• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

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

混合粒子-场分子动力学方法:生物膜高效粗粒模型的途径。

A hybrid particle-field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes.

机构信息

Dipartimento di Chimica e Biologia, Università di Salerno, I-84084 SA, Italy.

出版信息

Phys Biol. 2013 Aug;10(4):045007. doi: 10.1088/1478-3975/10/4/045007. Epub 2013 Aug 2.

DOI:10.1088/1478-3975/10/4/045007
PMID:23912010
Abstract

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle-field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle-field models. This feature makes these models very promising ones in the exploration of several problems in biophysics.

摘要

本文概述了作者最近在混合粒子-场分子动力学技术框架下开发的磷脂粗粒度模型。该技术采用了一类特殊的粗粒度模型,由于它们允许对大规模系统进行模拟,同时为所采用的映射方案提供了足够详细的化学信息,因此这些模型越来越受欢迎。我们的方法与标准分子动力学模拟的计算成本比较是系统大小和并行计算中使用的处理器数量的函数。由于数据交换量低,处理器数量越多,混合粒子-场模型的性能越好。这个特性使得这些模型在探索生物物理学中的几个问题方面非常有前途。

相似文献

1
A hybrid particle-field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes.混合粒子-场分子动力学方法:生物膜高效粗粒模型的途径。
Phys Biol. 2013 Aug;10(4):045007. doi: 10.1088/1478-3975/10/4/045007. Epub 2013 Aug 2.
2
Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids.用于生物磷脂的混合粒子-场粗粒度模型
J Chem Theory Comput. 2011 Sep 13;7(9):2947-62. doi: 10.1021/ct200132n. Epub 2011 Aug 12.
3
Coarse-grained stochastic processes for microscopic lattice systems.微观晶格系统的粗粒化随机过程。
Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):782-7. doi: 10.1073/pnas.242741499. Epub 2003 Jan 27.
4
Coarse-grained Monte Carlo simulations of non-equilibrium systems.非平衡系统的粗粒度蒙特卡罗模拟。
J Chem Phys. 2013 Jun 28;138(24):244111. doi: 10.1063/1.4811656.
5
Coarse-grained lattice Monte Carlo simulations with continuous interaction potentials.具有连续相互作用势的粗粒化晶格蒙特卡罗模拟。
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 2):026708. doi: 10.1103/PhysRevE.86.026708. Epub 2012 Aug 16.
6
Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system.用于界面膜蛋白模拟的改进采样:广义阴影混合蒙特卡罗方法在肽毒素/双层系统中的应用
J Phys Chem B. 2008 May 8;112(18):5710-7. doi: 10.1021/jp076712u. Epub 2008 Apr 16.
7
First example of multi-scale reverse Monte Carlo modeling for small-angle scattering experimental data using reverse mapping from coarse-grained particles to atoms.首次使用从粗粒粒子到原子的逆向映射,对小角散射实验数据进行多尺度逆向蒙特卡罗建模的示例。
J Phys Condens Matter. 2010 Oct 13;22(40):404215. doi: 10.1088/0953-8984/22/40/404215. Epub 2010 Sep 22.
8
The CUMULUS coarse graining method: transferable potentials for water and solutes.CUMULUS 粗粒化方法:水和溶质的可传递势能。
J Phys Chem B. 2011 Aug 25;115(33):10001-12. doi: 10.1021/jp201975m. Epub 2011 Jul 28.
9
Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.多肽主链中粗粒度和细粒度自由度所支配运动的时间尺度分离与耦合
J Chem Phys. 2007 Oct 21;127(15):155103. doi: 10.1063/1.2784200.
10
Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints.采用具有热力学约束的逆蒙特卡罗方法的磷脂/胆固醇双层粗粒度模型。
J Chem Phys. 2007 Feb 21;126(7):075101. doi: 10.1063/1.2646614.

引用本文的文献

1
Development of a Meshless Kernel-Based Scheme for Particle-Field Brownian Dynamics Simulations.用于粒子场布朗动力学模拟的基于无网格核的方案的开发。
J Phys Chem B. 2024 Jul 18;128(28):6907-6921. doi: 10.1021/acs.jpcb.4c01441. Epub 2024 Jul 10.
2
HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter.HylleraasMD:一种基于域分解的混合粒子-场软件,用于软物质的多尺度模拟。
J Chem Theory Comput. 2023 May 23;19(10):2939-2952. doi: 10.1021/acs.jctc.3c00134. Epub 2023 May 2.
3
Organizations of melittin peptides after spontaneous penetration into cell membranes.
蜂毒肽自发穿透细胞膜后的构象。
Biophys J. 2022 Nov 15;121(22):4368-4381. doi: 10.1016/j.bpj.2022.10.002. Epub 2022 Oct 4.
4
Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents?反相表面活性剂能否在非极性溶剂中自组装?
J Phys Chem B. 2020 Jul 23;124(29):6448-6458. doi: 10.1021/acs.jpcb.0c04842. Epub 2020 Jul 14.
5
Computational Modeling of Realistic Cell Membranes.真实细胞膜的计算建模。
Chem Rev. 2019 May 8;119(9):6184-6226. doi: 10.1021/acs.chemrev.8b00460. Epub 2019 Jan 9.