Eugene A. Grachev

Direct simulation of plastocyanin and cytochrome f interactions in solution

Most biological functions, including photosynthetic activity, are mediated by protein interactions. The proteins plastocyanin and cytochrome f are reaction partners in a photosynthetic electron transport chain. We designed a 3D computer simulation model of diffusion and interaction of spinach plastocyanin and turnip cytochrome f in solution. It is the first step in simulating the electron transfer from cytochrome f to photosystem 1 in the lumen of thylakoid. The model is multiparticle and it can describe the interaction of several hundreds of proteins. In our model the interacting proteins are represented as rigid bodies with spatial fixed charges. Translational and rotational motion of proteins is the result of the effect of stochastic Brownian force and electrostatic force. The Poisson-Boltzmann formalism is used to determine the electrostatic potential field generated around the proteins. Using this model we studied the kinetic characteristics of plastocyanin-cytochrome f complex formation for plastocyanin mutants at pH 7 and a variety of ionic strength values.

Computer Simulation of Plastocyanin-Cytochrome f Complex Formation in the Thylakoid Lumen

Plastocyanin diffusion in the thylakoid lumen and its binding to cytochrome f (a subunit of the membrane b6f complex) were studied with a direct multiparticle simulation model that could also take account of their electrostatic interaction. Experimental data were used to estimate the model parameters for plastocyanin-cytochrome f complexing in solution. The model was then employed to assess the dependence of the association rate constant on the dimensions of the lumen. Highest rates were obtained at a lumen span of 8–10 nm; narrowing of the lumen below 7 nm resulted in drastic deceleration of complexing. This corresponded to the experimentally observed effect of hyperosmotic stress on the interaction between plastocyanin and cytochrome f in thylakoids.

New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions

This review covers the methods of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. A direct multiparticle simulation method that simulates reactions describing interactions of ensembles of molecules in the heterogeneous interior of a cell is developed. In the models, protein molecules move according to the laws of Brownian dynamics, mutually orient themselves in the electrical field, and form complexes in the 3D scene. The method allows us to visualize the processes of molecule interactions and to calculate the rate constants for protein complex formation reactions in the solution and in the photosynthetic membrane. Three-dimensional multiparticle computer models for simulating the complex formation kinetics for plastocyanin with photosystem I and cytochrome bf complex, and ferredoxin with photosystem I and ferredoxin:NADP+-reductase are considered. Effects of ionic strength are featured for wild type and mutant proteins. The computer multiparticle models describe nonmonotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions.

Miltiparticle computer simulation of photosynthetic electron transport in the thylakoid membrane

Further developing the method for direct multiparticle modeling of electron transport in the thylakoid membrane, here we examine the influence of the shape of the reaction volume on the kinetics of the interaction of the mobile carrier with the membrane complex. Applied to cyclic electron transport around photosystem I, with account of the distribution of complexes in the membrane and restricted diffusion of the reactants, the model demonstrates that the biphasic character of the dark reduction of P700+ is quite naturally explained by the spatial heterogeneity of the system.

Software tool for advanced Monte Carlo simulation of electron scattering in EBL and SEM: CHARIOT

An advanced Monte Carlo model and software were developed to simulate electron scattering in electron beam lithography and signal formation in scanning electron microscopy at a new level of accuracy required for lithography and metrology. The model involves generation of fast secondary and slow secondary electrons, as well as generation of volume plasmons, and electron transfer between layers with regard to the difference between work functions of layers. To track SEM detector channel, the geometry of a detector and its energy transfer function were taken into account. This advanced model was used to simulate electron trajectories, deposited energy, signal from electron detector and images in SEM. Examples of simulations are presented for electron spectra, energy deposition in 50 kV maskmaking, and signals from patterned wafers in SEM.

Simulation of the fluctuations of energy and charge deposited during e-beam exposure

The stochastic nature of an energy and charge deposition process is examined using a model based on discrete loss approximation (DLA). Deposited energy deviations computed using the continuous slowing down approximation (CSDA) and DLA are compared. It is shown that CSDA underestimates fluctuations in deposited energy.

Electron beam with homogeneous solids interaction simulation using Monte-Carlo method in discrete looses approximation

Problems of backscattered and true-secondary spectra as far as transmission spectra simulation using discrete looses approximation are regarded in this article. Developed model allows acquiring the electron energy spectra from samples with complicated 3-d structure. Besides due to higher detailing of the discrete looses method one can evaluate the spatial energy and accumulated charge distributions more accurately. Simulation results are compared with the experimental ones, SEM image simulation examples are given.

Modeling of dielectric polarization during an electron beam exposure

On the basis of Monte-Carlo method a new approach to modeling of an electron interaction with a substance is offered. Some phenomena concerned with spatial energy distribution and accumulation of a charge in an irradiated sample are considered. Calculations of distributions of electric potential and resists polarization induced by an injected charge are presented. It is shown that charging is still the essential circumstance, capable to cause significant loss of accuracy in electron-beam lithography.

Modulation of the dynamics of mitochondrial calcium by buffer cytosolic proteins and plasma membrane fluxes

Buffer performance of mitochondria in intracellular calcium signaling is studied in relation to the amount of cytosolic calcium-binding proteins and calcium ion fluxes across the plasma membrane of the cell.

Computation of charge and energy deposited during electron beam irradiation depth distributions in discrete looses approximation

Problems of simulation of deposited during beam irradiation charge and energy (dose) simulation. Results obtained using Monte-Carlo method in discrete and continuous looses. Analytical approximations for depth-dose and charge-dose for Si, Au, Ag, Cu, GaN obtained.