Physical review. E最新文献

{"title":"Growth bistability in small bacterial populations exposed to antibiotics.","authors":"B Ledoux, D Lacoste","doi":"10.1103/hg5y-tqvt","DOIUrl":"https://doi.org/10.1103/hg5y-tqvt","url":null,"abstract":"<p><p>With the development of microfluidics, it has now become possible to assess the susceptibility of bacteria to antibiotics at the single-cell level instead of relying on population measurements. Such studies are particularly relevant when the growth of a bacterial population in the presence of antibiotics is heterogeneous. Here, we build a model to describe such a case and apply it to experimental measurements on a small population of E. coli exposed to ciprofloxacin, a drug which is well-known for triggering a bistable response.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034411"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207375","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":"Theory of β relaxation beyond mode-coupling theory: A microscopic treatment.","authors":"Corentin C L Laudicina, Liesbeth M C Janssen, Grzegorz Szamel","doi":"10.1103/57qw-rtrw","DOIUrl":"https://doi.org/10.1103/57qw-rtrw","url":null,"abstract":"<p><p>We develop a systematic extension of mode-coupling theory that incorporates critical dynamical fluctuations. Starting from a microscopic diagrammatic theory, we identify dominant classes of divergent diagrams near the mode-coupling transition and show that the corresponding asymptotic series dominates the mean-field prediction below an upper critical dimension d_{c}=8. To resum these divergences, we construct a mapping to a stochastic dynamical process in which the order parameter evolves under random spatiotemporal fields. This reformulation provides a controlled, fully dynamical derivation of an effective theory for β relaxation that remarkably coincides with stochastic beta relaxation theory [T. Rizzo, Long-wavelength fluctuations lead to a model of the glass crossover, Europhys. Lett. 106, 56003 (2014)10.1209/0295-5075/106/56003]. All coupling constants of the latter theory are expressed microscopically in terms of the liquid static structure factor and are computed for the paradigmatic hard-sphere system in the Percus-Yevick approximation. The analysis demonstrates that critical fluctuations alone restore ergodicity and replace the putative mean-field transition with a smooth crossover. Our results establish a predictive framework for structural relaxation beyond mean-field.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-2","pages":"035411"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207584","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":"Diffusion with conserved marginal distributions and information theory in fracton hydrodynamics.","authors":"Vaibhav Mohanty, Sunghan Ro","doi":"10.1103/8wsp-p1xb","DOIUrl":"https://doi.org/10.1103/8wsp-p1xb","url":null,"abstract":"<p><p>Diffusion with multipole-moment conservation gives rise to transport laws that generalize Fick's law and has attracted growing attention following experimental advances in strongly tilted optical lattices. It was recently shown that conserving complete multipole-moment groups leads to subdiffusive dynamics governed by a nonlinear diffusion equation, raising the question of whether hydrodynamic equations would also be nonlinear when the conservation law is imposed only at the subsystem level. Here we show that subsystem symmetries generically produce nonlinear hydrodynamic equations with shear-only transport, in which any localization present in the initial marginal distributions is preserved at long times by the conservation of those marginals. A linear regime emerges only as a limiting case for small fluctuations around a uniform background. We derive the deterministic and fluctuating parts of the hydrodynamic equations in arbitrary dimensions and obtain the corresponding maximum-entropy equilibrium distributions under constrained marginals. We also show that marginal-conserving diffusion provides a concrete hydrodynamic realization of partial multipole-moment conservation, and we offer an information-theoretic interpretation in which total correlation decays monotonically even when pairwise mutual information does not.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034129"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207564","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":"Introduction to random rule-based chemical networks.","authors":"Jérémie Unterberger","doi":"10.1103/wfn7-h898","DOIUrl":"https://doi.org/10.1103/wfn7-h898","url":null,"abstract":"<p><p>Large chemical networks appear in various branches of chemistry and biology, in particular, cellular metabolism and prebiotic chemistry. Detailed simulations of such networks are difficult, or even impossible for lack of kinetic data. Various strategies have been developed to produce synthetic random networks mimicking the large scale organizational properties of experimental chemical networks. These random networks are however mathematical artifacts, which fail to reflect the general reactivity structure of chemistry. We present here a class of random models of prebiotic (uncatalyzed) chemistry, based on context-independent rules, which is coherent with the general compositional logic of metabolism. The general organization of the random networks fits within the small-world paradigm. We get a phase diagram of the models through an approximate mapping to a solvable tree growth model. Our predictions go beyond a purely abstract connectivity analysis of the reaction graph by studying the diversity of chemical mechanisms, and singling out evolutionary patterns, such as autocatalysis and multistationarity, paving the road to possible open-ended evolution.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034307"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207581","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":"Anomalous diffusion and ergodicity breaking of subordinated random diffusivity processes in harmonic potential.","authors":"Xudong Wang, Zhenhai Wang, Yao Chen","doi":"10.1103/jtq7-379m","DOIUrl":"https://doi.org/10.1103/jtq7-379m","url":null,"abstract":"<p><p>It is an important physical property for a diffusion process to respond to an external force or a spatial confinement in experiments. This paper investigates the random diffusivity processes coupled with an inverse α-stable subordinator which characterizes the trapping events in crowded environment, and studies its dynamics under the harmonic potential by evaluating the ensemble-averaged and time-averaged mean-squared displacements (MSDs). We build three kinds of coupled Langevin equations based on different physical realities of the external force in crowded environment, e.g., the harmonic potential only modifies the particle's motion at the moments of particle-making jumps, and that exerts an effect throughout the whole physical time, and the case with the validity of fluctuation-dissipation theorem. By comparing these three models, we find that the crowding trapping effect and temporal dynamic fluctuation play different roles in the MSDs. Nevertheless, we also observe an interesting phenomenon that the ratio between two MSDs exhibits the same scaling form, which perhaps reveals an underlying mechanism of the ergodicity breaking within the subordinated diffusion processes.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034107"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207603","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":"Extended-range percolation for neighborhoods of rectangular shape on square lattice.","authors":"Zhipeng Xun, Dapeng Hao, Robert M Ziff","doi":"10.1103/xsyr-d79f","DOIUrl":"https://doi.org/10.1103/xsyr-d79f","url":null,"abstract":"<p><p>In this paper, extended-range percolation for neighborhoods of rectangular shape on a square lattice is investigated by means of Monte Carlo simulations. We choose a rectangle with an aspect ratio of 2 : 1, with the long side indicating its orientation. Three types of orientation are considered, namely horizontal (model I), horizontal or vertical randomly with equal probability (model II), and both horizontal and vertical simultaneously (thus in the shape of a cross) (model III). Simulations of both bond and site percolation are performed on the basis of an effective single-cluster growth algorithm, and precise percolation thresholds are found. The asymptotic and finite-size behaviors between the thresholds p_{c} and the coordination number z for each type are also discussed. For bond percolation, the asymptotic value zp_{c} of all three situations tends to Bethe-lattice behavior (zp_{c}∼1), and the finite-z correction is found to be consistent with zp_{c}∼1+a_{1}z^{-1/2}+a_{2}z^{-1}+a_{3}z^{-3/2} given by Deng et al. [J. Phys.: Conf. Ser. 1163, 012001, (2019)10.1088/1742-6596/1163/1/012001]. Regarding site percolation, for model I, data fitting gives the value of zp_{c}∼4.3951(1) for large z, compared to zp_{c}=2^{d}η_{c}∼4.3954, where η_{c}=1.09884280(9) [Phys. Rev. E 86, 061109 (2012)1539-375510.1103/PhysRevE.86.061109] is the continuum percolation threshold of aligned squares. For model II with site percolation, the nonlinear behavior of zp_{c} versus 1/z shows that the orientation of the rectangle has an effect on the asymptotic behavior of zp_{c}. A variation of model II in which reciprocal neighborhoods are taken into account however shows linear behavior on such a plot. For model III, the fitting of the data leads to zp_{c}∼4.414(2), which is in principle not related to the continuum threshold of overlapping crosses but close to the value zp_{c}≈4.51235 of overlapping disks. Some power laws of the simulation results are also discussed. The results show that the orientation of the rectangle has an impact on the thresholds of both bond percolation and site percolation, and a deeper analysis indicates that this effect gradually weakens as the coordination number z increases, following a power law of z^{-w} with w=1.49(1) for bond percolation and 0.91(1) for site percolation for the difference between models I and II.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034139"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207652","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":"Evolutionary chemical learning in dimerization networks.","authors":"Alexei V Tkachenko, Bortolo Matteo Mognetti, Sergei Maslov","doi":"10.1103/bszq-gftl","DOIUrl":"https://doi.org/10.1103/bszq-gftl","url":null,"abstract":"<p><p>We present a framework for chemical learning based on competitive dimerization networks (CDNs)-systems in which multiple molecular species, e.g., proteins or DNA-RNA oligomers, reversibly bind to form dimers. We show numerically that these networks can, in principle, be trained in vitro through directed evolution, enabling the implementation of complex learning tasks such as multiclass classification without digital hardware or prior knowledge of all microscopic association constants. Each molecular species functions analogously to a neuron, with binding affinities acting as tunable synaptic weights. A training protocol involving mutation, selection, and amplification of DNA-based components allows CDNs to robustly discriminate among noisy input patterns. The resulting classifiers exhibit strong output contrast and high mutual information between input and output, especially when guided by a contrast-enhancing loss function. Comparative analysis with in silico gradient descent training reveals closely correlated performance. These results establish CDNs as a promising platform for analog physical computation, bridging synthetic biology and machine learning, and advancing the development of adaptive, energy-efficient molecular computing systems.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-2","pages":"035404"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207691","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":"Critical scaling for dense granular flow between parallel plates near jamming.","authors":"Michio Otsuki, Kenta Hayashi, Kiwamu Yoshii","doi":"10.1103/tsvc-r78g","DOIUrl":"https://doi.org/10.1103/tsvc-r78g","url":null,"abstract":"<p><p>We numerically study the flow of dense granular materials between parallel plates driven by an external force. The granular materials form a jammed solidlike state when the external force is below a critical force, while they flow like fluids above the critical force. The transition is characterized by the mass flux. The critical force depends on the average packing fraction and the distance between the plates. The scaling laws for the critical force and the mass flux are theoretically predicted based on a continuum model, and are numerically verified.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-2","pages":"035412"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207699","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":"Granular clogging across gravities: A unified scaling.","authors":"Oliver Gaida, Olfa D'Angelo, Jonathan E Kollmer","doi":"10.1103/x3bt-63wt","DOIUrl":"https://doi.org/10.1103/x3bt-63wt","url":null,"abstract":"<p><p>Lacking a universal law for granular flows across gravitational environments, fundamental processes such as hopper discharge remain vulnerable to failure in low gravity environments. A central challenge is clogging, the spontaneous arrest of flow through a constriction; yet previous studies report contradictory results on its dependence on gravitational acceleration. We identify the granular Bond number as the missing control parameter, defined as the ratio of intrinsic cohesive interactions among particles to gravity. Based on an in-bulk measurement of this quantity, we propose to rescale Earth-measured data for predicting granular behavior in low gravity. We present experiments of granular flow through an orifice under true reduced gravity (Moon and Mars), using an active drop tower, and extraterrestrial soil simulants as model cohesive materials. Our experiments reveal substantial increases in clogging probability, contrary to previously predictions, which depends on the properties of the material itself. When rescaled by the Bond number, seemingly conflicting results can be explained and collapse into a unified state diagram, predicting clogging across materials and gravitational accelerations. This establishes a general framework for the cohesion-to-gravity competition. Future space missions to the Moon, Mars, and asteroids will rely on such predictions of granular behavior in low gravity.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-2","pages":"035405"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207757","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":"Stochastic thermodynamics of quantum-induced stochastic dynamics.","authors":"Pedro Ventura Paraguassú","doi":"10.1103/tgsz-1mm9","DOIUrl":"https://doi.org/10.1103/tgsz-1mm9","url":null,"abstract":"<p><p>Quantum-induced stochastic dynamics arises when a quantum system, strongly decohered by its coupling to a quantum environment, evolves as a genuine classical stochastic process. Depending on the environment's quantum state, the environment can act as a dynamic bath, capable of simultaneously exchanging heat and performing work. We formulate a thermodynamic framework for this semiclassical regime, defining heat, work, and entropy production. We derive a modified Second Law that accounts for nonequilibrium quantum features, such as squeezing. The framework is exemplified by an optomechanical setup, where we characterize the thermodynamics of the nonstationary noise induced by the cavity field.</p>","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"114 3-1","pages":"034130"},"PeriodicalIF":2.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207763","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}