Tetrahedral Finite Element Meshing for Bio-Molecules



The following contains applications of our tetrahedral meshing scheme [1, 2] for mouse acetylcholinesterase (mAChE) and a tetramer AChE (mAChE_4) which consists of four mAChE subunits.



1. mAChE



Figure 1: The molecular surface is extracted from solvent accessibility data with an isovalue 0.5. The color shows the distribution of the electrostatic potential over the molecular surface (red is negative, blue positive, and white neutral). The meshing is adaptive, and finer around the active gorge area.  The solvent accessibility and electrostatic potential data were generated by N. Baker et. al.



2. mAChE_4



Figure 3: Two crystal structures of the tetrameric mAChE (1C2O and 1C2B) and three intermediate structures.









Figure 4: Adaptive finite element tetrahedral meshes for a mAChE_4 molecular surface.





1.      Y. Zhang, C. Bajaj, B-S. Sohn. 3D Finite Element Meshing from Imaging Data. Accepted in the special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 2004.

2.      Y. Zhang, C. Bajaj, B-S. Sohn. Adaptive and Quality 3D Meshing from Imaging Data. Proceedings of 8th ACM Symposium on Solid Modeling and Applications, pp. 286-291. Seattle, WA. June 16-20, 2003.

3.      Y. Song, Y. Zhang, C. Bajaj, N. Baker. Continuum Diffusion Reaction Rate Calculations of Wild Type and Mutant Mouse Acetylcholinesterase: Adaptive Finite Element Analysis. Biophysical Journal, Vol. 87, No. 3, pp. 1558-1566, 2004.

4.      Y. Song, Y. Zhang, T. Shen, C. Bajaj, J. McCammon, N. Baker. Finite Element Solution of the Steady-state Smoluchowski Equation for Rate Constant Calculations. Biophysical Journal, Vol. 86, No. 4, pp. 2017-2029, 2004.


* Questions about these images, should be directed to jessica@ices.utexas.edu.