Physical Review E最新文献

Tunable glassy dynamics in models of dense cellular tissue. 致密细胞组织模型中的可调玻璃动力学。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/ryy4-2xt6

Helen S Ansell, Chengling Li, Daniel M Sussman

引用次数: 0

Predicting interface residues for protein polymers based on module division. 基于模块划分的蛋白质聚合物界面残基预测。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/pj5v-cdf4

Shuhong Yu, Zicheng Xie, Jiudong Wang, Xinqi Gong

{"title":"Predicting interface residues for protein polymers based on module division.","authors":"Shuhong Yu, Zicheng Xie, Jiudong Wang, Xinqi Gong","doi":"10.1103/pj5v-cdf4","DOIUrl":"10.1103/pj5v-cdf4","url":null,"abstract":"In the field of computational biology, AlphaFold has facilitated remarkable progress in predicting protein structures. However, for some multimeric complexes, the accuracy of its predictions still needs improvement. Enhancing the prediction of binding sites in protein oligomers contributes to the prediction of overall structures, and the details of binding sites are crucial for understanding the functional mechanism, affinity, and specificity of complexes. The approach presented here is independent of black-box modeling, thereby facilitating a clearer elucidation of the underlying biological mechanisms of protein-protein interaction interfaces. The study investigates protein interaction sites, mainly for trimers and tetramers, in the Protein Data Bank (PDB) database, using a modular division method. By ranking modules based on the linear combination of the square of the solvent-accessible surface area and the internal contact area (SSAIA), it was found that interface modules are more likely to appear in surface modules with lower values. Among 44 964 monomers, 92.25% of the monomer interface residues are found in the three modules with the smallest SSAIA values. In 5240 trimers, 98.63% of the complexes had at least one chain correctly predicted, and in 7311 tetramers, 98.92% of the complexes had at least one chain correctly predicted, with an average of approximately 3 out of 4 residues in the top-ranked interface modules being interface residues. The results of comparison with other methods in the Benchmark 3.0 dataset and 12 targets of the CASP15 competition validated the effectiveness of our approach, providing a new perspective for predicting binding sites in multimer interactions.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-1","pages":"014403"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876201","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}

引用次数: 0

Quantifying evolutionary rescue probabilities upon standing genetic variation and de novo mutations. 量化长期遗传变异和新生突变的进化拯救概率。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/f5c1-rpc4

Paulo R A Campos

引用次数: 0

Analytical insights from a model of opinion formation based on persuasive argument theory. 基于说服性论证理论的意见形成模型的分析见解。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/j5z4-5ry9

Lucía Pedraza, Nicolas Saintier, Juan Pablo Pinasco, Pablo Balenzuela, Celia Anteneodo

引用次数: 0

Simulating and analyzing the dynamics of collective movement with elastic interactions and leadership influence. 具有弹性相互作用和领导影响的集体运动动力学模拟与分析。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/2p2h-vz38

A Eddakoun, A Hader, I Tarras, I Bakkasi, M Tanasehte, R Moultif, M Eddahby, A El Bachiri

{"title":"Simulating and analyzing the dynamics of collective movement with elastic interactions and leadership influence.","authors":"A Eddakoun, A Hader, I Tarras, I Bakkasi, M Tanasehte, R Moultif, M Eddahby, A El Bachiri","doi":"10.1103/2p2h-vz38","DOIUrl":"10.1103/2p2h-vz38","url":null,"abstract":"This paper investigates the simulation and analysis of collective self-propelled motion in the presence of a leader, a phenomenon commonly observed in natural and artificial systems, such as bird flocks or robotic swarms. Using a dynamic approach based on the Langevin equation, the study models interactions between particles and a leader through elastic restoring forces and incorporates stochastic noise to simulate random fluctuations. These forces ensure group cohesion, avoid collisions, and mimic real-world conditions where unpredictability plays a significant role. The simulation starts with particles randomly distributed in a two-dimensional space. As the leader moves at a constant velocity, particles adjust their positions and velocities to follow it. The results demonstrate a two-phase evolution: an initial rapid clustering around the leader due to strong elastic forces, followed by a gradual alignment of particle velocities to match the leader. The velocity profile, represented by a linear increase followed by an exponential decay, captures the transition from disorder to order. Key parameters such as the spring constant k_{1}, which governs the leader-particle interaction, and the diffusion coefficient D, which regulates stochastic noise, are shown to significantly influence the system dynamics. High interaction strength accelerates synchronization and stabilizes the group, while weaker interactions lead to slower clustering and potential dispersion. Phase diagrams and susceptibility analyses confirm that the leader's role is critical in initiating and maintaining collective behavior. This study highlights the emergence of coordinated motion in a leader-follower context, offering insights into biological systems and inspiring applications in swarm robotics, where efficient and cohesive movement is essential.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-1","pages":"014130"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876144","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}

引用次数: 0

Temporal evolution of intralayer synchronizability in multiplex hypergraphs. 多重超图中层内同步性的时间演化。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/b3zq-c33r

Yinchao Yang, Xirong Xu, Xilong Qu, Qiang Zhang

{"title":"Temporal evolution of intralayer synchronizability in multiplex hypergraphs.","authors":"Yinchao Yang, Xirong Xu, Xilong Qu, Qiang Zhang","doi":"10.1103/b3zq-c33r","DOIUrl":"10.1103/b3zq-c33r","url":null,"abstract":"In practical applications, complex networks often model scenarios involving higher-order relationships, for which hypergraphs offer a suitable representation. This paper introduces synchronizability metrics to study the synchronization of a temporal two-layer multiplex hypergraph, where temporal characteristics are captured by time-evolving incidence matrix. By transforming hyperedges into maximal cliques, we construct a temporally evolving weighted network that reproduces the dynamics on the hypergraph under simple structure and symmetric coupling. The analysis focuses on intralayer synchronizability across different spatio-temporal scales. In the short term, we observe that the synchronizability of the hypergraph is positively correlated with network stochasticity. For the long term, we derive time-averaged approximation equations for fast-switching hypergraph and conduct both linear and global stability analyses to determine the necessary conditions for intralayer synchronization. Experimental results demonstrate that fast-switching hypergraph achieve superior long-term synchronizability compared to their short-term evolving counterparts under identical conditions.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-1","pages":"014207"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876149","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}

引用次数: 0

Top rank statistics for Brownian reshuffling. 布朗重组的顶级统计数据。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/tkd1-fk1l

Zdzislaw Burda, Mario Kieburg

{"title":"Top rank statistics for Brownian reshuffling.","authors":"Zdzislaw Burda, Mario Kieburg","doi":"10.1103/tkd1-fk1l","DOIUrl":"10.1103/tkd1-fk1l","url":null,"abstract":"We study the dynamical aspects of the top rank statistics of particles, performing Brownian motions on a half-line, which are ranked by their distance from the origin. For this purpose, we introduce an observable Ω(t) which we call the overlap ratio. The average overlap ratio is equal to the probability that a particle that is on the top-n list at some time will also be on the top-n list after time t. The overlap ratio is a local observable which is concentrated at the top of the ranking and does not require the full ranking of all particles. In practice, the overlap ratio is easy to measure. We derive an analytical formula for the average overlap ratio for a system of N particles in the stationary state that undergo independent Brownian motion on the positive real half-axis with a reflecting wall at the origin and a drift towards the wall. In particular, we show that for N→∞, the overlap ratio takes a rather simple form 〈Ω(t)〉=erfc(asqrt[t]) for n≫1 with some scaling parameter a>0. This result is a very good approximation even for moderate sizes of the top-n list such as n=10. Moreover, we observe in numerical studies that the overlap ratio exhibits universal behavior in many dynamical systems including geometric Brownian motion, Brownian motion with asymptotically linear drift, the Bouchaud-Mézard wealth distribution model, and Kesten processes. We conjecture the universality to hold for a broad class of one-dimensional stochastic processes.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-1","pages":"014114"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876153","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}

引用次数: 0

Complete wetting and drying at sinusoidal walls. 在正弦壁上完成润湿和干燥。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/2d7c-6t3t

Alexandr Malijevský, Martin Pospíšil, Miriam Magočiová, Jiří Janek

引用次数: 0

Ultradelayed material failure via shear banding after straining an amorphous material. 非晶材料在拉伸后通过剪切带破坏超延迟材料。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/b64y-61lt

Henry A Lockwood, Emily S Carrington, Suzanne M Fielding

{"title":"Ultradelayed material failure via shear banding after straining an amorphous material.","authors":"Henry A Lockwood, Emily S Carrington, Suzanne M Fielding","doi":"10.1103/b64y-61lt","DOIUrl":"10.1103/b64y-61lt","url":null,"abstract":"We predict a phenomenon of catastrophic material failure arising suddenly within an amorphous material, with an extremely long delay time since the material was last deformed. By simulating a mesoscopic soft glassy rheology model in one dimension (1D), a mesoscopic elastoplastic model in 1D and 2D, and a continuum fluidity model in 1D, we demonstrate the basic physics to involve a dramatic ultra-delayed shear banding instability, in which strain suddenly strongly localizes within the material and the stress drops precipitously. The delay time after the long historical shear strain was applied before failure occurs increases steeply with decreasing strain amplitude, decreasing working temperature, and increasing sample annealing prior to shear. In demonstrating the same physics-which is directly testable experimentally and in particle simulations-to obtain within three different constitutive models, we suggest it may be generic across amorphous materials. The counter-intuitive prediction of catastrophic material failure long after any deformation was last applied could have important consequences for material processing and performance.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-2","pages":"015404"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876213","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}

引用次数: 0

Convective and absolute instabilities in electrohydrodynamic flow for viscoelastic fluid. 粘弹性流体电流体动力流动中的对流和绝对不稳定性。

IF 2.4 3区物理与天体物理

Physical Review E Pub Date : 2025-07-01 DOI: 10.1103/wgh7-543b

Zhenze Yao, Mengqi Zhang, Jian Wu, Kang Luo, Hongliang Yi

{"title":"Convective and absolute instabilities in electrohydrodynamic flow for viscoelastic fluid.","authors":"Zhenze Yao, Mengqi Zhang, Jian Wu, Kang Luo, Hongliang Yi","doi":"10.1103/wgh7-543b","DOIUrl":"10.1103/wgh7-543b","url":null,"abstract":"The convective and absolute instabilities in electrohydrodynamic-Poiseuille mixed convection for viscoelastic fluids with the Oldroyd-B model are examined. In the absence of Poiseuille flow, based on the stationary and oscillatory characteristics at the onset of convection, we distinguish weakly and strongly elastic fluid, dominated by viscosity effects and elasticity effects, respectively. Their borderline of the two effects in terms of the critical electric Weissenberg W_{ec} satisfies the relation W_{ec}=a/(1-β)+b where β is viscosity ratio, and the parameters a and b depend on dimensionless ion mobility. In the presence of Poiseuille flow, with an increase in shear strength, the convective and absolute instability thresholds increase in both weakly and strongly elastic fluids, and the jump of phase speed and saddle point shift are observed at low polymer concentration with sufficient elasticity, causing the faster transverse rolls (TRs) to propagate downstream. However, at the high polymer concentration of large W_{e}, instead of downstream moving TRs, the upstream moving TRs can be the most unstable at the onset of absolute instability. Kinetic energy budget analysis reveals that with an increase in shear strength and elasticity, the suppressive effect of polymeric stresses on instability is enhanced in viscosity effects-dominated flow, while it is reduced in elasticity effects-dominated flow. Besides, the energy transfer from the wall-normal gradient of the perturbed electric field to the wall-normal gradient of the perturbed wall-normal velocity under the effect of the wall-normal gradient of the base electric field becomes the most destabilizing factor in the very strongly elastic fluids.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"112 1-2","pages":"015102"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876228","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}

引用次数: 0