Physical Review E最新文献_第2页

Paradise-disorder transition in structural balance dynamics on Erdös-Rényi graphs.

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.

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

Limits to positional information in boundary-driven systems.

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.L022102

Prashant Singh, Karel Proesmans

引用次数: 0

Hydrodynamics of a hard-core active lattice gas.

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024128

Ritwik Mukherjee, Soumyabrata Saha, Tridib Sadhu, Abhishek Dhar, Sanjib Sabhapandit

引用次数: 0

Inference of transcriptional regulation from STARR-seq data.

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

Crystal nucleation rates in one-component Yukawa systems.

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.025206

B Arnold, J Daligault, D Saumon, Antoine Bédard, S X Hu

引用次数: 0

Memory-induced current reversal of Brownian motors.

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024130

Mateusz Wiśniewski, Jakub Spiechowicz

引用次数: 0

Stabilization of a transition state by excited vibration and impact on the reaction rate in the three-body Lennard-Jones system.

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024204

Yoshiyuki Y Yamaguchi

引用次数: 0

Advecting scaffolds: Controlling the remodeling of actomyosin with anillin.

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

Emergence in kinetic roughening with long-range temporal correlations.

IF 2.2 3区物理与天体物理

Physical Review E Pub Date : 2025-02-01 DOI: 10.1103/PhysRevE.111.024124

Shuting Wang, Hui Xia

引用次数: 0