论文标题
简单:一种新型的成对潜力,用于与单位模型的隐式溶剂脂质模拟
SiMPLISTIC: A Novel Pairwise Potential for Implicit Solvent Lipid Simulations with Single-site Models
论文作者
论文摘要
具有成对相互作用的隐式溶剂,粗颗粒模型可以访问分子动力学模拟中最大的长度和时间尺度,这是因为与大量溶剂颗粒的相互作用没有相互作用,模型分子中的相互作用位点较少,并且缺乏快速的亚物质自由度。在本文中,我们描述了隐式水中脂质的最大粗粒模型。该模型被称为简单化,它缩写为单点模型与脂质的成对相互作用的隐式溶剂与可调固有曲率的隐式相互作用。简单的脂质快速自我组装成现实的非层状和层状相,例如倒置的胶束和双层,该相的自发曲率由模型的单个自由参数确定。与层状脂质的模型膜模拟显示出令人满意的液体和凝胶相,没有插头或倾斜。脂质模型遵循经验研究建议的刚体动力学,并产生与实验和其他模拟一致的双层弹性特性。简单化的还可以模拟脂质的混合物,它们的填料参数或长度有所不同,后者导致疏水不匹配驱动的结构域的形成现象。由于其速度,概念和计算简单性以及多功能性,该模型具有很大的范围。应用的应用可能从大规模的基于脂质的系统的学术和工业研究的模拟范围,例如溶晶液晶,生物学和生物映射膜,用于药物和基因递送的矢量,快速,轻巧,交互式模拟,以获得对自我组合,脂质多态性多态性多态性多态性多态性组织的见解,
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller number of interaction sites in the model molecules, and the lack of fast sub-molecular degrees of freedom. In this paper, we describe a maximally coarse-grained model for lipids in implicit water. The model is called SiMPLISTIC, which abbreviates for Single-site Model with Pairwise interaction for Lipids in Implicit Solvent with Tuneable Intrinsic Curvature. SiMPLISTIC lipids rapidly self-assemble into realistic non-lamellar and lamellar phases such as inverted micelles and bilayers, the spontaneous curvature of the phase being determined by a single free parameter of the model. Model membrane simulations with the lamellar lipids show satisfactory fluid and gel phases with no interdigitation or tilt. The model lipids follow rigid body dynamics suggested by empirical studies, and generate bilayer elastic properties consistent with experiments and other simulations. SiMPLISTIC can also simulate mixtures of lipids that differ in their packing parameter or length, the latter leading to the phenomenon of hydrophobic mismatch driven domain formation. The model has a large scope due to its speed, conceptual and computational simplicity, and versatility. Applications may range from large-scale simulations for academic and industrial research on various lipid-based systems, such as lyotropic liquid crystals, biological and biomimetic membranes, vectors for drug and gene delivery, to fast, lightweight, interactive simulations for gaining insights into self-assembly, lipid polymorphism, biomembrane organization etc.