Suppr超能文献

一种基于短程势计算自由能景观的几何方法。

A geometrical approach to computing free-energy landscapes from short-ranged potentials.

机构信息

School of Engineering and Applied Sciences and Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA 02138, USA.

出版信息

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E5-14. doi: 10.1073/pnas.1211720110. Epub 2012 Dec 17.

Abstract

Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free-energy landscape of such systems as the range of the potential goes to zero. In this limit, the landscape is entirely defined by geometrical manifolds, plus a single control parameter. These manifolds are fundamental objects that do not depend on the details of the interaction potential and provide the starting point from which any quantity characterizing the system--equilibrium or nonequilibrium--can be computed for arbitrary potentials. To consider dynamical quantities we compute the asymptotic limit of the Fokker-Planck equation and show that it becomes restricted to the low-dimensional manifolds connected by "sticky" boundary conditions. To illustrate our theory, we compute the low-dimensional manifolds for n ≤ 8 identical particles, providing a complete description of the lowest-energy parts of the landscape including floppy modes with up to 2 internal degrees of freedom. The results can be directly tested on colloidal clusters. This limit is a unique approach for understanding energy landscapes, and our hope is that it can also provide insight into finite-range potentials.

摘要

粒子与短程势相互作用引起了越来越多的关注,部分原因是它们能够模拟胶体通过 DNA 或耗尽相互作用等介观系统。我们考虑了势的范围趋于零时的自由能景观。在这个极限下,景观完全由几何流形以及单个控制参数定义。这些流形是基本的对象,不依赖于相互作用势的细节,并为任意势下计算任何描述系统的特性——平衡或非平衡——提供了起点。为了考虑动力学量,我们计算了福克-普朗克方程的渐近极限,并表明它被限制在由“粘性”边界条件连接的低维流形上。为了说明我们的理论,我们计算了 n ≤ 8 个相同粒子的低维流形,提供了景观中最低能量部分的完整描述,包括多达 2 个内部自由度的柔软模式。结果可以直接在胶体簇上进行测试。这个极限是理解能量景观的独特方法,我们希望它也能为有限范围势提供深入的了解。

相似文献

1
2
Free energy of singular sticky-sphere clusters.奇异粘性球体簇的自由能。
Phys Rev E. 2017 Feb;95(2-1):022130. doi: 10.1103/PhysRevE.95.022130. Epub 2017 Feb 22.
3
Dissipative self-assembly of particles interacting through time-oscillatory potentials.时频振荡势相互作用的粒子耗散自组装。
Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9751-6. doi: 10.1073/pnas.1406122111. Epub 2014 Jun 23.
8
Temperature-induced migration of electro-neutral interacting colloidal particles.温度诱导的电中性相互作用胶体颗粒的迁移
J Colloid Interface Sci. 2024 Jul 15;666:457-471. doi: 10.1016/j.jcis.2024.04.031. Epub 2024 Apr 9.
9
Feedback-induced oscillations in one-dimensional colloidal transport.一维胶体传输中反馈诱导的振荡。
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Nov;86(5 Pt 1):051405. doi: 10.1103/PhysRevE.86.051405. Epub 2012 Nov 30.
10
Master equation approach to molecular motors.分子马达的主方程方法。
Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Dec;64(6 Pt 1):061905. doi: 10.1103/PhysRevE.64.061905. Epub 2001 Nov 20.

引用本文的文献

4
Physical constraints on early blastomere packings.早期胚胎细胞的物理约束。
PLoS Comput Biol. 2021 Jan 26;17(1):e1007994. doi: 10.1371/journal.pcbi.1007994. eCollection 2021 Jan.
5
Mechanics of Multicentrosomal Clustering in Bipolar Mitotic Spindles.多中心体簇集在双极有丝分裂纺锤体中的机制。
Biophys J. 2020 Jul 21;119(2):434-447. doi: 10.1016/j.bpj.2020.06.004. Epub 2020 Jun 12.
6
Rigidity for sticky discs.粘性椎间盘的僵硬
Proc Math Phys Eng Sci. 2019 Feb;475(2222):20180773. doi: 10.1098/rspa.2018.0773. Epub 2019 Feb 27.
7
Size limits of self-assembled colloidal structures made using specific interactions.使用特定相互作用自组装胶体结构的尺寸限制。
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15918-23. doi: 10.1073/pnas.1411765111. Epub 2014 Oct 27.
8
Energy landscapes of planar colloidal clusters.平面胶体团簇的能量景观。
Nanoscale. 2014 Sep 21;6(18):10717-26. doi: 10.1039/c4nr02670e. Epub 2014 Aug 6.
9
Mesoscale molecular network formation in amorphous organic materials.无定形有机材料中的介观分子网络形成。
Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10055-60. doi: 10.1073/pnas.1409514111. Epub 2014 Jun 30.

本文引用的文献

2
Nanoparticle superlattice engineering with DNA.DNA 引导的纳米颗粒超晶格工程。
Science. 2011 Oct 14;334(6053):204-8. doi: 10.1126/science.1210493.
5
Geometric frustration in small colloidal clusters.小胶体团簇中的几何阻挫
J Phys Condens Matter. 2009 Oct 21;21(42):425103. doi: 10.1088/0953-8984/21/42/425103. Epub 2009 Sep 22.
6
Markov state models based on milestoning.基于里程碑的马尔可夫状态模型。
J Chem Phys. 2011 May 28;134(20):204105. doi: 10.1063/1.3590108.
7
Design principles for self-assembly with short-range interactions.短程相互作用自组装的设计原则。
Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5193-8. doi: 10.1073/pnas.1014094108. Epub 2011 Mar 7.
9
Protein folded states are kinetic hubs.蛋白质折叠状态是动力学枢纽。
Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10890-5. doi: 10.1073/pnas.1003962107. Epub 2010 Jun 1.

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验