Repository: Freie Universit├Ąt Berlin, Math Department

Spatial averaging for small molecule diffusion in condensed phase environments

Plattner, N. and Doll, J. D. and Meuwly, M. (2010) Spatial averaging for small molecule diffusion in condensed phase environments. The Journal of Chemical Physics, 133 (4). 044506. ISSN 00219606

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Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems for typical problems arising in physical chemistry. They include (I) a CO molecule diffusing on an amorphous ice surface, (II) a hydrogen molecule probing favorable positions in amorphous ice, and (III) CO migration in myoglobin. The systems encompass a wide range of energy barriers and for all of them spatial averaging is found to outperform conventional Metropolis Monte Carlo. It is also found that optimal simulation parameters are surprisingly similar for the different systems studied, in particular, the radius of the point cloud over which the potential energy function is averaged. For H2 diffusing in amorphous ice it is found that facile migration is possible which is in agreement with previous suggestions from experiment. The free energy barriers involved are typically lower than 1 kcal/mol. Spatial averaging simulations for CO in myoglobin are able to locate all currently characterized metastable states. Overall, it is found that spatial averaging considerably improves the sampling of configurational space.

Item Type:Article
Subjects:Physical Sciences > Physics > Chemical Physics
ID Code:1256
Deposited By: BioComp Admin
Deposited On:19 Apr 2013 15:22
Last Modified:19 Apr 2013 15:22

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