Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054216
L Friedland, A G Shagalov
{"title":"Multiphase autoresonant excitations in the Korteweg-de Vries system.","authors":"L Friedland, A G Shagalov","doi":"10.1103/PhysRevE.111.054216","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054216","url":null,"abstract":"<p><p>Autoresonant (continuously phase-locked) two-phase waves of the Korteweg-de Vries equation are excited and controlled using a two-component, small amplitude, chirped frequency driving. These solutions are analyzed in the weakly nonlinear regime. The theory is based on Whitham's averaged variational principle. The problem is reduced to a fully separated two degrees of freedom dynamical problem. This separation allows for simple derivation of the autoresonant thresholds on the driving wave amplitudes. We also excite more complex four-phase autoresonant waves. The inverse scattering analysis of this case indicates again the separation of all four degrees of freedom in the associated weakly nonlinear dynamical problem.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054216"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327357","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054413
Kiran Kumari
{"title":"Nonequilibrium replication process generates the initial template for chromatin folding.","authors":"Kiran Kumari","doi":"10.1103/PhysRevE.111.054413","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054413","url":null,"abstract":"<p><p>DNA replication is a fundamental process required for duplicating the genome before cell division. However, how epigenetic information is preserved during replication remains poorly understood. DNA replication occurs within specific domains, with replication initiation following a time-regulated pattern. After replication, chromatin must be refolded to restore the 3D structure of the parental chromatin. In this work, we investigate the nonequilibrium problem of how chromatin folds in 3D soon after replication, using stochastic simulation methods, to generate the contact probability map for a specific replicating domain. Our findings indicate that the initial post-replication chromatin structure is influenced by the location of replication origins, the nonequilibrium nature of the replication process, and the speed of the replication fork. Specifically, replication fork speed can significantly impact the organization of newly synthesized chromatin, affecting contact density and enabling the formation of euchromatin-like and heterochromatin-like structures.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054413"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327361","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054125
Arpita Goswami, Ravi Kumar, Monikana Gope, Shaon Sahoo
{"title":"Phase transitions in the q-state clock model.","authors":"Arpita Goswami, Ravi Kumar, Monikana Gope, Shaon Sahoo","doi":"10.1103/PhysRevE.111.054125","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054125","url":null,"abstract":"<p><p>The q-state clock model, sometimes called the discrete XY model, is known to show a second-order (symmetry-breaking) phase transition in two dimensions for q≤4 (q=2 corresponds to the Ising model). On the other hand, the q→∞ limit of the model corresponds to the XY model, which shows the infinite order (non-symmetry-breaking) Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions. Interestingly, the two-dimensional clock model with q≥5 is predicted to show three different phases and two associated phase transitions. There are varying opinions about the actual characters of phases and the associated transitions. In this work, we develop the basic and higher-order mean-field (MF) theories to study the q-state clock model systematically. Our MF calculations reaffirm that, for large q, there are three phases: (broken) Z_{q} symmetric ferromagnetic phase at the low temperature, emergent U(1) symmetric BKT phase at the intermediate temperature, and paramagnetic (disordered) phase at the high temperature. The phase transition at the higher temperature is found to be of the BKT type, and the other transition at the lower temperature is argued to be a large-order spontaneous symmetry-breaking type (the largeness of transition order yields the possibility of having some of the numerical characteristics of a BKT transition). The higher-order MF theory developed here better characterizes phases by estimating the spin-spin correlation between two neighbors.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054125"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327369","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054406
Robert P Gowers, Magnus J E Richardson
{"title":"Resonances in the voltage statistics and upcrossing rate of a minimal dendritic neuron model with a passive membrane.","authors":"Robert P Gowers, Magnus J E Richardson","doi":"10.1103/PhysRevE.111.054406","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054406","url":null,"abstract":"<p><p>A dendritic neuron model subject to spatiotemporal fluctuating synaptic drive and a pointlike oscillating current stimulation is considered. Unlike for dendritic models that are statistically homogeneous in space, this experimentally plausible scenario allows for the electrotonic length constant to feature in quantities like the modulated firing rate as a function of the distance to current stimulation. The cable equation for the voltage is solved to find the modulated first- and second-order moments featuring the voltage and its rate of change. These are then used to calculate the frequency dependence of the firing-rate response in the upcrossing approximation as a function of the distance between a nominal soma and current stimulation. With an isopotential model as a reference, this minimal dendritic model exhibits some surprising features such as modulated first-order moments that grow with frequency. In addition, despite the model's passive membrane, the voltage moments and upcrossing rate exhibit frequency preferences in the form of resonances and troughs. These features are in the same class of morphological resonance phenomena previously seen in Purkinje cells and in models of cells driven by external electrical fields.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054406"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327377","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054301
K Fortuna, J Szwabiński
{"title":"Role of debt valuation factors in systemic risk assessment.","authors":"K Fortuna, J Szwabiński","doi":"10.1103/PhysRevE.111.054301","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054301","url":null,"abstract":"<p><p>The fragility of financial systems was starkly demonstrated in early 2023 through a cascade of major bank failures in the United States, including the second, third, and fourth largest collapses in U.S. history. The highly interdependent financial networks and the associated high systemic risk have been deemed the cause of the crashes. The goal of this paper is to enhance existing systemic risk analysis frameworks by incorporating essential debt valuation factors. Our results demonstrate that these additional elements substantially influence the outcomes of risk assessment. Notably, by modeling the dynamic relationship between interest rates and banks' credibility, our framework can detect potential cascading failures that standard approaches might miss. The proposed risk assessment methodology can help regulatory bodies prevent future failures, while also allowing companies to more accurately predict turmoil periods and strengthen their survivability during such events.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054301"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327379","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.054210
Kin'ya Takahashi, Kensuke S Ikeda
{"title":"Semiclassical reproducibility of sawtooth structure observed for a periodically perturbed rounded-rectangular potential.","authors":"Kin'ya Takahashi, Kensuke S Ikeda","doi":"10.1103/PhysRevE.111.054210","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.054210","url":null,"abstract":"<p><p>In the previous work [Takahashi and Ikeda, Phys. Rev. E 109, 044203 (2024)2470-004510.1103/PhysRevE.109.044203], we found that tunneling probabilities for a periodically perturbed rounded rectangular potential form a sawtoothlike structure as a function of either the Planck constant ℏ or the angular frequency of the perturbation ω owing to multiquanta absorption tunneling. The replacement of the dominant harmonic channel with the change of either ℏ or ω occurs in every transition region of the sawtooth structure, which causes a sudden change in the tunneling probability. The tunneling probability in the potential region forms a resonance peak reflecting the fundamental resonance scattering state at each edge of the sawtooth structure. In this paper, we explore the underlying mechanism of the sawtooth structure in terms of semiclassics. The semiclassical method reproduces the sawtooth structure except for narrow transition regions accompanied by resonance peaks. The sawtooth structure is constructed by superpositioning a sufficiently large number of complex branches as an analogy of the Fourier decomposition of a sawtoothlike wave. The baseline of tunneling probability, i.e., the average line of the sawtooth structure, is well reproduced by the Melnikov method, i.e., the semiclassical weight estimated based on the theory of stable-unstable manifold guided tunneling. When ℏ and ω are fixed, the average line changes as exponentiation with the base ε, i.e., ∝ε^{α}, where α is roughly estimated as ∼c/ℏω.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-1","pages":"054210"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327382","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.055413
Arindam Panda, Roland G Winkler, Sunil P Singh
{"title":"Activity-enhanced shear thinning of flexible linear polar polymers.","authors":"Arindam Panda, Roland G Winkler, Sunil P Singh","doi":"10.1103/PhysRevE.111.055413","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055413","url":null,"abstract":"<p><p>The rheological properties of tangentially propelled flexible polymers under linear shear flow are studied by computer simulations and are compared with analytical calculations. We find a significant impact of the coupled nonequilibrium active and shear forces on the polymer characteristics. The polar activity enhances shear-induced stretching along the flow direction, shrinkage in the transverse direction, and implies a strongly amplified shear-thinning behavior. The characteristic shear rate for the onset of these effects is determined by the activity. In the asymptotic limit of large activities, the shear-induced features become independent of activity and, for asymptotically large shear rates, shear dominates over activity with passive polymer behavior.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055413"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327400","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.055304
Yong Zhao, Xinyue Liu, Zhenyu Chen, Lei Wang
{"title":"Alternative multiple-relaxation-time lattice Boltzmann method for simulating conjugate heat transfer.","authors":"Yong Zhao, Xinyue Liu, Zhenyu Chen, Lei Wang","doi":"10.1103/PhysRevE.111.055304","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055304","url":null,"abstract":"<p><p>In this paper, an alternative multiple-relaxation-time lattice Boltzmann (LB) scheme for conjugate heat transfer is proposed. We have derived the correct energy governing equation from the first law of thermodynamics and clarified that the thermal boundary for conjugate heat transfer should be the continuity of the conductive heat flux, which is essential to guarantee Galilean invariance. The development of the present model has two distinct features. First, the temperature evolution equation is modified to include the effect of the specific heat capacity. Second, the convection term is considered as a source term and is calculated in moment space, thus preserving the inherent advantages of the LB method without finite difference calculations. To verify the thermal governing equations, we conduct numerical simulations of heat conduction in a moving rod configuration with varying thermal capacities. Furthermore, to validate the present model's in accuracy, we examine several benchmark problems, including the effective thermal conductivity of parallel and series dual-component materials, steady and unsteady coupled heat transfer in horizontal interface channels, stable heat conduction in a two-layer annulus, natural convection in a square cavity with 16 solid blocks, and thermocapillary flow with two superimposed planar fluids. In the realm of application research, we apply our model to simulate the cooling process in random porous media. The results demonstrate that our model achieves satisfactory accuracy and exhibits a second-order convergence rate in space. The simulation results show the potential of the current LB method to simulate complex applications, highlighting its versatility and accuracy.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055304"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327401","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.055407
Partha Sarathi Majee, Hiroyuki Ohshima
{"title":"Analytical study on diffusiophoresis of soft particles: Role of surface-charge-mobility-dependent hydrophobic core.","authors":"Partha Sarathi Majee, Hiroyuki Ohshima","doi":"10.1103/PhysRevE.111.055407","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.055407","url":null,"abstract":"<p><p>This paper theoretically analyzes the diffusiophoretic motion of a soft particle comprising a surface charge-dependent hydrophobic rigid core coated with a polyelectrolyte layer. The surface hydrophobicity of the inner core is considered to depend on the lateral mobility of the surface charge ions. A modified slip boundary condition is employed at the inner core interface to account for the hydrodynamic frictional and tangential electric forces on the flow due to the mobile adsorbed ions. The dielectric permittivity of the porous layer is assumed to be lower than the background electrolyte's permittivity constant, yielding the ion partitioning effect. The electrolyte concentration is considered sufficiently high so that the electric double layer around the particle becomes very thin compared to the porous layer thickness, and the inner core surface can be regarded as a flat plate. Considering the particle to be weakly charged, for which the Debye-Hückel approximation can be applied, a closed-form general diffusiophoretic mobility expression is derived, valid to a thin Debye layer. Analytic expressions for the electrophoretic and chemiphoretic components are also reported separately. Asymptotic mobility solutions are further deduced for various limiting situations. Results show that the lateral mobility of the surface charge ions significantly influences the diffusiophoretic motion of the particle, and the impact is extensive for a highly hydrophobic surface. Additionally, the ion partitioning effect strengthens the influence of the surface charge mobility on the flow by augmenting the effective charge of the particle. The contribution of the surface charge-dependent hydrophobic inner core and the ion partitioning effect is substantial for a highly permeable porous layer and insignificant for a thinner hydrodynamic screening length.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"055407"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327403","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}
Physical Review EPub Date : 2025-05-01DOI: 10.1103/PhysRevE.111.056201
J B Bell, A Nonaka, A L Garcia
{"title":"Comment on \"Brownian motion of droplets induced by thermal noise\".","authors":"J B Bell, A Nonaka, A L Garcia","doi":"10.1103/PhysRevE.111.056201","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.056201","url":null,"abstract":"<p><p>We simulate phase separated fluids using the Cahn-Hillard fluctuating hydrodynamic (CH-FHD) model and measure the statistical properties of capillary waves generated by thermal fluctuations. Our measurements are in good agreement with stochastic lubrication theory and molecular dynamics simulations but differ significantly from recent CH-FHD results by Zhang et al. [Phys. Rev. E 109, 024208 (2024)2470-004510.1103/PhysRevE.109.024208]. Specifically, we find that capillary wave statistics at thermodynamic equilibrium are independent of transport properties, namely viscosity and species diffusion.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 5-2","pages":"056201"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327408","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}