Michal Pudlak

Primary charge separation in the bacterial reaction center: Validity of incoherent sequential model

A description of electron transfer (ET) by the incoherent sequential model was employed to elucidate the unidirectionality of the primary charge separation process in bacterial reaction centers (RC). The model assumes that the vibrational relaxation of the medium modes is sufficiently fast and that the system relaxes to thermal equilibrium after each ET step. ET was investigated for 5-sites (molecules) arranged in two branches. Beginning at molecule 1, ET can proceed in two directions with each branch composed of two molecules. Analysis shows that the model can successfully explain the asymmetry of primary electron transfer both in the wild type and several mutants of Rb capsulatus RC. In these cases the dependence of ET asymmetry on temperature was also evaluated. It was shown that in order to obtain the correct temperature dependence of ET asymmetry in the mutants, the superexchange mechanism operating in parallel with the sequential process must be used.

Electronic structure of disclinated graphene in a uniform magnetic field

The electronic structure in the vicinity of the 1-heptagonal and 1-pentagonal defects in the carbon graphene plane is investigated for the case of hyperboloidal geometry. Using a continuum gauge field-theory model, the local density of states around the Fermi energy is calculated for both cases. In this model, the disclination is represented by a SO(2) gauge vortex and the corresponding metrics follows from the elasticity properties of the graphene membrane. To enhance the interval of energies, a self-consistent perturbation scheme is used. The Landau states are investigated and compared with the predicted values. A discussion on the influence of the Zeeman effect is included.

Electronic pathway in reaction centers from Rhodobacter sphaeroides and Chloroflexus aurantiacus.

The reaction centers (RC) of Chloroflexus aurantiacus and Rhodobacter sphaeroidesH(M182)L mutant were investigated. Prediction for electron transfer (ET) at very low temperatures was also performed. To describe the kinetics of the C. aurantiacus RCs, the incoherent model of electron transfer was used. It was shown that the asymmetry in electronic coupling parameters must be included to explain the experiments. For the description of R. sphaeroidesH(M182)L mutant RCs, the coherent and incoherent models of electron transfer were used. These two models are discussed with regard to the observed electron transfer kinetics. It seems likely that the electron transfer asymmetry in R. sphaeroides RCs is caused mainly by the asymmetry in the free energy levels of L- and M-side cofactors. In the case of C. aurantiacus RCs, the unidirectionality of the charge separation can be caused mainly by the difference in the electronic coupling parameters in two branches.

The role of accessory bacteriochlorophylls in the primary charge transfer in the photosynthetic reaction centers

In this work we present a model to elucidate the unidirectionality of the primary charge separation process in the bacterial reaction centers (RCs) where two symmetric ways of electron transfer (ET), starting from the common electron donor, are possible. We have used a model of three sites/molecules with ET beginning at site 1 with an option to proceed to site 2 or site 3. The dependence of the asymmetry in ET on the value of the sink parameter, introduced through an additional imaginary diagonal matrix element of the Hamiltonian, was investigated. Results show indeed that the unidirectionality of the ET generated in the system of three molecules depends strongly on the value of the energy levels of the accessory bacteriochlorophyll molecules.

Electron transfer driven by conformational variations

In this paper is given a general formulation of electron transfer (ET) in the system where the conformational transitions are present. The conformation changes of the system were described as a classical telegraphic noise. In the work was assumed that electron transfer reaction can be completely interrupted by the fluctuation of the electronic coupling. A functional-integral approach to the dynamics of a two-state system was used. We have got exact analytical nonperturbative expression for the probability to find electron on donor at time t. We derived two limiting cases for the electron transfer—the nonadiabatic limit and the conformational-controlled adiabatic ET case.

The influence of the molecular dynamics of exchanging groups on the electron transfer rate

Abstract The present work rests on non-adiabatic electron transfer theory. The influence of the molecular dynamics (MD) of exchanging groups on the electron transfer rate is treated. The MD of exchanging groups is described as a stochastic process with two possible states. The transfer between these two states is expressed by master equations.

Spin-orbit interaction in the graphitic nanocone

The Hamiltonian for nanocones with curvature-induced spin-orbit coupling have been derived. The effect of curvature-induced spin-orbit coupling on the electronic properties of graphitic nanocones is considered. Energy spectra for different numbers of the pentagonal defects in the tip of the nanocones are calculated. It was shown that the spin-orbit interaction considerably affects the local density of states of the graphitic nanocone. This influence depends on the number of defects present at the tip of the nanocone. This property could be applied in atomic force microscopy for the construction of the probing tip.

Effect of the molecular dynamics of exchanging groups on electron transport. Stochastic Liouville equation approach

We developed a theory of nonadiabatic electron transfer reactions in the systems where conformational variations are present. This is done with the use of the stochastic Liouville equation approach. The conformational changes of the system are described as a two-state jump Markov process. Limiting regime analytic results for rate constants are presented for high and slow Markovian modulation.

Calculation of the electronic structure near the tip of a graphitic nanocone

Abstract In earlier works, the electronic structure of the graphitic nanocone for the long distance from the tip was investigated. Here, we investigate the behaviour of the given nanostructure near the tip where in our approach hybridizations of π orbitals need to be included. In this case, the curvature dependence of π orbital energy has to be included in the model. For this purpose, we use an approximation valid for small values of the corresponding parameters. We consider different numbers of the pentagonal defects in the tip. This localization of the electrons on the nanocone tip could be used as a real application in the electron microscopes.

The influence of energy-level fluctuation and acceptor local diffusion on electron transport in biological systems

The present work is a modification of nonadiabatic electron transfer theory for fixed electron exchanging groups. We attempt to account for the role of the relative motion of exchanging groups on electron transfer processes. We also show how the fluctuation of the potential surfaces of the initial and final states of solute molecules (here, the donor-acceptor pari) affect electron transfer.