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EnCurv:分子动力学模拟中保持全局膜曲率的简单技术。

EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.

机构信息

Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028 Kyiv, Ukraine.

Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France.

出版信息

J Chem Theory Comput. 2021 Feb 9;17(2):1181-1193. doi: 10.1021/acs.jctc.0c00800. Epub 2021 Jan 29.

Abstract

The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into the system and without restrictions on lateral and transversal lipid diffusion and distribution. The current implementation is limited to the membranes curved in a single plane but generalization to arbitrary curvature and membrane topology is possible. The method is simple, easy to implement, and scales linearly with the system size. EnCurv is agnostic to the force field, simulation parameters, and membrane composition. The proof of principle implementation (https://github.com/yesint/EnCurv) is compatible with the majority of modern simulation packages and shows consistent results on the model systems.

摘要

介绍了一种在分子动力学模拟中保持膜曲率的 EnCurv 方法。该方法允许在单个平面内弯曲的脂质膜的扇形区域中保持任何所需的曲率,而不会向系统中添加任何非物理相互作用,也不会限制侧向和横向脂质扩散和分布。当前的实现仅限于在单个平面内弯曲的膜,但可以推广到任意曲率和膜拓扑。该方法简单、易于实现,并且与系统大小呈线性比例缩放。EnCurv 与力场、模拟参数和膜组成无关。原理实现的证明(https://github.com/yesint/EnCurv)与大多数现代模拟包兼容,并在模型系统上显示出一致的结果。

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