Modeling of kinetic processes in biological systems

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Abstract

Endocytosis of viruses and nanoparticles. We study cellular uptake of viruses and nanoparticles via clathrin-mediated endocytosis focusing on how the kinetics of this process depends on the virus/nanoparticle size. Rate of bimolecular reactions in crowded cytoplasm. We developed a theory of bimolecular reactions in crowded cytoplasm, which explains how the presence of crowders modifies the reaction rate compared to that in the absence of crowding agents. Stochastic gating in insect respiration. We proposed a model that accounts for the effect of stochastic gating on transport of oxygen molecules in insect respiration. Our analysis explains how the rates of closing and opening of the stochastic gate affect the diffusive flux of oxygen molecules. Transport in channels of varying width. Our analysis of transport in channels with corrugated walls focuses on the slowdown of diffusion in such channels, compared to that in channels with flat walls, due to entropy wells and barriers. Trapping by striped channel walls. The major finding of our analysis of trapping of diffusing particles by striped channel walls is that the effective trapping rate of the wall is independent of the wall curvature. This rate is determined only by the stripe surface fraction.