Biomedical subjects

A M Dykhne

Publications and source records attributed to A M Dykhne.

3 recordsLinked to original sources

PubMed1991

Computer simulation of DNA supercoiling.

We treat supercoiled DNA within a wormlike model with excluded volume. A modified Monte Carlo approach has been used, which allowed computer statistical-mechanical simulations of moderately and highly supercoiled DNA molecules. Even highly supercoiled molecules do not have a regular shape, though with an increase in writhing the chains look more and more like branched interwound helixes. The averaged writhing (Wr) approximately 0.7 delta Lk. The superhelical free energy F is calculated as a function of the linking number. Lk. The calculations have shown that the generally accepted quadratic dependence of F on Lk is valid for a variety of conditions, though it is by no means universal. Significant deviations from the quadratic dependence are expected at high superhelical density under ionic conditions where the effective diameter of DNA is small. The results are compared with the available experimental data.

Computer Simulation↗

PubMed1989

Variance of writhe for wormlike DNA rings with excluded volume.

We have calculated the variance of the equilibrium distribution of a circular wormlike polymer chain over the writhing number, less than (Wr)2 greater than, with allowance for the excluded volume effects. Within this model the less than (Wr)2 greater than value is a function of the number of Kuhn statistical segments, n, and the chain diameter, d measured in Kuhn statistical lengths, b. Simulated DNA chains varied from 200 to 10,000 base pairs and the d value varied from 0.02 to 0.2. Theory predicts a considerable ionic strength dependence of the DNA superhelix energy as a consequence of the change in the DNA diameter. A comparison with the available experimental data has yielded an estimate of the DNA torsional rigidity, the Kuhn statistical length, and the effective diameter of the double helix under conditions of the complete screening of the DNA electrostatic potential.

DNA↗

PubMed1988

Effect of excluded volume on topological properties of circular DNA.

We have performed computer simulations of closed polymer chains with allowance for the excluded volume effects within the framework of the free-joint model. The probability of knot formation, the linking probability of a pair of chains and the variance in the writhing number proved to be significantly affected by the excluded volume effects. This is true even for DNA with completely screened charges for which the b/d ratio (where b is the Kuhn statistical length and d is the diameter of the double helix) is as large as 50. Allowance for the electrostatic repulsion (change of the DNA effective diameter d) further increases the effects. The most dramatic dependence on d is found for the probability of knot formation. The data on the dependence of the variance of writhing, mean value of (WR)2, on d indicate that the DNA superhelix energy should be significantly ionic strength-dependent. Special calculations have shown that the free-joint model underestimates the mean value of (Wr)2 value by about 20% as compared with the wormlike model.

DNA, Circular↗