Physical Review E最新文献_第7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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11605730/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neuromodulatory effects on synchrony and network reorganization in networks of coupled Kuramoto oscillators. 神经调节对耦合仓本振荡器网络的同步性和网络重组的影响

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044401

Sinan Aktay, Leonard M Sander, Michal Zochowski

{"title":"Neuromodulatory effects on synchrony and network reorganization in networks of coupled Kuramoto oscillators.","authors":"Sinan Aktay, Leonard M Sander, Michal Zochowski","doi":"10.1103/PhysRevE.110.044401","DOIUrl":"10.1103/PhysRevE.110.044401","url":null,"abstract":"Neuromodulatory processes in the brain can critically change signal processing on a cellular level, leading to dramatic changes in network level reorganization. Here, we use coupled nonidentical Kuramoto oscillators to investigate how changes in the shape of phase response curves from Type 1 to Type 2, mediated by varying ACh levels, coupled with activity-dependent plasticity may alter network reorganization. We first show that, when plasticity is absent, the Type 1 networks with symmetric adjacency matrix, as expected, exhibit asynchronous dynamics with oscillators of the highest natural frequency robustly evolving faster in terms of their phase dynamics. However, interestingly, Type 1 networks with an asymmetric connectivity matrix can produce stable synchrony (so-called splay states) with complex phase relationships. At the same time, Type 2 networks synchronize independent of the symmetry of their connectivity matrix, with oscillators locked so that those with higher natural frequency have a constant phase lead as compared to those with lower natural frequency. This relationship establishes a robust mapping between the frequency and oscillators' phases in the network, leading to structure and frequency mapping when plasticity is present. Finally, we show that biologically realistic, phase-locking dependent, connection plasticity naturally produces splay states in Type 1 networks that do not display the structure-frequency reorganization observed in synchronized Type II networks. These results indicate that the formation of splay states in the brain could be a common phenomenon.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044401"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677427","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

Classification of beating solitons, their physical spectra, and second-order nonlinear superpositions. 跳动孤子的分类、其物理光谱和二阶非线性叠加。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044210

Chong Liu, Wen-Juan Che, Nail Akhmediev

引用次数: 0

Molecular modeling of odd viscoelastic fluids. 奇异粘弹性流体的分子建模。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044605

Paweł Matus, Ruben Lier, Piotr Surówka

引用次数: 0

Hippocampal synchronization in a realistic CA1 neuron model. 在逼真的 CA1 神经元模型中实现海马同步

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044406

Alessandro Fiasconaro, Michele Migliore

引用次数: 0

Network analysis for the steady-state thermodynamic uncertainty relation. 稳态热力学不确定性关系的网络分析。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044103

Yasuhiro Utsumi

引用次数: 0

Lattice model for percolation on a plane of partially aligned sticks with length dispersity. 具有长度分散性的部分排列棍平面上的渗滤网格模型。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044115

Avik P Chatterjee, Yuri Yu Tarasevich

引用次数: 0

Mean back relaxation for position and densities. 位置和密度的平均背弛。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044137

Gabriel Knotz, Matthias Krüger

引用次数: 0

Resetting by rescaling: Exact results for a diffusing particle in one dimension. 通过重新缩放进行重置：一维扩散粒子的精确结果

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044142

Marco Biroli, Yannick Feld, Alexander K Hartmann, Satya N Majumdar, Grégory Schehr

{"title":"Resetting by rescaling: Exact results for a diffusing particle in one dimension.","authors":"Marco Biroli, Yannick Feld, Alexander K Hartmann, Satya N Majumdar, Grégory Schehr","doi":"10.1103/PhysRevE.110.044142","DOIUrl":"https://doi.org/10.1103/PhysRevE.110.044142","url":null,"abstract":"In this paper, we study a simple model of a diffusive particle on a line, undergoing a stochastic resetting with rate r, via rescaling its current position by a factor a, which can be either positive or negative. For |a|<1, the position distribution becomes stationary at long times and we compute this limiting distribution exactly for all |a|<1. This symmetric distribution has a Gaussian shape near its peak at x=0, but decays exponentially for large |x|. We also studied the mean first-passage time (MFPT) T(0) to a target located at a distance L from the initial position (the origin) of the particle. As a function of the initial position x, the MFPT T(x) satisfies a nonlocal second order differential equation and we have solved it explicitly for 0≤a<1. For -1<a≤0, we also solved it analytically but up to a constant factor κ whose value can be determined independently from numerical simulations. Our results show that, for all -1<a<1, the MFPT T(0) (starting from the origin) shows a minimum at r=r^{*}(a). However, the optimized MFPT T_{opt}(a) turns out to be a monotonically increasing function of a for -1<a<1. This demonstrates that, compared to the standard resetting to the origin (a=0), while the positive rescaling is not beneficial for the search of a target, the negative rescaling is. Thus resetting via rescaling followed by a reflection around the origin expedites the search of a target in one dimension.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"110 4-1","pages":"044142"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677602","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

Spectral energy transfers in domain growth problems. 域增长问题中的光谱能量转移。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2024-10-01 DOI: 10.1103/PhysRevE.110.044130

Pradeep Kumar Yadav, Mahendra Kumar Verma, Sanjay Puri

引用次数: 0