Ivannikov Institute for System Programming of the RAS


Parallel Monte Carlo study on caffeine-DNA interaction in aqueous solution.

Authors

Kalugin, M.D., Teplukhin, A.V.

Abstract

Monte Carlo simulation of the caffeine-DNA interaction in aqueous solution at room temperature was carried out using parallel calculations on supercomputer. Very large simulation boxes were used containing superhelical B-DNA fragment surrounded by caffeine and water molecules. The most probable binding sites of caffeine molecules on the DNA surface as well as structural features of the respective caffeine-DNA complexes were revealed for several solutions' concentrations.

Full text of the paper in pdf

Keywords

DNA, Monte Carlo methods, biology computing, molecular biophysics, parallel algorithms

Edition

Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium, 2009.

Research Group

Compiler Technology

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