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Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches. 跨尺度的生物分子凝聚物建模：原子，粗粒度和数据驱动的方法。
IF 10.8 2区 物理与天体物理
Advances in Physics: X Pub Date : 2025-01-01 Epub Date: 2025-12-05 DOI: 10.1080/23746149.2025.2592547
Maria Julia Maristany, Alina Emelianova, Pin Yu Chew, Anne Aguirre, Rosana Collepardo-Guevara, Jerelle A Joseph
{"title":"Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.","authors":"Maria Julia Maristany, Alina Emelianova, Pin Yu Chew, Anne Aguirre, Rosana Collepardo-Guevara, Jerelle A Joseph","doi":"10.1080/23746149.2025.2592547","DOIUrl":"10.1080/23746149.2025.2592547","url":null,"abstract":"<p><p>Biomolecular condensates are integral to processes underlying cellular function and dysfunction, and they also present a versatile platform for engineering living cells. Understanding how molecular interactions give rise to condensate form and function is therefore a major area of research. Computational modeling has emerged as a powerful tool for uncovering the biophysical principles underlying condensates. Because condensate biophysics spans multiple spatiotemporal scales, from interactions of amino acid side chains to the emergent material properties of entire condensates, decoding their behavior requires multiscale strategies. In this review, we discuss three core classes of computational modeling approaches that extend our ability to probe condensates. We first examine atomistic modeling, which enables a detailed examination of interactions that encode condensate behaviors. We then discuss coarse-grained modeling, with a focus on residue-resolution models, which advance our ability to predict condensate properties with both precision and efficiency. Finally, we summarize advances in data-driven and machine learning approaches, which leverage molecular simulations to map sequence-property relationships of condensates at a fraction of the cost. Throughout the review, we highlight the key ingredients of each approach, the types of simulations and modeling strategies employed, and the primary observables that can be measured. In doing so, we aim for this review to serve as both an informative and practical guide for leveraging these approaches to understand and engineer biomolecular condensates.</p>","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"10 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13004485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147497211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Orbital angular momentum of Bloch electrons: equilibrium formulation, magneto-electric phenomena, and the orbital Hall effect 布洛赫电子的轨道角动量：平衡公式、磁电现象和轨道霍尔效应
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-07-04 DOI: 10.1080/23746149.2024.2371972
Rhonald Burgos Atencia, Amit Agarwal, Dimitrie Culcer
{"title":"Orbital angular momentum of Bloch electrons: equilibrium formulation, magneto-electric phenomena, and the orbital Hall effect","authors":"Rhonald Burgos Atencia, Amit Agarwal, Dimitrie Culcer","doi":"10.1080/23746149.2024.2371972","DOIUrl":"https://doi.org/10.1080/23746149.2024.2371972","url":null,"abstract":"The investigation of orbital angular momentum (OAM) of delocalised Bloch electrons has advanced our understanding of magnetic, transport, and optical phenomena in crystals, drawing widespread inter...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"60 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141614039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Fundamental physics and other applications using nonneutral plasma 使用非中性等离子体的基础物理学和其他应用
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-06-26 DOI: 10.1080/23746149.2024.2367438
G. Maero, E. D. Hunter, D. J. Murtagh, E. V. Stenson
{"title":"Fundamental physics and other applications using nonneutral plasma","authors":"G. Maero, E. D. Hunter, D. J. Murtagh, E. V. Stenson","doi":"10.1080/23746149.2024.2367438","DOIUrl":"https://doi.org/10.1080/23746149.2024.2367438","url":null,"abstract":"During the last fifty years, nonneutral plasma physics has developed into a definite subfield of basic research, whose main focus has been on the collective properties of systems comprising many ch...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"53 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Performance limits of information engines 信息引擎的性能极限
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-05-21 DOI: 10.1080/23746149.2024.2352112
Johan du Buisson, David A. Sivak, John Bechhoefer
{"title":"Performance limits of information engines","authors":"Johan du Buisson, David A. Sivak, John Bechhoefer","doi":"10.1080/23746149.2024.2352112","DOIUrl":"https://doi.org/10.1080/23746149.2024.2352112","url":null,"abstract":"We review recent studies of a colloidal information engine that consists of a bead in water and held by an optical trap. The bead is ratcheted upward without any apparent external work, by taking a...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"17 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141151337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Insight into the interactions of fullerenes with biological membranes through molecular dynamics simulations 通过分子动力学模拟深入了解富勒烯与生物膜的相互作用
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-05-10 DOI: 10.1080/23746149.2024.2350160
Nililla Nisoh, Viwan Jarerattanachat, Cristiano Dias, Jirasak Wong-Ekkabut
{"title":"Insight into the interactions of fullerenes with biological membranes through molecular dynamics simulations","authors":"Nililla Nisoh, Viwan Jarerattanachat, Cristiano Dias, Jirasak Wong-Ekkabut","doi":"10.1080/23746149.2024.2350160","DOIUrl":"https://doi.org/10.1080/23746149.2024.2350160","url":null,"abstract":"This paper reviews our current understanding of how fullerene molecules interact with biological membranes. First, we discuss how fullerenes permeate into biological membranes. Next, the putative m...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"20 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140925805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
3D assembly of Janus spheres: potentials, dynamics, and experiments 杰纳斯球的三维组装：潜力、动力学和实验
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-04-28 DOI: 10.1080/23746149.2024.2341759
Stephen Chung, Sina Safaei, Geoff R. Willmott
{"title":"3D assembly of Janus spheres: potentials, dynamics, and experiments","authors":"Stephen Chung, Sina Safaei, Geoff R. Willmott","doi":"10.1080/23746149.2024.2341759","DOIUrl":"https://doi.org/10.1080/23746149.2024.2341759","url":null,"abstract":"Asymmetric colloidal Janus particles (JPs) have stimulated research which spans many disciplines, often due to possibilities for their assembly into larger structures. This review aims to identify ...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"31 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140925811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Reconfigurable nanoionic and photoionic material and device platforms 可重构的纳米和光电离子材料与器件平台
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-04-16 DOI: 10.1080/23746149.2024.2338285
Ahmed H. Elfarash, Behrad Gholipour
{"title":"Reconfigurable nanoionic and photoionic material and device platforms","authors":"Ahmed H. Elfarash, Behrad Gholipour","doi":"10.1080/23746149.2024.2338285","DOIUrl":"https://doi.org/10.1080/23746149.2024.2338285","url":null,"abstract":"Nanoionic and photoionic reconfigurable oxides and chalcogenide semiconductors are emerging material platforms for field-based, non-volatile control of electrons and photons in nanoscale optoelectr...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"34 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Progress in high-power and high-intensity structured light 高功率和高强度结构光的进展
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-03-26 DOI: 10.1080/23746149.2024.2327453
Justin Harrison, Darryl Naidoo, Andrew Forbes, Angela Dudley
{"title":"Progress in high-power and high-intensity structured light","authors":"Justin Harrison, Darryl Naidoo, Andrew Forbes, Angela Dudley","doi":"10.1080/23746149.2024.2327453","DOIUrl":"https://doi.org/10.1080/23746149.2024.2327453","url":null,"abstract":"Structured light refers to the ability to tailor light in its many degrees of freedom, from the traditional control in time and space to more exotic multi-dimensional control for new forms of light...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"20 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140312309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Recent development in integrated Lithium niobate photonics 集成铌酸锂光子学的最新发展
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-03-12 DOI: 10.1080/23746149.2024.2322739
Zhenda Xie, Fang Bo, Jintian Lin, Hui Hu, Xinlun Cai, Xiao-Hui Tian, Zhiwei Fang, Jinming Chen, Min Wang, Feng Chen, Ya Cheng, JingJun Xu, Shining Zhu
{"title":"Recent development in integrated Lithium niobate photonics","authors":"Zhenda Xie, Fang Bo, Jintian Lin, Hui Hu, Xinlun Cai, Xiao-Hui Tian, Zhiwei Fang, Jinming Chen, Min Wang, Feng Chen, Ya Cheng, JingJun Xu, Shining Zhu","doi":"10.1080/23746149.2024.2322739","DOIUrl":"https://doi.org/10.1080/23746149.2024.2322739","url":null,"abstract":"The lithium niobate on insulator devices confine the light field to submicron size in monocrystalline lithium niobate, to achieve ultra-strong electro-optical interaction and nonlinear optical inte...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"47 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140115262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Liquid metal phase change materials for thermal management of electronics 用于电子设备热管理的液态金属相变材料
IF 6 2区 物理与天体物理
Advances in Physics: X Pub Date : 2024-03-11 DOI: 10.1080/23746149.2024.2324910
Yuchen Yao, Wei Li, Jing Liu, Zhongshan Deng
{"title":"Liquid metal phase change materials for thermal management of electronics","authors":"Yuchen Yao, Wei Li, Jing Liu, Zhongshan Deng","doi":"10.1080/23746149.2024.2324910","DOIUrl":"https://doi.org/10.1080/23746149.2024.2324910","url":null,"abstract":"With the rapid development of various chips towards high performance and integration, the ‘thermal barrier’ difficulty facing electronic devices has become ever increasingly challenging, while at t...","PeriodicalId":7374,"journal":{"name":"Advances in Physics: X","volume":"5 1","pages":""},"PeriodicalIF":6.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140115191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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