Physical Review E最新文献_第8页

Density estimation for ordinal biological sequences and its applications. 序生物序列的密度估计及其应用。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044408

Wei-Chia Chen, Juannan Zhou, David M McCandlish

{"title":"Density estimation for ordinal biological sequences and its applications.","authors":"Wei-Chia Chen, Juannan Zhou, David M McCandlish","doi":"10.1103/PhysRevE.110.044408","DOIUrl":"10.1103/PhysRevE.110.044408","url":null,"abstract":"Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence space is thus a natural first step toward understanding the underlying mechanisms. Here we propose a method for inferring the probability distribution from which a sample of biological sequences were drawn for the case where the sequences are composed of elements that admit a natural ordering. Our method is based on Bayesian field theory, a physics-based machine learning approach, and can be regarded as a nonparametric extension of the traditional maximum entropy estimate. As an example, we use it to analyze the aneuploidy data pertaining to gliomas from The Cancer Genome Atlas project. In addition, we demonstrate two follow-up analyses that can be performed with the resulting probability distribution. One of them is to investigate the associations among the sequence sites. This provides a way to infer the governing biological grammar. The other is to study the global geometry of the probability landscape, which allows us to look at the problem from an evolutionary point of view. It can be seen that this methodology enables us to learn from a sample of sequences about how a biological system or phenomenon in the real world works.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044408"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677352","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

Relation between critical exponent of the conductivity and the morphological exponents of percolation theory. 电导率临界指数与渗流理论形态指数之间的关系。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.L042104

Carl Fredrik Berg, Muhammad Sahimi

{"title":"Relation between critical exponent of the conductivity and the morphological exponents of percolation theory.","authors":"Carl Fredrik Berg, Muhammad Sahimi","doi":"10.1103/PhysRevE.110.L042104","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.L042104","url":null,"abstract":"A central unsolved problem in percolation theory over the past five decades has been whether there is a direct relationship between the critical exponents that characterize the power-law behavior of the transport properties near the percolation threshold, particularly the effective electrical conductivity σ_{e}, and the exponents that describe the morphology of percolation clusters. The problem is also relevant to the relation between the static exponents of percolation clusters and the critical dynamics of spin waves in dilute ferromagnets, the elasticity of gels and composite solids, hopping conductivity in semiconductors, solute transport in porous media, and many others. We propose an approach to address the problem by showing that the contributions to σ_{e} can be decomposed into several groups representing the structure of percolation networks, including their mass and tortuosity, as well as constrictivity that describes the fluctuations in the driving potential gradient along the transport paths. The decomposition leads to a relationship between the critical exponent t of σ_{e} and other percolation exponents in d dimensions, t/ν=(d-D_{bb})+2(D_{op}-1)+d_{C}, where ν, D_{bb}, D_{op}, and d_{C} are, respectively, the correlation length exponent, the fractal dimensions of the backbones and the optimal paths, and the exponent that characterizes the constrictivity. Numerical simulations in two and three dimensions, as well as analytical results in d=1 and d=6, the upper critical dimension of percolation, validate the relationship. We, therefore, believe that the solution to the 50-year-old problem has been derived.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4","pages":"L042104"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677291","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

Exploring noisy Jeffery orbits: A combined Fokker-Planck and Langevin analysis in two and three dimensions. 探索噪声杰弗里轨道：二维和三维福克-普朗克和朗格文综合分析。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044143

J Talbot, C Antoine, P Claudin, E Somfai, T Börzsönyi

{"title":"Exploring noisy Jeffery orbits: A combined Fokker-Planck and Langevin analysis in two and three dimensions.","authors":"J Talbot, C Antoine, P Claudin, E Somfai, T Börzsönyi","doi":"10.1103/PhysRevE.110.044143","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.044143","url":null,"abstract":"The behavior of nonspherical particles in a shear flow is of significant practical and theoretical interest. These systems have been the object of numerous investigations since the pioneering work of Jeffery a century ago. His eponymous orbits describe the deterministic motion of an isolated, rodlike particle in a shear flow. Subsequently, the effect of adding noise was investigated. The theory has been applied to colloidal particles, macromolecules, anisometric granular particles, and most recently to microswimmers, for example, bacteria. We study the Jeffery orbits of elongated (uniaxial, prolate) particles subject to noise using Langevin simulations and a Fokker-Planck equation. We extend the analytical solution for infinitely thin needles (β=1) obtained by Doi and Edwards to particles with arbitrary shape factor (0≤β≤1) and validate the theory by comparing it with simulations. We examine the rotation of the particle around the vorticity axis and study the orientational order matrix. We use the latter to obtain scalar order parameters s and r describing nematic ordering and biaxiality from the orientational distribution function. The value of s (nematic ordering) increases monotonically with increasing Péclet number, while r (measure of biaxiality) displays a maximum value. From perturbation theory, we obtain simple expressions that provide accurate descriptions at low noise (or large Péclet numbers). We also examine the orientational distribution in the v-grad v plane and in the perpendicular direction. Finally, we present the solution of the Fokker-Planck equation for a strictly two-dimensional (2D) system. For the same noise amplitude, the average rotation speed of the particle in 3D is larger than in 2D.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044143"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677363","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

Fracture process of composite materials in a spring network model. 弹簧网络模型中复合材料的断裂过程

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.045001

Haruka Noguchi, Satoshi Yukawa

引用次数: 0

Model for random internalization of nanoparticles by cells. 细胞随机内化纳米粒子的模型。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044101

Sergei Fedotov, Dmitri V Alexandrov

{"title":"Model for random internalization of nanoparticles by cells.","authors":"Sergei Fedotov, Dmitri V Alexandrov","doi":"10.1103/PhysRevE.110.044101","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.044101","url":null,"abstract":"We propose a stochastic model for the internalization of nanoparticles by cells formulating cellular uptake as a compound Poisson process with a random probability of success. This is an alternative approach to the one presented by Rees et al. [Nat. Commun. 10, 2341 (2019)2041-172310.1038/s41467-018-07882-8] who explained overdispersion in nanoparticle uptake and associated negative binomial distribution by considering a Poisson distribution for particle arrival and a gamma-distributed cell area. In our stochastic model, the formation of new pits is represented by the Poisson process, whereas the capturing process and the population heterogeneity are described by a random Bernoulli process with a beta-distributed probability of success. The random probability of success generates ensemble-averaged conditional transition probabilities that increase with the number of newly formed pits (self-reinforcement). As a result, an ensemble-averaged nanoparticle uptake can be represented as a Polya process. We derive an explicit formula for the distribution of the random number of pits containing nanoparticles. In the limit of the fast nucleation and low probability of nanoparticle capture, we find the negative binomial distribution.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044101"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677473","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

Non-Hermitian diluted banded random matrices: Scaling of eigenfunction and spectral properties. 非ermitian 稀释带状随机矩阵：特征函数的缩放和频谱特性

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044124

M Hernández-Sánchez, G Tapia-Labra, J A Méndez-Bermúdez

引用次数: 0

Theoretical framework for learning through structural plasticity. 通过结构可塑性学习的理论框架。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044311

Gianmarco Tiddia, Luca Sergi, Bruno Golosio

引用次数: 0

Effective diffusion constant of stochastic processes with spatially periodic noise. 具有空间周期性噪声的随机过程的有效扩散常数。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044123

Stefano Giordano, Ralf Blossey

引用次数: 0

Interplay of the complete-graph and Gaussian fixed-point asymptotics in finite-size scaling of percolation above the upper critical dimension. 完整图和高斯定点渐近线在高于上临界维度的渗滤的有限大小缩放中的相互作用。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044140

Mingzhong Lu, Sheng Fang, Zongzheng Zhou, Youjin Deng

{"title":"Interplay of the complete-graph and Gaussian fixed-point asymptotics in finite-size scaling of percolation above the upper critical dimension.","authors":"Mingzhong Lu, Sheng Fang, Zongzheng Zhou, Youjin Deng","doi":"10.1103/PhysRevE.110.044140","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.044140","url":null,"abstract":"For statistical mechanical systems with continuous phase transitions, there are two closely related but subtly different mean-field treatments, the Gaussian fixed point (GFP) in the renormalization group framework and the Landau mean-field theory or the complete-graph (CG) asymptotics. By large-scale Monte Carlo simulations, we systematically study the interplay of the GFP and CG effects to the finite-size scaling of percolation above the upper critical dimension d_{c}=6 with periodic and cylindrical boundary conditions. Our results suggest that, with periodic boundaries, the unwrapped correlation length scales as L^{d/6} at the critical point, diverging faster than L above d_{c}. As a consequence, the scaling behaviors of macroscopic quantities with respect to the linear system size L follow the CG asymptotics. The distance-dependent properties, such as the short-distance behavior of the two-point correlation function and the Fourier transformed quantities with nonzero modes, are still controlled by the GFP. With cylindrical boundaries, due to the interplay of the GFP and CG effects, the correlation length along the axial direction of the cylinder scales as ξ_{L}∼L^{(d-1)/5} within the critical window of size O(L^{-2(d-1)/5}), distinct from periodic boundary. A field-theoretical calculation for deriving the scaling of ξ_{L} is also presented. Moreover, the one-point surface correlation function along the axial direction of the cylinder is observed to scale as τ^{(1-d)/2} when the distance τ is short, but then enter a plateau of order L^{-3(d-1)/5} before it decays significantly fast.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044140"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677373","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

Multivariate opinion evolution analysis on individual opinion differences: An agent-based model. 个体意见差异的多变量意见演变分析：基于代理的模型

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044301

Shan Liu, Hanfei Zhao

{"title":"Multivariate opinion evolution analysis on individual opinion differences: An agent-based model.","authors":"Shan Liu, Hanfei Zhao","doi":"10.1103/PhysRevE.110.044301","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.044301","url":null,"abstract":"The spiral of silence is a classic theory originating from the age of mass media, which posits that individuals may suppress dissenting opinions to avoid social exclusion. In the digital era, despite the persistence of this phenomenon, the rise of social media has catalyzed the emergence of an antispiral of silence-a counterphenomenon fueled by growing self-awareness and online anonymity. In this paper, we focus on an interesting phenomenon: how these two spirals compete with each other to promote pluralism in social networks. To this end, we propose the spiral competition model (SCM) to quantify the two spirals and explore the impact of this phenomenon on the evolution of public opinion. In the SCM, agents can generate pseudo-opinions as well as antiopinions. In addition, we propose a time-varying network topology updating algorithm based on triangle closure, which simulates the fluid nature of social connections. Furthermore, we propose a community-based opinion initialization method with Gaussian distribution for enhancing simulation fidelity. Finally, we applied complex network theory to information dissemination, and the model was then simulated and analyzed in Erdős-Rényi random networks. And the rationality of SCM was verified using Sina Weibo data. The experimental results show that while the spiral of silence initially holds sway, the antispiral of silence can precipitate significant opinion divergence during critical junctures, challenging the status quo. And if the antispiral of silence fails to prevail, the trend of public opinion will be difficult to reverse. This research helps us recognize the influence that can be brought about by the awakening of individual consciousness, and provides an important reference for public opinion prediction.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044301"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677417","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