Physical Review E最新文献_第2页

Inference of transcriptional regulation from STARR-seq data. 从STARR-seq数据推断转录调控。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024402

Amin Safaeesirat, Hoda Taeb, Emirhan Tekoglu, Tunc Morova, Nathan A Lack, Eldon Emberly

{"title":"Inference of transcriptional regulation from STARR-seq data.","authors":"Amin Safaeesirat, Hoda Taeb, Emirhan Tekoglu, Tunc Morova, Nathan A Lack, Eldon Emberly","doi":"10.1103/PhysRevE.111.024402","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024402","url":null,"abstract":"One of the primary regulatory processes in cells is transcription, during which RNA polymerase II (Pol-II) transcribes DNA into RNA. The binding of Pol-II to its site is regulated through interactions with transcription factors (TFs) that bind to DNA at enhancer cis-regulatory elements. Measuring the enhancer activity of large libraries of distinct DNA sequences is now possible using massively parallel reporter assays (MPRAs), and computational methods have been developed to identify the dominant statistical patterns of TF binding within these large datasets. Such methods are global in their approach and may overlook important regulatory sites that function only within the local context. Here we introduce a method for inferring functional regulatory sites (their number, location, and width) within an enhancer sequence based on measurements of its transcriptional activity from an MPRA method such as STARR-seq. The model is based on a mean-field thermodynamic description of Pol-II binding that includes interactions with bound TFs. Our method applied to simulated STARR-seq data for a variety of enhancer architectures shows how data quality impacts the inference and also how it can find local regulatory sites that may be missed in a global approach. We also apply the method to recently measured STARR-seq data on androgen receptor (AR) bound sequences, a TF that plays an important role in the regulation of prostate cancer. The method identifies key regulatory sites within these sequences, which are found to overlap with binding sites of known coregulators of AR.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024402"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659204","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

Unitary description of the Jaynes-Cummings model under fractional-time dynamics. 分数时间动力学下Jaynes-Cummings模型的统一描述。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024110

Danilo Cius

引用次数: 0

Advecting scaffolds: Controlling the remodeling of actomyosin with anillin. 血管支架：用苯胺控制肌动球蛋白的重构。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024403

Denni Currin-Ross, Sami C Al-Izzi, Ivar Noordstra, Alpha S Yap, Richard G Morris

{"title":"Advecting scaffolds: Controlling the remodeling of actomyosin with anillin.","authors":"Denni Currin-Ross, Sami C Al-Izzi, Ivar Noordstra, Alpha S Yap, Richard G Morris","doi":"10.1103/PhysRevE.111.024403","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024403","url":null,"abstract":"We propose and analyze an active hydrodynamic theory that characterizes the effects of the scaffold protein anillin. Anillin is found at major sites of cortical activity, such as adherens junctions and the cytokinetic furrow, where the canonical regulator of actomyosin remodeling is the small GTPase, RhoA. RhoA acts via intermediary \"effectors\" to increase both the rates of activation of myosin motors and the polymerization of actin filaments. Anillin has been shown to scaffold this action of RhoA-improving critical rates in the signaling pathway without altering the essential biochemistry-but its contribution to the wider spatiotemporal organization of the cortical cytoskeleton remains poorly understood. Here we combine analytics and numerics to show how anillin can nontrivially regulate the cytoskeleton at hydrodynamic scales. At short times, anillin can amplify or dampen existing contractile instabilities, as well as alter the parameter ranges over which they occur. At long times, it can change both the size and speed of steady-state traveling pulses. The primary mechanism that underpins these behaviors is established to be the advection of anillin by myosin II motors, with the specifics relying on the values of two coupling parameters. These codify anillin's effect on local signaling kinetics and can be traced back to its interaction with the acidic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP_{2}), thereby establishing a putative connection between actomyosin remodeling and membrane composition.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024403"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659309","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

Comparing temporal and aggregated network descriptions of fluid transport in the Mediterranean Sea. 比较地中海流体输送的时间和聚集网络描述。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024211

Kishor Acharya, Javier Aguilar, Lorenzo Dall'Amico, Kyriacos Nicolaou, Sandro Meloni, Enrico Ser-Giacomi

{"title":"Comparing temporal and aggregated network descriptions of fluid transport in the Mediterranean Sea.","authors":"Kishor Acharya, Javier Aguilar, Lorenzo Dall'Amico, Kyriacos Nicolaou, Sandro Meloni, Enrico Ser-Giacomi","doi":"10.1103/PhysRevE.111.024211","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024211","url":null,"abstract":"Ocean currents exhibit strong time dependence at all scales that influences physical and biochemical dynamics. Network approaches to fluid transport permit to address explicitly how connectivity across the seascape is affected by the spatiotemporal variability of currents. However, such temporal aspect is mostly neglected, relying on a static representation of the flow. We here investigate the role of current variability on networks describing physical transport across the Mediterranean basin. We first focus on degree distributions and community structure comparing ensembles of temporal networks that explicitly resolve time dependence and their aggregated, i.e., time-averaged, counterparts. Furthermore, we explore the implications of the two approaches in a simple reaction dispersal model for a generic tracer. Our analysis evidences that aggregation induces structural network changes that cannot be easily avoided, not even introducing a pruning of the aggregated adjacency matrix. We also highlight that, depending on the time scales considered, the importance of the temporal features of the networks can vary significantly. Finally, we find that the tracer evolution obtained from a temporal dispersal kernel cannot be always approximated by aggregated adjacency matrices, in particular during transients of the dynamics.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024211"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659535","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

Competing social contagions with opinion-dependent infectivity. 与意见依赖传染性相竞争的社会传染。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024313

Corbit R Sampson, Juan G Restrepo

{"title":"Competing social contagions with opinion-dependent infectivity.","authors":"Corbit R Sampson, Juan G Restrepo","doi":"10.1103/PhysRevE.111.024313","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024313","url":null,"abstract":"The spread of disinformation (maliciously spread false information) in online social networks has become an important problem in today's society. Disinformation's spread is facilitated by the fact that individuals often accept false information based on cognitive biases which predispose them to believe information that they have heard repeatedly or that aligns with their beliefs. Moreover, disinformation often spreads in direct competition with corresponding true information. To model these phenomena, we develop a model for two competing beliefs spreading on a social network, where individuals have an internal opinion that models their cognitive biases and modulates their likelihood of adopting one of the competing beliefs. By numerical simulations of an agent-based model and a mean-field description of the dynamics, we study how the long-term dynamics of the spreading process depend on the initial conditions for the number of spreaders and the initial opinion of the population. We find that the addition of cognitive biases enriches the transient dynamics of the spreading process, facilitating behavior such as the revival of a dying belief and the overturning of an initially widespread opinion. Finally, we study how external recruitment of spreaders can lead to the eventual dominance of one of the two beliefs.","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024313"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659536","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

Describing self-organized criticality as a continuous phase transition. 将自组织临界描述为连续的相变。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024111

S S Manna

引用次数: 0

Helicity modulus and chiral symmetry breaking for boundary conditions with finite twist. 有限扭转边界条件下的螺旋模和手性对称破缺。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024114

Gaurav Khairnar, Thomas Vojta

引用次数: 0

Paradise-disorder transition in structural balance dynamics on Erdös-Rényi graphs. Erdös-Rényi图上结构平衡动力学中的天堂-无序过渡。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024310

Krishnadas Mohandas, Krzysztof Suchecki, Janusz A Hołyst

引用次数: 0

Patterns of link reciprocity in directed, signed networks. 定向、签名网络中的链接互惠模式。

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024312

Anna Gallo, Fabio Saracco, Renaud Lambiotte, Diego Garlaschelli, Tiziano Squartini

{"title":"Patterns of link reciprocity in directed, signed networks.","authors":"Anna Gallo, Fabio Saracco, Renaud Lambiotte, Diego Garlaschelli, Tiziano Squartini","doi":"10.1103/PhysRevE.111.024312","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024312","url":null,"abstract":"Most of the analyses concerning signed networks have focused on balance theory, hence identifying frustration with undirected, triadic motifs having an odd number of negative edges; much less attention has been paid to their directed counterparts. To fill this gap, we focus on signed, directed connections, with the aim of exploring the notion of frustration in such a context. When dealing with signed, directed edges, frustration is a multifaceted concept, admitting different definitions at different scales: if we limit ourselves to consider cycles of length 2, frustration is related to reciprocity, i.e., the tendency of edges to admit the presence of partners pointing in the opposite direction. As the reciprocity of signed networks is still poorly understood, we adopt a principled approach for its study, defining quantities and introducing models to consistently capture empirical patterns of the kind. In order to quantify the tendency of empirical networks to form either mutualistic or antagonistic cycles of length 2, we extend the exponential random graph framework to binary, directed, signed networks with global and local constraints and then compare the empirical abundance of the aforementioned patterns with the one expected under each model. We find that the (directed extension of the) balance theory is not capable of providing a consistent explanation of the patterns characterizing the directed, signed networks considered in this work. Although part of the ambiguities can be solved by adopting a coarser definition of balance, our results call for a different theory, accounting for the directionality of edges in a coherent manner. In any case, the evidence that the empirical, signed networks can be highly reciprocated leads us to recommend to explicitly account for the role played by bidirectional dyads in determining frustration at higher levels (e.g., the triadic one).","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024312"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659157","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

Enhancing Otto refrigerator performance with a precooling strategy. 提高奥托冰箱性能与预冷策略。

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.L022101

Yang Xu, Huilin Ruan, Shaolin Luo, Shouhui Guo, Xian He, Jianhui Wang

引用次数: 0