Physical Review E最新文献

Injection and confinement of positron bunches in a magnetic dipole trap 正电子束在磁偶极阱中的注入和束缚

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-08-09 DOI: 10.1103/physreve.110.l023201

A. Deller, J. von der Linden, S. Nißl, K. Michishio, N. Oshima, H. Higaki, E. Stenson

引用次数: 0

Brownian particle diffusion in generalized polynomial shear flows 广义多项式剪切流中的布朗粒子扩散

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-08-08 DOI: 10.1103/physreve.110.024117

Nan Wang, Y. Dagan

引用次数: 0

Combinatorics and topological weights of chromatin loop networks. 染色质环路网络的组合学和拓扑权重

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.064405

Andrea Bonato, Michael Chiang, Dom Corbett, Sergey Kitaev, Davide Marenduzzo, Alexander Morozov, Enzo Orlandini

{"title":"Combinatorics and topological weights of chromatin loop networks.","authors":"Andrea Bonato, Michael Chiang, Dom Corbett, Sergey Kitaev, Davide Marenduzzo, Alexander Morozov, Enzo Orlandini","doi":"10.1103/PhysRevE.109.064405","DOIUrl":"https://doi.org/10.1103/PhysRevE.109.064405","url":null,"abstract":"Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network-i.e., its partition function in statistical mechanics language-in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141634982","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

Behavioral transition of a fish school in a crowded environment. 鱼群在拥挤环境中的行为转变。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.064403

Bruno Ventéjou, Iris Magniez-Papillon, Eric Bertin, Philippe Peyla, Aurélie Dupont

{"title":"Behavioral transition of a fish school in a crowded environment.","authors":"Bruno Ventéjou, Iris Magniez-Papillon, Eric Bertin, Philippe Peyla, Aurélie Dupont","doi":"10.1103/PhysRevE.109.064403","DOIUrl":"https://doi.org/10.1103/PhysRevE.109.064403","url":null,"abstract":"In open water, social fish gather to form schools, in which fish generally align with each other. In this work, we study how this social behavior evolves when perturbed by artificial obstacles. We measure the behavior of a group of zebrafish in the presence of a periodic array of pillars. When the pillar density is low, the fish regroup with a typical interdistance and a well-polarized state with parallel orientations, similarly to their behavior in open-water conditions. Above a critical density of pillars, their social interactions, which are mostly based on vision, are screened and the fish spread randomly through the aquarium, orienting themselves along the free axes of the pillar lattice. The abrupt transition from natural to artificial orientation happens when the pillar interdistance is comparable to the social distance of the fish, i.e., their most probable interdistance. We develop a stochastic model of the relative orientation between fish pairs, taking into account alignment, antialignment, and tumbling, from a distribution biased by the environment. This model provides a good description of the experimental probability distribution of the relative orientation between the fish and captures the behavioral transition. Using the model to fit the experimental data provides qualitative information on the evolution of cognitive parameters, such as the alignment or the tumbling rates, as the pillar density increases. At high pillar density, we find that the artificial environment imposes its geometrical constraints to the fish school, drastically increasing the tumbling rate.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141634977","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

Generalized spectral form factor in random matrix theory. 随机矩阵理论中的广义谱形式因子。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.064208

Zhiyang Wei, Chengming Tan, Ren Zhang

{"title":"Generalized spectral form factor in random matrix theory.","authors":"Zhiyang Wei, Chengming Tan, Ren Zhang","doi":"10.1103/PhysRevE.109.064208","DOIUrl":"https://doi.org/10.1103/PhysRevE.109.064208","url":null,"abstract":"The spectral form factor (SFF) plays a crucial role in revealing the statistical properties of energy-level distributions in complex systems. It is one of the tools to diagnose quantum chaos and unravel the universal dynamics therein. The definition of SFF in most literature only encapsulates the two-level correlation. In this manuscript, we extend the definition of SSF to include the high-order correlation. Specifically, we introduce the standard deviation of energy levels to define correlation functions, from which the generalized spectral form factor (GSFF) can be obtained by Fourier transforms. GSFF provides a more comprehensive knowledge of the dynamics of chaotic systems. Using random matrices as examples, we demonstrate dynamics features that are encoded in GSFF. Remarkably, the GSFF is complex, and the real and imaginary parts exhibit universal dynamics. For instance, in the two-level correlated case, the real part of GSFF shows a dip-ramp-plateau structure akin to the conventional counterpart, and the imaginary part for different system sizes converges in the long-time limit. For the two-level GSFF, the analytical forms of the real part are obtained and consistent with numerical results. The results of the imaginary part are obtained by numerical calculation. Similar analyses are extended to three-level GSFF.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635085","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

Melting curve of two-dimensional Yukawa systems predicted by isomorph theory. 同构理论预测的二维汤川系统熔化曲线。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.065212

Nichen Yu, Dong Huang, Yan Feng

引用次数: 0

Rescaled mode-coupling scheme for the quantitative description of experimentally observed colloid dynamics. 用于定量描述实验观察到的胶体动力学的重比例模式耦合方案。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.064605

Joel Diaz Maier, Joachim Wagner

{"title":"Rescaled mode-coupling scheme for the quantitative description of experimentally observed colloid dynamics.","authors":"Joel Diaz Maier, Joachim Wagner","doi":"10.1103/PhysRevE.109.064605","DOIUrl":"https://doi.org/10.1103/PhysRevE.109.064605","url":null,"abstract":"We describe experimentally observed collective dynamics in colloidal suspensions of model hard-sphere particles using a modified mode coupling theory (MCT). This rescaled MCT is capable of describing quantitatively the wave-vector and time-dependent diffusion in these systems. Intermediate scattering functions of liquidlike structured dispersions are determined by means of static and dynamic light-scattering experiments. The structure and short-time dynamics of the systems can be described quantitatively employing a multicomponent Percus-Yevick ansatz for the partial structure factors and an effective, one-component description of hydrodynamic interactions based on the semianalytical δγ expansion. Combined with a recently proposed empirical modification of MCT in which memory functions are calculated using effective structure factors at rescaled number densities, the scheme is able to model the collective dynamics over the entire accessible time and wave-vector range and predicts the volume-fraction-dependence of long-time self-diffusion coefficients and the zero-shear viscosity quantitatively. This highlights the potential of MCT as a practical tool for the quantitative analysis and prediction of experimental observations.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635100","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

Extinction and coexistence in a binary mixture of proliferating motile disks. 增殖运动盘二元混合物中的消亡与共存。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.064140

Alejandro Almodóvar, Tobias Galla, Cristóbal López

引用次数: 0

From cavitation to astrophysics: Explicit solution of the spherical collapse equation. 从空化到天体物理学：球形塌缩方程的显式求解。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.065102

Danail Obreschkow

引用次数: 0

Soliton gas: Theory, numerics, and experiments. 孤子气体：理论、数值和实验。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-06-01 DOI: 10.1103/PhysRevE.109.061001

Pierre Suret, Stephane Randoux, Andrey Gelash, Dmitry Agafontsev, Benjamin Doyon, Gennady El

{"title":"Soliton gas: Theory, numerics, and experiments.","authors":"Pierre Suret, Stephane Randoux, Andrey Gelash, Dmitry Agafontsev, Benjamin Doyon, Gennady El","doi":"10.1103/PhysRevE.109.061001","DOIUrl":"https://doi.org/10.1103/PhysRevE.109.061001","url":null,"abstract":"The concept of soliton gas was introduced in 1971 by Zakharov as an infinite collection of weakly interacting solitons in the framework of Korteweg-de Vries (KdV) equation. In this theoretical construction of a diluted (rarefied) soliton gas, solitons with random amplitude and phase parameters are almost nonoverlapping. More recently, the concept has been extended to dense gases in which solitons strongly and continuously interact. The notion of soliton gas is inherently associated with integrable wave systems described by nonlinear partial differential equations like the KdV equation or the one-dimensional nonlinear Schrödinger equation that can be solved using the inverse scattering transform. Over the last few years, the field of soliton gases has received a rapidly growing interest from both the theoretical and experimental points of view. In particular, it has been realized that the soliton gas dynamics underlies some fundamental nonlinear wave phenomena such as spontaneous modulation instability and the formation of rogue waves. The recently discovered deep connections of soliton gas theory with generalized hydrodynamics have broadened the field and opened new fundamental questions related to the soliton gas statistics and thermodynamics. We review the main recent theoretical and experimental results in the field of soliton gas. The key conceptual tools of the field, such as the inverse scattering transform, the thermodynamic limit of finite-gap potentials, and generalized Gibbs ensembles are introduced and various open questions and future challenges are discussed.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635104","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