| Issue |
Europhys. Lett.
Volume 34, Number 6, May III 1996
|
|
|---|---|---|
| Page(s) | 471 - 476 | |
| Section | Cross-disciplinary physics and related areas of science and technology | |
| DOI | https://doi.org/10.1209/epl/i1996-00481-1 | |
| Published online | 01 September 2002 | |
A method for the computer simulation of the free-energy difference in conformational changes of polyelectrolytes. Application to the B- to Z-DNA transition
Departamento de Química-Física, Facultad de Ciencias Químicas,
Universidad Complutense de Madrid, E-28040 Madrid, Spain
Received:
11
December
1995
Accepted:
2
April
1996
A method for calculating the free-energy difference between two dissimilar
conformational states of a nucleic acid is proposed.
The procedure is especially suited for computer simulation.
The calculation of the free energy of each conformer is split into two
steps; the first one consists in the build-up of the uncharged
conformers while the other one —which leads to the more important
contribution— corresponds to the charging process of such structures.
We report preliminary results on the application of the method to evaluate
the free-energy difference for the salt-induced conformational
change between the B and Z forms of DNA.
This is the first rigorous evaluation of the 
dependence on the added salt concentration.
PACS: 87.15.By – Structure, bonding, conformation, configuration, and isomerism of biomolecules / 87.15.He – Molecular dynamics and conformational changes / 61.20.Ja – Computer simulation
© EDP Sciences, 1996
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