Mathematical Modeling in Biology: Part 2. Models of Protein Interaction Processes in a Photosynthetic Membrane

The second part of the article concerns agent-based, multiparticle, Brownian and molecular dynamic models. In these models, the motion and interaction of individual proteins—electron carriers (Brownian multiparticle models) and individual atoms in molecules—electron carriers and their complexes (molecular dynamics) are described based on the apparatus of Brownian and molecular modeling. Direct multiparticle models explicitly simulate the Brownian diffusion of mobile protein carriers and their electrostatic interactions with multienzyme complexes, both in solution and in the interior of a biomembrane. Analysis of these models reveals the role of diffusion and electrostatic factors in the regulation of electron transport, the effect of the of reaction volume geometry, and ionic strength and pH of the cell medium on the rate of electron transport reactions between protein carriers. Through joint application methods of kinetic and Brownian multiparticle modeling make it possible to study the regulation mechanisms of electron transport processes at the subcellular and molecular levels and also mechanisms of electron-flow switching in plant and algae cells and to evaluate the optimal conditions for the obtainment of target products in microalgae cells, e.g., hydrogen as an alternative fuel. The prospects for various methods of mathematical modeling used to study subcellular systems are discussed in the conclusion. The paper is based on the results obtained at the Department of Biophysics, Biological Faculty, Moscow State University.