Paper Citing NAMD - Abstract
Nowak, Wieslaw; Marszalek, Piotr E.
Molecular Dynamics Simulations of Single Molecule Atomic Force Microscope Experiments
COMPUTATIONAL CHEMISTRY: REVIEWS OF CURRENT TRENDS, VOL 9, 9:47-83, 2005
The ultimate goal of nanosciences is to develop tools for spatial and chemical control of single molecules. A number of experimental techniques have emerged in recent years which allow for mechanical manipulations of single molecules including single molecule fluorescence, optical and magnetic tweezers, atomic force spectroscopy. Proper understanding of experimental results requires adequate theory. In this paper we present an overview of recent advances and trends in applications of computer simulations aimed at understanding of atomic force microscope (AFM) experiments. Special attention is devoted to those variants of classical molecular dynamics (MD) simulations, such as steered MD or biased MD, which are particularly helpful in interpretation of experimental data obtained for single biopolymer molecules. A short meta-review (review of recent reviews) of advances in the MD technology is also presented.
