Mark Thompson, Ph.D.

Dr. Thompson is an expert in theoretical and computational chemistry.  He has published and spoken widely in the areas of photosynthesis, molecular recognition, and the development of hybrid QM/MM methods.  He has 20 years experience developing and implementing novel algorithms to solve challenging scientific and industrial problems in computational chemistry, drug modeling, scientific visualization, and enterprise business software systems.  

He lives in Seattle Washington.

At Planaria, he authored the ArgusLab molecular modeling program currently used by more than 20,000 scientists and students worldwide. 

As a Chief Research Scientist for the Department of Energy at Pacific Northwest National Laboratory, he developed new algorithms for modeling solvent effects by combining quantum mechanics with classical mechanics.  These methods were used to simulate molecules that sequester radionuclides from complex waste.  He also developed genetic algorithm approaches for automating the design of molecules with targeted properties.  

As a Staff Scientist at Brookhaven National Laboratory, he was one of the first to apply quantum mechanics to study the photochemistry of the entire bacterial photosynthetic reaction center and explain the photochemistry of the bacteriochlorophyll-b dimer that initiates the primary photochemical event.  

Selected publications & presentations:

1. Poster Presentation:  Molecular docking using ArgusLab: An efficient shape-based search algorithm and the AScore scoring function.  Fall 2004 ACS meeting, Philadelphia, August, 2004.  

2. Submitted Talk: “Docking ligands into flexible proteins”, G. D. Purvis and Mark Thompson, Spring 2003 ACS meeting, New Orleans,  March 27, 2003.

3. Book: “Combined Quantum Mechanical and Molecular Mechanical Methods”  Eds. Gao, J, and Mark A. Thompson. ACS Symposium Series 172, 1997.

4.  Feller, D.; Thompson, M. A.; and Rick A. Kendall "A Theoretical Case Study of Substituent Effects and Microsolvation on the Binding Specificity of Crown Ethers" J. Phys. Chem. A 1997, 101, 7292-7298.

5.  Thompson, M. A. "QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone" J. Phys. Chem. 1996, 100, 14492-14507.

6.  Thompson, Mark A. "Molecular Dynamics Study of Li and Still's New Rigidified 18-Crown-6 Derivative Using a QM/MM Method" Int. J. Quantum Chemistry, 1996, 60, 1133-1141.

7.  Thompson, Mark A. "Studies of Molecular Recognition Using QM/MM Methods. The Potential of Mean Force for the Association of K+ with 1,2-Dimethoxyethane in Aqueous Solution" Proceedings from the 34th Hanford Symposium on the Environment 1996.

8.  Brooks, B. R.; Field, M. J.; Gao, J.; and Mark A. Thompson "Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution" in Pacific Symposium on Biocomputing Eds. L. Hunter and T. E. Klein. 1996. World Scientific, New Jersey.

9.  Thompson, Mark A. " A QM/MM Molecular Dynamics Study of the Potential of Mean Force for the Association of K+ with Dimethylether" in Aqueous Solution" J. Am. Chem. Soc., 1995, 117, 11341-11344.

10.  Thompson, Mark A. and Gregory K. Schenter. "Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization" J. Phys. Chem. 1995, 99, 6374-6386.