Molecular dynamics, Monte Carlo simulations, and langevin dynamics: a computational review

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DOIResolve DOI: https://doi.org/10.1155/2015/183918
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  1. National Research Council of Canada. Information and Communication Technologies
FormatText, Article
Journal titleBioMed Research International
ISSN2314-6133
2314-6141
Volume2015
Pages1–18
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.
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PublisherHindawi Publishing Corporation
LanguageEnglish
Peer reviewedYes
NPARC number23001557
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Record identifier3d35879a-c4d3-4c24-a06c-7e67a97bf7df
Record created2017-03-06
Record modified2020-05-30
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