Paper Citing NAMD - Abstract
Kosztin, Ioan; Schulten, Klaus
Molecular dynamics methods for bioelectronic systems in photosynthesis
Advances in Photosynthesis and Respiration, 26:445-464, 2008
With the widespread availability of high performance computer clusters and efficient parallel molecular modeling software, molecular dynamics (MD) simulations became an indispensable tool for the study of the structure function relationship in proteins with known crystal structures. However, understanding at atomic level the functioning of membrane bound pigment-protein complexes (PPCs), which in photosynthetic organisms convert the energy of the absorbed light into electronic excitations and electrochemical potential gradients, continues to remain a challenging problem. Indeed, the theoretical description of PPCs at physiological temperature in their native environment is a complicated stochastic quantum mechanics problem that requires determining and characterizing the quantum states of the interacting pigment molecules in the presence of thermal fluctuations. Until recently most theoretical approaches for calculating the optical spectra and the electronic transfer rates of PPCs were based on empirical stochastic models in which several fitting parameters are adjusted to simulate the corresponding experimental results. In this chapter a general approach, which combines MD simulations, quantum chemistry (QC) calculations and quantum many-body theory, for predicting and characterizing charge transfer, spectral and optical properties (e.g., linear absorption and circular dichroism spectra) of PPCs is presented. The method requires only atomic-level crystal structure information and consists of three major steps: (i) the conformational dynamics of the protein matrix embedded into a fully solvated lipid bilayer is followed by means of classical MD simulations; (ii) the lowest energy quantum states of each pigment molecule are determined along the MD trajectory by means of QC calculations; and (iii) the transfer rate and/or optical spectra are determined in terms of a lineshape function which, within the cumulant approximation, can be calculated from the results of the QC calculations. To demonstrate its features, the combined MD/QC method is applied to calculate the linear optical spectra of the light harvesting complex LH2 from Rhodospirillum molischianum and the electron transfer rates in photosynthetic reaction center from Rhodobacter sphaeroides.
