Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, the excitation energy transfer in the CP29 complex has been studied using ensemble-average wave packet dynamics.
Minimization of disorder as a key design principle for natural sizes of light harvesting 2 complexes
Korea Institute for Advanced Study（韩国高等研究院）；Queens College, City University of New York（纽约市立大学皇后学院）；Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）
Nanofluidics shows great promise for energy conversion and desalination applications. The performance of nanofluidic devices is controlled by liquid-solid friction, quantified by the Navier friction coefficient (FC). Despite decades of research, there is no well-established generic framework to determine the frequency dependent Navier FC from atomistic simulations. Here, we have derived analytical expressions to connect the Navier FC to the random force autocorrelation on the confining wall, from the observation that the random force autocorrelation can be related to the hydrodynamic boundary …
We formulate a comprehensive theoretical description of excitation harvesting in molecular aggregates photoexcited by weak incoherent radiation. An efficient numerical scheme that respects the continuity equation for excitation fluxes is developed to compute the nonequilibrium steady state (NESS) arising from the interplay between excitation generation, excitation relaxation, dephasing, trapping at the load, and recombination. The NESS is most conveniently described in the so-called preferred basis in which the steady-state excitonic density matrix is diagonal. The NESS properties are examined…
Oscillations in time-dependent 2D electronic spectra appear as evidence of quantum coherence in light-harvesting systems related to electronic-vibrational resonant interactions. Nature, however, takes place in a non-equilibrium steady-state, so the relevance of these arguments to the natural process is unclear. Here we examine the role of intramolecular vibrations in the non-equilibrium steady-state of photosynthetic dimers in the natural scenario of incoherent light excitation. It is found that vibrations resonant with the energy difference between exciton states do not increase the quantum y…
We present molecular mechanics {and spectroscopic} calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker, and Oregon Green 488, when th…
The vapor-liquid-solid (VLS) method is considered a plausible technique for synthesizing germanium (Ge) nanostructures (e.g. nanowires), which have a broad range of applications due to their unique electronic properties and intrinsic compatibility with silicon. However, crystallization failures and material defects are still frequently observed in VLS processes, with insufficient understanding of their underlying mechanisms due to instrumental limitations for high-resolution in-situ characterizations. Employing an accurate interatomic potential well fitted to the gold-germanium (Au-Ge) phase d…
Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting systems in purple bacteria. It is found that inclusion of long-range dipolar interactions in the two methods results in significant increases in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking…
