Abstract
Numerical solution of the quantum mechanical Schrodinger 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.
Highlights
Application of ab initio quantum-chemical algorithms aiming at numerical solutions of the Schrdinger equation for molecules has served as a polygon for testing high-performance computers for a long period of time
In attempts to reduce the high scaling of ab initio methods and novel numerical algorithms based on fragmentation of a large molecular aggregate have begun to extend the traditional quantum-chemistry approaches
We show here how this method can be applied for a photosynthetic light harvesting (LH)-reaction centers (RC) complex comprising a half of million atoms
Summary
Application of ab initio quantum-chemical algorithms aiming at numerical solutions of the Schrdinger equation for molecules has served as a polygon for testing high-performance computers for a long period of time. That is why the routine calculations are usually conducted for moderate sized systems containing several hundreds of atoms in total. They usually scale well for up to 256 cores on the Infiniband clusters. In this respect characterization of the photosynthetic molecular machines responsible for conversion of solar energy to chemical energy presents one of the greatest challenges for quantumbased simulations. In attempts to reduce the high scaling of ab initio methods and novel numerical algorithms based on fragmentation of a large molecular aggregate have begun to extend the traditional quantum-chemistry approaches. In this work we check the corresponding options using current implementation of the FMO algorithms in modern facilities utilizing both large and small computational clusters
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