In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free energy of all possible interfaces separating solutes (e.g., proteins) from solvent (e.g., water). Previously, such a functional is minimized numerically by the level set method to determine the stable equilibrium conformations and solvation free energies. We vastly improve the speed by applying the binary level set method, in which the interface is approximated by a binary level set function that only takes value $\pm 1$ on the solute/solvent region, leading to a discrete formulation of VISM energy. The surface area is approximated by convolution of an indicator function with a compactly supported kernel. The VISM energy can be minimized by iteratively "flipping" the binary level set function in a steepest descent fashion. Numerical experiments are performed to demonstrate the accuracy and performance of our method.
翻译:在本条中,我们将二元级设定方法应用于多功能隐性溶解模型(VISM),这是一个理论和计算工具,用于研究具有复杂地形的生物分子系统。VISM中心是将溶液(例如蛋白质)与溶剂(例如水)分离的所有可能的界面的有效自由能源。以前,这种功能通过确定稳定平衡一致性和无溶解能量的定级方法从数字上最小化。我们通过应用二元级设定方法大大提高了速度,该方法的界面被一个二元级设定功能所近似,该二元级设定功能仅需要溶液/溶液区域1美元的价值,从而导致VISM能量的离散配方。表面区域被一个指标函数与一个紧凑支持的内核的组合相近。通过迭接式“滑动”将VISM能量以最陡峭的基位函数最小化。进行了数字实验,以显示我们的方法的准确性和性。