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BioMed Research International
Volume 2015, Article ID 183918, 18 pages
http://dx.doi.org/10.1155/2015/183918
Review Article

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

1Vaccine Program, National Research Council, 1200 Montreal Road, Ottawa, ON, Canada K1A 0R6
2School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Road, Ottawa, ON, Canada K1N 6N5

Received 28 August 2014; Accepted 5 November 2014

Academic Editor: Xuguang Li

Copyright © 2015 Eric Paquet and Herna L. Viktor. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.