Physical Review E最新文献_第8页

Local topology and perestroikas in protein structure and folding dynamics. 蛋白质结构和折叠动力学中的局部拓扑和重构。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024406

Alexander Begun, Maxim N Chernodub, Alexander Molochkov, Antti J Niemi

{"title":"Local topology and perestroikas in protein structure and folding dynamics.","authors":"Alexander Begun, Maxim N Chernodub, Alexander Molochkov, Antti J Niemi","doi":"10.1103/PhysRevE.111.024406","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024406","url":null,"abstract":"Methods of local topology are introduced to the field of protein physics. This is done by interpreting the folding and unfolding processes of a globular protein in terms of conformational bifurcations that alter the local topology of the proteins Cα backbone. The mathematical formulation extends Arnold's perestroikas to piecewise linear chains using the discrete Frenet frame formalism. In the low-temperature folded phase, the backbone geometry generalizes the concept of a Peano curve, with its modular building blocks modeled by soliton solutions of a discretized nonlinear Schrödinger equation. The onset of thermal unfolding begins when perestroikas change the flattening and branch points that determine the centers of solitons. When temperature increases, the perestroikas cascade, which leads to a progressive disintegration of the modular structures. The folding and unfolding processes are quantitatively characterized by a correlation function that describes the evolution of perestroikas under temperature changes. The approach provides a comprehensive framework for understanding the Physics of protein folding and unfolding transitions, contributing to the broader field of protein structure and dynamics.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024406"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659229","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

Oscillatory and chaotic pattern dynamics driven by surface curvature. 曲面曲率驱动下的振荡和混沌模式动力学。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.L022202

Ryosuke Nishide, Shuji Ishihara

引用次数: 0

Wrinkling and imaging of thin curved sheets. 弯曲薄板的起皱和成像。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.025501

Megha Emerse, Lucas Goehring

{"title":"Wrinkling and imaging of thin curved sheets.","authors":"Megha Emerse, Lucas Goehring","doi":"10.1103/PhysRevE.111.025501","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.025501","url":null,"abstract":"Thin films or sheets subjected to external forces often undergo mechanical instability, leading to regular patterns of wrinkles, folds, and creases. As can be anticipated from the difficulty of flattening a curved globe, any natural curvature of the sheet will have a strong influence on these instabilities. Here, we develop a noninvasive synthetic schlieren imaging technique to image and reconstruct the surface of wrinkling curved sheets, confined to float on water. Our method circumvents the small-amplitude limit of related imaging techniques, and we demonstrate robust means to estimate the reconstruction accuracy. We then evaluate how the sign and magnitude of Gaussian curvature affect the wrinkling of thin curved sheets, and compare observations of the wrinkle wavelength, amplitude, and domain structure with recent theoretical predictions. While generally validating model predictions, we find that the assumption of a conserved surface area during wrinkling should be treated with some care. The control of wrinkling behavior demonstrated here can have applications in the design of liquid lenses, microfluidics, active textured surfaces, and flexible electronic components.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-2","pages":"025501"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659473","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

Compounded random walk for space-fractional diffusion on finite domains. 有限域上空间-分数扩散的复合随机漫步。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024136

Christopher N Angstmann, Daniel S Han, Bruce I Henry, Boris Z Huang, Zhuang Xu

引用次数: 0

Weakly nonlinear analysis of Turing pattern dynamics on curved surfaces. 曲面上图灵图案动力学的弱非线性分析。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024208

Ryosuke Nishide, Shuji Ishihara

{"title":"Weakly nonlinear analysis of Turing pattern dynamics on curved surfaces.","authors":"Ryosuke Nishide, Shuji Ishihara","doi":"10.1103/PhysRevE.111.024208","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024208","url":null,"abstract":"Pattern dynamics on curved surfaces are ubiquitous. Although the effect of surface topography on pattern dynamics has gained much interest, there is a limited understanding of the roles of surface geometry and topology in pattern dynamics. Recently, we reported that a static pattern on a flat plane can become a propagating pattern on a curved surface [Phys. Rev. Lett. 128, 224101 (2022)10.1103/PhysRevLett.128.224101]. By examining reaction-diffusion equations on axisymmetric surfaces, certain conditions for the onset of pattern propagation were determined. However, this analysis was limited by the assumption that the pattern propagates at a constant speed. Here, we investigate the pattern propagation driven by surface curvature using weakly nonlinear analysis, which enables a more comprehensive approach to the aforementioned problem. The analysis reveals consistent conditions of the pattern propagation similar to our previous results, and further predicts that rich dynamics other than pattern propagation, such as periodic and chaotic behaviors, can arise depending on the surface geometry. This study provides a perspective on the relationship between surfaces and pattern dynamics and a basis for controlling pattern dynamics on surfaces.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024208"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658796","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

Local nearby bifurcations lead to synergies in critical slowing down: The case of mushroom bifurcations. 局部附近分岔导致临界减速的协同效应：蘑菇分岔的情况。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024213

Mariona Fucho-Rius, Smitha Maretvadakethope, Àlex Haro, Tomás Alarcón, Josep Sardanyés, Rubén Pérez-Carrasco

{"title":"Local nearby bifurcations lead to synergies in critical slowing down: The case of mushroom bifurcations.","authors":"Mariona Fucho-Rius, Smitha Maretvadakethope, Àlex Haro, Tomás Alarcón, Josep Sardanyés, Rubén Pérez-Carrasco","doi":"10.1103/PhysRevE.111.024213","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024213","url":null,"abstract":"The behavior of nonlinear systems near critical transitions has significant implications for stability, transients, and resilience in complex systems. Transient times, τ, become extremely long near phase transitions (or bifurcations) in a phenomenon known as critical slowing down, and are observed in electronic circuits, circuit quantum electrodynamics, ecosystems, and gene regulatory networks. Critical slowing down typically follows universal laws of the form τ∼|μ-μ_{c}|^{β}, with μ being the control parameter and μ_{c} its critical value. For instance, β=-1/2 close to saddle-node bifurcations. Despite intensive research on slowing down phenomena for single bifurcations, both local and global, the behavior of transients when several bifurcations are close to each other remains unknown. Here, we investigate transients near two saddle-node bifurcations merging into a transcritical one. Using a nonlinear gene-regulatory model and a normal form exhibiting a mushroom bifurcation diagram we show, both analytically and numerically, a synergistic, i.e., nonadditive, lengthening of transients due to coupled ghost effects and transcritical slowing down. We also show that intrinsic and extrinsic noise play opposite roles in the slowing down of the transition, allowing us to control the timing of the transition without compromising the precision of timing. This establishes molecular strategies to generate genetic timers with transients much larger than the typical timescales of the reactions involved.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024213"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659224","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

Memory of rotation in residual stress of paste. 膏体残余应力中的旋转记忆。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.025502

Hiroki Matsuda, Michio Otsuki

引用次数: 0

Spallation of polycarbonate on nanosecond timescales. 聚碳酸酯在纳秒级时间尺度上的剥落。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.025503

Jacob M Diamond, K T Ramesh

引用次数: 0

Fluctuations and persistence in quantum diffusion on regular lattices. 规则晶格上量子扩散的波动和持续性。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024126

Cheng Ma, Omar Malik, G Korniss

{"title":"Fluctuations and persistence in quantum diffusion on regular lattices.","authors":"Cheng Ma, Omar Malik, G Korniss","doi":"10.1103/PhysRevE.111.024126","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024126","url":null,"abstract":"We investigate quantum persistence by analyzing amplitude and phase fluctuations of the wave function governed by the time-dependent free-particle Schrödinger equation. The quantum system is initialized with local random uncorrelated Gaussian amplitude and phase fluctuations. In analogy with classical diffusion, the persistence probability is defined as the probability that the local (amplitude or phase) fluctuations have not changed sign up to time t. Our results show that the persistence probability in quantum diffusion exhibits exponential-like tails. More specifically, in d=1 the persistence probability decays in a stretched exponential fashion, while in d=2 and d=3 as an exponential. We also provide some insights by analyzing the two-point spatial and temporal correlation functions in the limit of small fluctuations. In particular, in the long-time asymptotic limit, the temporal correlation functions for both local amplitude and phase fluctuations become time-homogeneous. Hence, the zero-crossing events correspond to those governed by a stationary Gaussian process, with an autocorrelation-function power-law tail decaying sufficiently fast to imply an exponential-like tail of the persistence probabilities.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024126"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658965","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

Comparison of the clock, stochastic cutoff, and Tomita Monte Carlo methods in simulating the dipolar triangular lattice at criticality. 时钟，随机截止，和富田蒙特卡罗方法在模拟临界偶极三角形晶格的比较。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.025308

S Ismailzadeh, M D Niry

{"title":"Comparison of the clock, stochastic cutoff, and Tomita Monte Carlo methods in simulating the dipolar triangular lattice at criticality.","authors":"S Ismailzadeh, M D Niry","doi":"10.1103/PhysRevE.111.025308","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.025308","url":null,"abstract":"Magnetic nanostructures find application in diverse technological domains, and their behavior is significantly influenced by long-range dipolar interactions. However, simulating these systems using the traditional Metropolis Monte Carlo method poses high computational demand. Several methods, including the clock, stochastic cutoff, and Tomita approaches, can reduce the computational burden of simulating 2D systems with dipolar interactions. Although these three methods rely on distinct theoretical concepts, they all achieve complexity reduction by a common strategy. Instead of calculating the energy difference between a spin and all its neighbors, they evaluate the energy difference with only a limited number of randomly chosen neighbors. This is achieved through methods like the dynamic thinning and Fukui-Todo techniques. In this article, we compared the performance of the clock, SCO, Tomita, and Metropolis methods near the critical point of the dipolar triangular lattice to identify the most suitable algorithm for this type of simulation. Our findings show that while these methods are less suitable for simulating this system in their untuned implementation, incorporating the boxing near-neighbors method and overrelaxation moves makes them significantly more efficient and better suited than the Metropolis method with overrelaxation.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-2","pages":"025308"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659031","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