Multi-Scale Supercomputing of Large Molecular Aggregates: A Case Study of the Light-Harvesting Photosynthetic Center

Alexander V. Nemukhin; Igor V. Polyakov; Alexander I. Moskovsky

doi:10.14529/jsfi150403

Authors

Alexander V. Nemukhin Lomonosov Moscow State University, Moscow
Igor V. Polyakov Lomonosov Moscow State University, Moscow
Alexander I. Moskovsky Lomonosov Moscow State University, Moscow

DOI:

https://doi.org/10.14529/jsfi150403

Abstract

Numerical solution of the quantum mechanical Schrödinger equation is required to model electronic excitations in the light-harvesting photosynthetic complexes composed of up to millions of atoms. We demonstrate that the modern supercomputers can be used to treat electronic structure calculations in such large molecular aggregates if proper multi-scale massive-parallel approaches are applied. We show that the three-level parallelization scheme based on the novel numerical algorithms assuming fragmentation of a light-harvesting complex allows us to reduce considerably the high scaling of ab initio quantum chemistry methods. More specifically we applied the time-dependent density functional theory based upon the fragment molecular orbital presentation (FMO-TDDFT) implemented at the modern supercomputers to obtain a realistic estimate of the electronic excitation in the complex. The application shows a good overall scaling.

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