DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex

2020 ◽  
Vol 11 (20) ◽  
pp. 8660-8667
Author(s):  
Sayan Maity ◽  
Beatrix M. Bold ◽  
Jigneshkumar Dahyabhai Prajapati ◽  
Monja Sokolov ◽  
Tomáš Kubař ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Light Harvesting ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

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.

scholarly journals Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II

2015 ◽  
Vol 17 (22) ◽  
pp. 14405-14416 ◽  
Author(s):  
Sandro Jurinovich ◽  
Lucas Viani ◽  
Ingrid G. Prandi ◽  
Thomas Renger ◽  
Benedetta Mennucci
Keyword(s):  
Molecular Dynamics ◽  
Photosystem Ii ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Light Harvesting ◽  
Optical Spectra ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

Only going beyond the static crystal picture through molecular dynamics simulations can a realistic excitonic picture of the light-harvesting complex CP29 be obtained using a multiscale polarizable QM/MM approach.

Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II

2021 ◽  
Vol 23 (12) ◽  
pp. 7407-7417
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Light Harvesting ◽  
Spectral Densities ◽  
Light Harvesting Complex ◽  
Complex Ii ◽  
Light Harvesting Complex Ii ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Remarkable Agreement

The site energies and spectral densities of the major light-harvesting complex LHCII have been determined using QM/MM molecular dynamics simulations. In particular, the spectral densities show a remarkable agreement with experimental findings.

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.

scholarly journals Chromophore arrangement in light-harvesting complex II influenced by the protein dynamics on the microsecond time scale

2019 ◽  
Vol 205 ◽  
pp. 09039
Author(s):  
Sebastian Thallmair ◽  
Siewert J. Marrink
Keyword(s):  
Molecular Dynamics ◽  
Energy Transfer ◽  
Protein Dynamics ◽  
Thylakoid Membrane ◽  
Light Harvesting ◽  
Coarse Grained ◽  
Light Harvesting Complex ◽  
Complex Ii ◽  
Light Harvesting Complex Ii ◽  
Dynamics Simulations

Coarse-grained molecular dynamics simulations of light-harvesting complex II in thylakoid membrane reveal its microsecond dynamics. We analyze the fluctuations of the relative chromophore orientations which set the stage for the energy transfer.

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