Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA

Abstract

In this work an implementation of a linearized Poisson-Boltzmann equation solver based on a Finite Differences scheme on the GPU architecture is presented. The algorithm exploits the checkerboard structure of the discretized Laplace operator and follows the footprints of a popular solver called DelPhi, which is widely used in the Computational Biology community. The algorithm has been implemented using CUDA. This implementation has then been integrated with the DelPhi solver and tested over a few representative cases of biological interest. Details of the implementation as well as performance test results are illustrated.