Smoluchowski Solver @ Molecular level (SMOL)

Smoluchowski Solver provides an efficient way to solve Smoluchowski diffusion equation with Finite Element Tool Kit (FETK). It reads the potential profile from APBS or Dr. Benzhuo Lu's PB-BEM solver. It can calculate the k_on constant of an enzyme during the steady-state and time-dependent Smoluchowski diffusion ( Currently only steady-state Smoluchowski solver was released.) It is also able to output concentration values of each finite element node in the diffusion domain and the output can be viewed by OpenDX. SMOL was programmed by Yuhui Cheng , and is free for download and use. Comments from users are welcome (please include SMOL in the subject of your email).

Smoluchowski Solver @ Sub-cellular level (CSMOL)

Recently we continue developing the SMOL solver and successfully applied it to cardiac ventricular myocytes. It read meshes directly deriving from experimental EM images and predict Ca2+ time-dependent distribution, as well as its mobile or immobile buffers. Users can model the detailed 3D Ca2+ signaling transduction information by running this version of CSMOL. The output snpshots can be viewed by GMV or OpenDX. It need to libraries from Finite Element Tool Kit (FETK). Users need to download and install the most recent version of FETK before installing CSMOL. The detailed installation guide can be found in the source code. CSMOL was programmed by Yuhui Cheng, and is free for download and use. Comments from users are welcome (please include CSMOL in the subject of your email).

Please visit the following links for more information about SMOL and CSMOL:

Supporting Organizations

National Biomedical Computation Resource

Availability

Please acknowledge your use of Steady-state SMOL Solver by citing:

Cheng, Y. H., Suen, J. K., Zhang D. Q., Bond S. D., Zhang, Y. J., Song, Y. H., Baker, N. A., Bajaj, C. L., Holst, M. J. and McCammon, J. A. FiniteElement Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations. Biophys. J., 2007, 92: 3397-3406.
Song, Y. H., Y. J. Zhang, T. Y. Shen, C. L. Bajaj, J. A. McCammon, and N. A. Baker. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J.86:2017–2029. (Link)
Song, Y. H., Y. J. Zhang, C. L. Bajaj, and N. A. Baker. Continuum diffusion reaction rate calculations of wildtype and mutant acetylcholinesterase: adaptive finite element analysis. Biophys.J. 87:1558–1566. (Link)
Zhang, D. Q., J. Suen, Y. J. Zhang, Y. H. Song, Z. Radic, P. Taylor, M. J. Holst, C. Bajaj, N. A. Baker, and J. A. McCammon. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys. J. 88:1659-1665. (Link)

Please acknowledge your use of the Holst group software by citing:

M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics15, 139-191, 2001. (Link).

for FEtk (the finite element solver).

Download

The most recent (beta) version of SMOL can be obtained in source code here: smol.0.0.3.tar.gz.

The most recent (beta) version of sub-cellular SMOL can be obtained in source code and sample input here: csmol.0.0.1.tar.gz.