Fast and Accurate Numerical Methods of Electrostatic Interactions in Biomolecules

描述（由申请人提供）：静电相互作用在分子和细胞过程中起着至关重要的作用，包括突触连接的信号传递、离子运输、分子识别以及DNA、RNA和蛋白质的稳定性和功能。最重要的生物学意义是离子，分子和大分子的集体行为具有不均匀的电荷分布在一个活细胞的水拥挤的环境。这种环境的核心是水，它是一种复杂的溶剂，在离子、分子和水-生物聚合物界面附近具有非体积性质。作为分子动力学和蒙特卡罗模拟的核心计算，静电建模的主要挑战是平衡电荷之间相互作用的准确性和现实生物系统所需的效率。在全原子模拟中，对于周期边界效应可以忽略不计的大系统，Ewald方法是目前最精确的方法。不幸的是，大分子的模拟需要很大的模拟体积，使得Ewald方法和类似的方法过于昂贵，而较小的系统尺寸会损害准确性。与此同时，使用连续介质静电学对溶剂进行建模要快得多，但由于忽略了分子尺度上的不均匀性，例如溶质表面附近的原子细节，准确性受到损害。

DESCRIPTION (provided by applicant): Electrostatic interactions play an essential role in molecular and cellular processes that include signal transmission at synaptic junctions, ion-transport, molecular recognition, and stability and function of DNA, RNA and proteins. Of paramount biological importance is the collective behavior of ions, molecules, and macromolecules having inhomogeneous charge distributions in the aqueous crowded environment of a living cell. Central to this environment is water, which is a complex solvent with non-bulk properties near ions, molecules and water-biopolymer interfaces. The main challenge for modeling electrostatics, as the core calculation of Molecular Dynamics and Monte Carlo simulations, is to balance the accuracy of interactions among charges and the efficiency required for realistic biological systems. For all-atom simulations the Ewald method is currently the most accurate method for large enough system where periodic boundary effects are negligible. Unfortunately, the simulation of a macromolecule requires a large simulation volume, making the Ewald method and similar methods too expensive while a smaller system size compromises accuracy. Meanwhile, modeling the solvent using continuum electrostatics is much faster, but accuracy is compromised by neglecting molecular scale inhomogeneity, such as atomic details near the surface of the solute.