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Exciton transport in the PE545 complex: insight from atomistic QM/MM-based quantum master equations and elastic network models

Pouyandeh , S ; Iubini, S. ; Jurinovich, S. ; Omar, Y. ; Mennucci, B. ; Piazza, F.

Physical Biology Vol. 14, Nº 6, pp. 066001 - 0660025, November, 2017.

ISSN (print): 1478-3967
ISSN (online): 1478-3975

Journal Impact Factor: (in )

Digital Object Identifier: 10.1088/1478-3975/aa90ea

Abstract
In this paper, we work out a parameterization of environmental noise within the Haken–Strobl–Reinenker (HSR) model for the PE545 light-harvesting complex, based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of various auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments. Interestingly, several cross-correlations of the latter kind, together with coupling–coupling cross-correlations, display clear low-frequency signatures in their spectral densities in the 30–70 ${
m cm}^{-1}$ region. These slow components lie at the limits of validity of the HSR approach, which requires that environmental fluctuations be faster than typical exciton transfer time scales. We show that a simple coarse-grained elastic-network-model (ENM) analysis of the PE545 protein naturally spotlights collective normal modes in this frequency range that represent specific concerted motions of the subnetwork of cysteines covalenty linked to the pigments. This analysis strongly suggests that protein scaffolds in light-harvesting complexes are able to express specific collective, low-frequency normal modes providing a fold-rooted blueprint of exciton transport pathways. We speculate that ENM-based mixed quantum classical methods, such as Ehrenfest dynamics, might be promising tools to disentangle the fundamental designing principles of these dynamical processes in natural and artificial light-harvesting structures.