Synergetic mechanisms of structural regulation of the electron transfer and other reactions of biological macromolecules

Use of a system of differential equations to analyze the functioning of a catalytic bio macromolecule under non equilibrium conditions

The aim of the work is to analyze the response of a biomolecule to an external influence based on the study of its hidden states by identifying differential equations with constant coefficients.

The relevance of the work lies in the fact that often the main reaction of an object to an external action can be represented as a sum of various exponential functions with a common starting point and a material balance equation. In this case, the response of an object to an external action corresponds to a system of differential equations with constant coefficients. This character of the main reaction may be due to the influence of the hidden properties of the object, which play the role of regulatory parameters.

The problem is that the hidden factors and the system of differential equations are not identified. As an object, isolated reaction centers (RC) of the bacteria Rhodobacter sphaeroides, which possess the above properties, has used. Their structure is well studied.

As result of studying of photo excitation processes of the reaction center has shown that electron transfer kinetics (the main reaction) can be approximated by three normalized exponential functions. Program was developed to identify for four differential equations of electron transfer and the balance equation, the behavior of hidden states of the reaction center.

It was concluded that time the dependence the probability density of finding an electron in different conformational states of the reaction center characterizes the space-time changes in the structure of the reaction center.

Theory of single-file multiparticle diffusion in narrow pores

Single-file diffusion of multiple strongly interacting particles in a one-dimensional pore is described within a general analytical framework. The theory accounts for nonequilibrium conditions, explicit particle-particle interactions, external potential acting on the particles and the fluctuations of the number of particles due to their exchange with external equilibrium reservoirs. It is shown that the problem can be reduced to a closed hierarchical set of partial differential equations of increasing dimensionality, which can be solved numerically. Our framework allows computing any macroscopic characteristic of multiparticle diffusion in the pore. It is shown that the pore occupancy probabilities and the current are rational functions of external concentrations in the steady state. The theory is tested on a simplified model of the narrow rigid pore inspired by the selectivity filter of biological ion channel. Perspectives and limitations of the theory are discussed.