Cerebras Systems, Sunnyvale, California 94085, United States.
Department of Mathematics, Southern Methodist University, Dallas, Texas 75275, United States.
J Phys Chem B. 2022 Sep 22;126(37):7104-7113. doi: 10.1021/acs.jpcb.2c04604. Epub 2022 Sep 13.
This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy. The new implementation utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a fast multipole method based on barycentric Lagrange interpolation and dual tree traversal. Performance-critical portions of the code were implemented on a GPU. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code's accuracy and efficiency.
本文描述了 TABI-PB 2.0，这是树码加速边界积分泊松-玻尔兹曼求解器的改进版本。该代码计算了溶剂化生物分子分子表面的静电势，进一步处理得到静电溶剂化能。新的实现利用了 NanoShaper 表面三角化代码、节点补丁边界积分离散化、块预条件器以及基于重心拉格朗日插值和对偶树遍历的快速多极方法。代码的性能关键部分在 GPU 上实现。针对蛋白 1A63 和两种病毒衣壳（Zika、H1N1）的数值结果证明了该代码的准确性和效率。
