David Zapletal

Computer Simulation of the Anisotropy of Fluorescence in Ring Molecular Systems: Tangential vs. Radial Dipole Arrangement

Time dependence of the anisotropy of fluorescence in recently discovered cyclic antenna units of the BChl photosystem is modeled. Interaction with a bath and a static disorder here modeled as uncorrelated Gaussian disorder in the transfer integrals is taken into account. Parallel computer enviroment is used because one is forced to recalculate every physical quantity for several thousands of different realizations of disorder. Results for the ring LH4 with radial optical transition dipole arrangement are compared with those for the ring LH2 with the tangential one. The difference between LH2 and LH4 results for the static disorder in transfer integrals has an opposite sign in comparison with that one for the static disorder in local energies. Equivalent differences are shifted to a smaller times for the stronger interaction with a bath.

Computer Simulation of the Anisotropy of Fluorescence in Ring Molecular Systems: Influence of Disorder and Ellipticity

We use massively parallelized system for computer simulation of time dependence of the anisotropy of fluorescence for the ring LH2 from Rhodopseudomonas acidophila with tangential optical transition dipole arrangements. Different models of uncorrelated static disorder and also ellipticity (correlated static disorder) in local molecular energies are taken into account. Dynamical disorder, interaction with a bath, is included in Markovian approximation of the equations of motion for the so called exciton density matrix. In this paper we compare the results for two different models of the spectral density of phonon bath.

Computer Simulation of Emission and Absorption Spectra for LH2 Ring

Computer simulation of absorption and steady state fluorescence spectra for molecular system is presented. We focus on the B850 ring from peripheral cyclic antenna unit LH2 of the bacterial photosystem from purple bacteria. Uncorrelated static disorder in radial positions of molecules on the ring is taking into account in our simulations. We consider also influence of dynamic disorder, interaction with phonon bath, in Markovian approximation. Spectral responses are calculated by the cumulant-expansion method of Mukamel et al. Procedure in Fortran was created for calculation of single ring spectra within full Hamiltonian model. These new results are compared with our previous ones (within the nearest neighbour approximation model) that were obtained by software package Mathematica.