Irradiation-driven molecular dynamics: a review
European Physical Journal D
This paper reviews Irradiation-Driven Molecular Dynamics (IDMD)-a novel computationalmethodology for atomistic simulations of the irradiation-driven transformations of complex molecularsystems implemented in the MBN Explorer software package. Within the IDMD framework, variousquantum processes occurring in irradiated systems are treated as random, fast and local transformationsincorporated into the classical MD framework in a stochastic manner with the probabilities elaborated onthe basis of quantum mechanics. Major transformations of irradiated molecular systems (such as topologicalchanges, redistribution of atomic partial charges, alteration of interatomic interactions) and possible paths of their further reactive transformations can be simulated by means of MD with reactive force fields in particular with the reactive CHARMM (rCHARMM) force field implemented in MBN Explorer. This paper reviews the general concept of the IDMD methodology and the rCHARMM force field and provides several exemplary case studies illustrating the utilization of these methods.
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