3D离子通道的有限元模拟

Based on the work of finite element method part developed in our previous program, this renewed project aims to develop new approaches to achieve breakthrough of completely removing current limitations in computational efficiency and stability, and finnaly bridge the gap between FEM and its real application in molecular modeling area, and develop a simulation software platform for ion channels as typical systems. Ion channels are the “nano valves of life” that have selectivity for ion permeations. Ion channel is one of the most important research areas in biology. However, because there are much difficulties in the physical mathematical model as well as in numerical methods originated from the complexity of the molecular system and the multi-physics multi-scale properties of the ion transport process, so far, there still lack efficient method and software for effective simulation of the full ion permeation procedure in realistic 3D ion channels. Recently we made a first successful application of finite element method to simulation of ionic transport in in ion channel at molecular level. But there is still an urgent need to improve the stability, robustness, and practicability of the algorithms and software, as well as the accuracy of the coupled electro-diffusion model. This study is to develop more effective and stabilized finite element algorithms, including convenient and robust new approaches for mesh generation and improvement of the physical models, to finally achieve an interface-friendly, automatic meshing, stable, efficient, and accurate simulation approach for ion permeation in general channel systems.

本研究旨在在前一期项目中有限元部分的工作基础上，进一步发展新方法，完全突破计算效率和稳定性等的限制，实现有限元方法在分子模拟中的真正应用，并推出针对典型体系离子通道的模拟软件平台。离子通道是“生命的纳米阀门”，对离子通透输运具有选择性。它一直是生物学里最重要的研究领域之一。但由于其分子系统的复杂性和离子输运过程的多物理多尺度特征带来物理数学模型上以及数值方法上的困难，使得至今仍缺乏能有效模拟整个3D离子通道系统内离子通透过程的方法和软件。我们最近首次实现了有限元模拟分子水平上的离子通道内的输运过程，但有限元模拟的稳定性、强壮性和实用性以及电扩散耦合模型的准确性还需要极大提高。本项目将发展更有效的稳定的有限元方法，包括新的、方便稳健的网格产生方法，同时改进物理模型，最终实现能够方便、自动生成网格、稳定高效和准确的模拟一般通道系统中的离子输运过程。

本研究旨在在前一期项目中有限元部分的工作基础上，进一步发展新方法，完全突破计算效率和稳定性等的限制，实现有限元方法在分子模拟中的真正应用，并推出针对典型体系离子通道的模拟软件平台。离子通道是“生命的纳米阀门”，对离子通透输运具有选择性。它一直是生物学里最重要的研究领域之一。但由于其分子系统的复杂性和离子输运过程的多物理多尺度特征带来物理数学模型上以及数值方法上的困难，使得有限元模拟的稳定性、强壮性和实用性以及电扩散耦合模型的准确性还需要极大提高。本项目发展了更有效的稳定的有限元方法，包括新的、方便稳健的网格产生方法，同时改进物理模型，实现了能够方便、自动生成网格、稳定高效和准确的模拟一般通道系统中的离子输运过程。