Title :
Error analysis of the Poisson P/sup 3/M force field scheme for particle-based simulations of biological systems
Author :
Marreiro, D. ; Aboud, S. ; Saraniti, M. ; Eisenberg, R.
Author_Institution :
Dept. of Electr. & Comput. Eng., Illinois Inst. of Technol., Chicago, IL, USA
Abstract :
The particle-particle-particle-mesh (P/sup 3/M) force field scheme by Hockney and Eastwood (1988) and Wordelman Ravaioli (2000) is an efficient approach to account for both the long-range and short-range electrostatic interactions in the simulation of biological systems. Resolving the particle-mesh term in real-space according to Wordelman Ravaioli (2000) and Saraniti et al. (2002) improves the original approach of Hockney et al. (1988) by allowing for the inclusion of non-periodic boundary conditions. In this work, a complete analysis of the error associated with the real space P/sup 3/M approach for biologically relevant systems is presented. Methods to improve the accuracy and efficiency of the P/sup 3/M are also discussed.
Keywords :
Poisson equation; differential equations; electrolytes; electrostatics; error analysis; finite difference methods; molecular biophysics; physiological models; stochastic processes; van der Waals forces; Poisson P/sup 3/M force field; biological system simulation; biological systems; electrostatic interactions; error analysis; nonperiodic boundary conditions; particle-based simulations; particle-mesh; particle-particle-particle-mesh; real space P/sup 3/M method; Biological system modeling; Differential equations; Electrochemical processes; Electrostatic analysis; Error analysis; Finite difference methods; Stochastic processes;
Conference_Titel :
Computational Electronics, 2004. IWCE-10 2004. Abstracts. 10th International Workshop on
Conference_Location :
West Lafayette, IN, USA
Print_ISBN :
0-7803-8649-3
DOI :
10.1109/IWCE.2004.1407398
