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首页> 外文期刊>Computer Methods in Applied Mechanics and Engineering >A fast variational method for the construction of resolution adaptive C~2-smooth molecular surfaces
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A fast variational method for the construction of resolution adaptive C~2-smooth molecular surfaces

机译：构造分辨率自适应C〜2光滑分子表面的快速变分方法

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摘要

We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo-atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C~2 interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C~2 smooth and resolution adaptive molecular surfaces.
机译：从蛋白质和核酸数据库中的原子坐标开始，我们提出了一种变通的方法来平滑分子（蛋白质，核酸）的表面结构。传统上用于了解蛋白质和核酸折叠过程的分子动力学（MD）模拟是基于分子力场，并且需要这些分子表面的平滑模型。为了加速MD模拟，一种流行的方法是采用粗糙的颗粒分子模型，该模型通过伪原子表示具有相似物理特性的原子簇，从而产生较粗糙的分子表面。我们考虑生成这些混合分辨率或自适应分子表面。我们的方法是通过最小化一阶能量函数（它还包括一个正则项）来最小化化学上不可行的分子表面口袋或隧道状伪像的发生，从而在水平集公式中推导出一般形式的二阶几何偏微分方程。为了获得更高的计算效率，还使用了快速三次B样条C〜2插值算法。然后使用窄带三三次B样条能级设置方法提供C〜2平滑和分辨率自适应的分子表面。

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