Conformation Control of DNA Molecules by Means Geometric and Physical Parameters

A conceptual approach to the problem of managing spatial configurations of DNA molecules is considered. The work is problematic in nature and is a synthesis of the authors’ research in the field of modeling the behavior and structure of DNA by the methods of the mechanics of a deformable solid. The subject of research in this paper is the question of the applicability of methods of control theory to a living object by the example of a DNA molecule. The paper considers both issues of controllability on examples of the influence of the parameters of a molecule on its configuration, and questions of observability and identification of parameters of a molecule, based on the visible configuration in the natural environment. A brief review of the authors’ results in terms of adaptation to the objects of research of existing and development of new mathematical models of deformable elastic objects with regard to their internal structure is given. The proposed approach is based on the concept of transition using known methods of molecular dynamics from a multi-element discrete medium to a continuum containing momentary stresses. To this end, in previous works, the authors obtained the dependence of the components of the strain tensors, force and moment stresses on various types of interatomic interaction potentials (LennardJones potential, Born-Meyer potential, etc.). The need to choose as the base model of a continuum containing momentary stresses is dictated by the peculiarities of the main object of study - nucleic acid molecules and biopolymers - which have several degrees of freedom of rotational motions. Also, as an example, we consider the case for which the reduction from the three-dimensional problem of the asymmetric theory of elasticity to a one-dimensional one was carried out by splitting the three-dimensional problem into a set of two-dimensional and one-dimensional problems. The kinematic parameters that are necessary to attract in order to obtain a closed system of equations of the one-dimensional moment theory of rods with the system of Kirchhoff’s differential equations are indicated. The remaining geometrical values are found from the relations defining them. The proposed approach is consistent with current trends in the field of molecular modeling in biophysics and physico-chemical biology, and it seems promising in solving the problems of controlling genetic and biochemical processes involving DNA.

DNA conformation management, elastic rod, identification of parameters of dynamic systems

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