Memory Effects in the Fluorescence Depolarization Dynamics Studied within the B850 Ring of Purple Bacteria

Time-dependent atomistic view on the electronic relaxation in light-harvesting system II

Aiming at a better understanding of the molecular details in light absorption during photosynthesis, spatial and temporal correlation functions as well as spectral densities have been determined. At the focus of the present study are the light-harvesting II complexes of the purple bacterium Rhodospirillum molischianum. The calculations are based on a time-dependent combination of molecular dynamics simulations and quantum chemistry methods. Using a 12 ps long trajectory, different quantum chemical methods have been compared to each other. Furthermore, several approaches to determine the couplings between the individual chromophores have been tested. Correlations between energy gap fluctuations of different individual pigments are analyzed but found to be negligible. From the energy gap fluctuations, spectral densities are extracted which serve as input for calculations of optical properties and exciton dynamics. To this end, the spectral densities are tested by determining the linear absorption of the complete two-ring system. One important difference from earlier studies is given by the severely extended length of the trajectory along which the quantum chemical calculations have been performed. Due to this extension, more accurate and reliable data have been obtained in the low frequency regime which is important in the dynamics of electronic relaxation.

Quest for spatially correlated fluctuations in the FMO light-harvesting complex

The light absorption in light-harvesting complexes is performed by molecules such as chlorophyll, carotenoid, or bilin. Recent experimental findings in some of these complexes suggest the existence of long-lived coherences between the individual pigments at low temperatures. In this context, the question arises if the bath-induced fluctuations at different chromophores are spatially correlated or not. Here we investigate this question for the Fenna-Matthews-Olson (FMO) complex of Chlorobaculum tepidum by a combination of atomistic theories, i.e., classical molecular dynamics simulations and semiempirical quantum chemistry calculations. In these investigations at ambient temperatures, only weak correlations between the movements of the chromophores can be detected at the atomic level and none at the more coarse-grained level of site energies. The often-employed uncorrelated bath approximations indeed seem to be valid. Nevertheless, correlations between fluctuations in the electronic couplings between the pigments can be found. Depending on the level of theory employed, also correlations between the fluctuations of site energies and the fluctuations in electronic couplings are discernible.

Non-Markovian theories based on a decomposition of the spectral density

For the description of dynamical effects in quantum mechanical systems on ultrashort time scales, memory effects play an important role. Meier and Tannor [J. Chem. Phys. 111, 3365 (1999)] developed an approach which is based on a time-nonlocal scheme employing a numerical decomposition of the spectral density. Here we propose two different approaches which are based on a partial time-ordering prescription, i.e., a time-local formalism and also on a numerical decomposition of the spectral density. In special cases such as the Debye spectral density the present scheme can be employed even without the numerical decomposition of the spectral density. One of the proposed schemes is valid for time-independent Hamiltonians and can be given in a compact quantum master equation. In the case of time-dependent Hamiltonians one has to introduce auxiliary operators which have to be propagated in time along with the density matrix. For the example of a damped harmonic oscillator these non-Markovian theories are compared among each other, to the Markovian limit neglecting memory effects and time dependencies, and to exact path integral calculations. Good agreement between the exact calculations and the non-Markovian results is obtained. Some of the non-Markovian theories mentioned above treat the time dependence in the system Hamiltonians nonperturbatively. Therefore these methods can be used for the simulation of experiments with arbitrary large laser fields.

Simulated data sets for single molecule kinetics: some limitations and complications of data analysis

When the fluorescence intensity of a chromophore attached to or bound in an enzyme relates to a specific reactive step in the enzymatic reaction, a single molecule fluorescence study of the process reveals a time sequence in the fluorescence emission that can be analyzed to derive kinetic and mechanistic information. Reports of various experimental results and corresponding theoretical studies have provided a basis for interpreting these data and understanding the methodology. We have found it useful to parallel experiments with Monte Carlo simulations of potential models hypothesized to describe the reaction kinetics. The simulations can be adapted to include experimental limitations, such as limited data sets, and complexities such as dynamic disorder, where reaction rates appear to change over time. By using models that are known a priori, the simulations reveal some of the challenges of interpreting finite single-molecule data sets by employing various statistical signatures that have been identified.