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Registration Number

0223U000752, 0121U111838 , R & D reports

Title

Computer simulations of the dynamics of a DNA double helix and its ion-hydration environment in an external electric field

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Head

Bubon Tetiana Leonidivna,

Registration Date

19-01-2023

Organization

М.М.Bogolyubov Institute of Theoretical Physics of the National Academy of Sciences of Ukraine

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 The aim of the present work is to study the dynamics of a DNA macromolecule under the action of an external electric field, as well as the interaction of DNA atomic groups with its ion-hydrate environment within modern computer simulation methods. The DNA macromolecule in a cell nucleus is situated in a solution, which consists mainly of water molecules and counterions. The composition of this solution plays a crucial role in the stabilization of DNA as a double helix, determines its shape, and also affects its stability. Accordingly, if the nature of this solution is somehow changed, it will affect all subsequent processes of DNA function in the cell, as well as the genetic information transfer processes. In the interaction of DNA with its ion-hydrate environment, two important aspects can be distinguished - interaction with counterions, as well as interaction with the hydration shell (water molecules). In the first part of the present work, classical all-atom molecular dynamics will be used to study the mechanics of the DNA macromolecule under the action of an external electric field. The system consisting of a DNA macromolecule in an aqueous-ionic solution will be simulated for different values of frequency and amplitude of the external periodic electric field. From the obtained simulation results, the conformational parameters of the DNA double helix will be calculated, in particular, the parameters of nucleic bases in complementary pairs, as well as the parameters of base-pair movements in general with respect to the other base pairs. The frequency of the external field at which the amplitude of oscillations of these parameters is maximal will also be found. The second part of the work will investigate the interaction of the DNA macromolecule with its hydration shell. The vibrational density of states for water molecules with respect to the DNA atomic groups in different hydration shells of the macromolecule will be calculated.

Product Description

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Zdorevskyi Oleksii Oleksandrovych

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2023-01-19