Simulation of a kink movement in homogeneous and heterogeneous DNA sequences taking into account the dissipation
-
Ludmila V. Yakushevich
Abstract
The problem of modelling the movement of a nonlinear conformational perturbation (i.e., kink) along a DNA molecule is considered taking into account the dissipation. The study of movement peculiarities is performed using a homogeneous sequence of nucleotides and a heterogeneous one consisting of two homogeneous parts separated by a boundary. Using analytic and numerical methods, it is shown that the effect of dissipation leads to a decrease of the energy of kink E, its velocity v, and the mass M. It is also shown that the consideration of the dissipation near the boundary leads to a smoothing of kink motion trajectories in the plane {z, t} in comparison with trajectories calculated without taking into account the dissipation and characterized by a sharp bend on the boundary caused by effects of reflection from the boundary or by a passage through the boundary with an increase or decrease of motion velocity.
© 2014 by Walter de Gruyter Berlin/Boston
Articles in the same Issue
- Masthead
- A polynomial algorithm for the quadratic programming problem
- A difference scheme for equations of ocean dynamics on unstructured grids
- Energy equation for certain approximate models of long-wave hydrodynamics
- Quasi-two-layer finite-volume scheme for modelling shallow water flows over an arbitrary bed in the presence of external force. II. Algorithm applications and numerical results
- Simulation of a kink movement in homogeneous and heterogeneous DNA sequences taking into account the dissipation
Articles in the same Issue
- Masthead
- A polynomial algorithm for the quadratic programming problem
- A difference scheme for equations of ocean dynamics on unstructured grids
- Energy equation for certain approximate models of long-wave hydrodynamics
- Quasi-two-layer finite-volume scheme for modelling shallow water flows over an arbitrary bed in the presence of external force. II. Algorithm applications and numerical results
- Simulation of a kink movement in homogeneous and heterogeneous DNA sequences taking into account the dissipation
