Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation

2016 ◽  
Vol 37 (21) ◽  
pp. 1983-1992 ◽  
Author(s):  
Hiroaki Nishizawa ◽  
Yoshifumi Nishimura ◽  
Masato Kobayashi ◽  
Stephan Irle ◽  
Hiromi Nakai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Parallel Computation ◽  
Density Functional ◽  
Tight Binding ◽  
Divide And Conquer ◽  
Massively Parallel ◽  
Quantum Mechanical ◽  
Dynamics Simulations ◽  
Quantum Mechanical Molecular Dynamics

scholarly journals Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II

2021 ◽  
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chlorophyll A ◽  
Density Functional ◽  
Light Harvesting ◽  
Higher Plants ◽  
Tight Binding ◽  
Spectral Densities ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born–Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.

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