Department of Mathematics, West Chester University of Pennsylvania, West Chester, Pennsylvania 19383, USA.
Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487, USA.
Math Biosci Eng. 2020 Sep 21;17(6):6259-6277. doi: 10.3934/mbe.2020331.
DelPhi is a popular scientific program which numerically solves the Poisson-Boltzmann equation (PBE) for electrostatic potentials and energies of biomolecules immersed in water via finite difference method. It is well known for its accuracy, reliability, flexibility, and efficiency. In this work, a new edition of DelPhi that uses a novel Newton-like method to solve the nonlinear PBE, in addition to the already implemented Successive Over Relaxation (SOR) algorithm, is introduced. Our tests on various examples have shown that this new method is superior to the SOR method in terms of stability when solving the nonlinear PBE, being able to converge even for problems involving very strong nonlinearity.
DelPhi 是一个流行的科学程序,它通过有限差分法数值求解生物分子在水中的泊松-玻尔兹曼方程(PBE)的静电势和能量。它以其准确性、可靠性、灵活性和效率而闻名。在这项工作中,引入了一个新版本的 DelPhi,该版本使用一种新的牛顿类方法来求解非线性 PBE,除了已经实现的超松弛(SOR)算法。我们在各种示例上的测试表明,这种新方法在求解非线性 PBE 时的稳定性方面优于 SOR 方法,即使对于涉及非常强非线性的问题也能够收敛。