title: Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.
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.
authors.affiliation: Vaccine Program, National Research Council, 1200 Montreal Road, Ottawa, ON, Canada K1A 0R6 ; School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Road, Ottawa, ON, Canada K1N 6N5.
authors.forename: Eric
authors.initials: E
authors.lastname: Paquet
authors.affiliation: School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Road, Ottawa, ON, Canada K1N 6N5.
authors.forename: Herna L
authors.initials: HL
authors.lastname: Viktor
mesh_terms: D039301:Computers, Molecular; D006801:Humans; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009010:Monte Carlo Method