分子模拟中隐式溶剂模型及应用软件的新发展

Implicit solvent models are commonly adopted in molecular modeling to accelerate computing and effectively treat large time-spatial scale processes. The currently used implicit models are mainly based on the Poisson or Poisson-Boltzmann equation describing the electrostatic interactions in equilibrium state, and the algorithms are mainly based on finite difference methods. Recently, new developments (including our work) emerge in on continuum models and their computational technologies of molecular electrostatics and diffusion, but there is still a distant way to their widely applications. The goal of this program is to promote the new developments in models, methods, and software tools of implicit solvent modeling, and widen its applications. The contents are: developing a computational framework for both the equilibrium PB electrostatics and the more general but less studied non-equilibrium electro-diffusion processes; modifying the traditional mean-field PB model, and developing more accurate physical models such as variable dielectric coefficient model and beyond mean-filed models with ionic size and correlation effects; developing and implementing new numerical approaches using such as finite element/boundary element methods, and providing systematic, comprehensive, and practical software systems and tools, at the same time improving our developed software systems, and promoting their wide applications in computational chemistry/biology communities.

隐式溶剂模型是分子模拟中常用的加速计算及有效处理大时空尺度过程的方法。目前的隐式溶剂模型基本上是以描述平衡态静电相互作用的Poisson或Poisson-Boltzmann方程为基础的，算法上主要是有限差分方法。近年，包括我们工作在内，在分子体系的静电、扩散等连续模型及数值计算方面出现若干新的进展，但离广泛运用仍有相当距离。本项目旨在推动隐式模型在模型、方法、和工具上的新发展，拓展其应用范围，包括：发展从平衡态PB静电到较少研究的、更一般的非平衡态电扩散过程的计算框架；改进传统平均场静电模型，发展变系数模型及考虑离子尺寸和关联效应的超越平均场模型；发展和使用有限元/边界元等新的数值计算方法，提供系统、完整、实用的软件系统和应用工具, 同时完善我们的核心软件，推广它们在国际计算化学/生物学界的广泛应用。

隐式溶剂模型是分子模拟中常用的加速计算及有效处理大时空尺度过程的方法。常用的隐式溶剂模型基本上是以描述平衡态静电相互作用的Poisson或Poisson-Boltzmann方程为基础的，算法上主要是有限差分方法。本项目在隐式模型的模型、方法、和工具上取得新的发展，拓展其应用范围，包括：发展从平衡态PB静电到更一般的非平衡态电扩散过程（PNP模型）的计算框架；改进传统平均场静电模型，发展变系数模型及考虑离子尺寸和关联效应的超越平均场模型；发展和使用有限元/边界元等新的数值计算方法，提供系统、完整、实用的软件系统和应用工具, 同时完善我们的核心软件，扩大了在该领域的国际影响。