain. Based on the atomic charge values reported in literature, three distinct quasiphases are reproduced, comprising a fully hydrogen-bonded water chain at lower temperatures, a more ordered dipolar orientation along the tube axis at intermediate temperatures, and a completely disordered structure at higher temperatures. Then by increasing the atomic charge values, we find that the fragmentation of the entire water chain into shorter water segments, the orientational ordering of water dipoles along the tube axis, and the transition towards complete disorder are all inhibited. Consequently, the transition temperatures between three quasiphases have been shifted to higher temperatures. The thermodynamic analysis demonstrates that the increased atomic charge values enhance the hydrogen bonding between neighboring water molecules and also the electrostatic attraction within the water chain, leading to a longer water dipole correlation length even at higher temperatures. These findings highlight the vital role of atomic charges in water models and also the electrostatic interaction in regulating the orientational ordering of water molecules under nanoconfinement.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-2","pages":"015419"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458905","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":"Factors influencing the stability of the motor-clutch model on compliant substrates under external load.","authors":"Beibei Shen, Yunxin Zhang","doi":"10.1103/PhysRevE.111.014417","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.014417","url":null,"abstract":"<p><p>Cellular migration is crucial for biological processes, including embryonic development, immune response, and wound healing. The myosin-clutch model is a framework that describes how cells control migration through the interactions between myosin, the clutch mechanism, and the substrate. This model is related to how cells regulate adhesion, generate traction forces, and move on compliant substrates. In this study, we present a five-dimensional nonlinear autonomous system to investigate the influences of myosin, clutches, substrate, and external load on the system's stability. Moreover, we analyze the effects of various parameters on fixed points and explore the frequency and amplitude of the limit cycle associated with oscillations. We discovered that the system demonstrates oscillatory behavior when the velocity of the myosin motor is relatively low or when the ratio of motor attachment rate to motor detachment rate is relatively high. The external load shares a fraction of the force exerted by myosin motors, thereby diminishing the force endured by the clutches. Within a specific range, an increase in external load not only diminishes and eventually eliminates the region lacking fixed points but also decelerates clutch detachment, enhancing clutch protein adherence.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"111 1-1","pages":"014417"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458916","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}