3D Finite Volume Poisson Solver For Ion Channels

FVM-based numerical solution of Poisson electrostatic equation in 3D Cartesizan coordinates

C-Library & Matlab Toolbox implement a numerical solution of Poisson equation

div(e*grad(u))=f

in Cartesizan 3D coordinates with respect to steeply varying dielectrical permittivity e. Library uses regular rectangular grid with mixed boundary conditions, FVM-based equation discretization and iterative methods for solving sparse linear system.

The solver can accommodate the severe jumps in dielectric permittivity typical of ion channels (ε=80 and ε=2 respectively for water and protein) and includes a Poisson-Boltzmann (PB) extension providing a solution of the linearized PB equation. The solver has been designed to calculate forces and potentials for single/multiple charges in model ion channel model with different parameters

MATLAB VERSION: 6.5 - 7.9

FILES:
C-LIBRARY:
COMMON.C, COMMON.H - data types, memory management
PSN_3D.C, PSN_3D.H - 3D Poisson solver

MATLAB TOOLBOX 3D:
PSN_3D_MEX.C - POISSON 3D MATLAB MEX SOURCE
PSN_3D_MAKE.M - MAKE MEX-DLL SCRIPT
PSN_3D_DEMO.M - POISSON 3D DEMO, CARTESIAN COORDINATES

FAST START:
1. Copy all files to appropriate folder
2. Make this folder to be current Matlab folder
3. Type "psn_3d_make" from Matlab command line to compile MEX for you platform
4. Type "psn_3d_demo" from Matlab command line to start demo