Paper Citing NAMD - Abstract
Matthai, C. C.; March, N. H.
The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes
THEORETICAL CHEMISTRY ACCOUNTS, 130:1155-1167, DEC 2011
The review draws on earlier interests of the authors and especially in two areas. The first of these consists of modelling polymers in different solvent conditions using Langevin molecular dynamics. For fully flexible polymers, it was found that in good solvents the polymer conformation had extended structure while in poor solvents, a globular-like conformation resulted. Stiffness in semi-flexible polymers allows for the description of a polymer with non-zero persistence length, thereby allowing biological polymers to be modelled. The second area focuses on the transport of DNA through cell membranes and in the related area of using molecular dynamics simulations in understanding biomolecular processes. Finally, under future directions, some of the areas in which techniques from condensed matter have been used in recent years point to how they may be employed in the future.
