Irradiation driven molecular dynamics: A review

Abstract

This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software package. Within the IDMD framework, various quantum processes occurring in irradiated systems are treated as random, fast and local transformations incorporated into the classical MD framework in a stochastic manner with the probabilities elaborated on the basis of quantum mechanics. Major transformations of irradiated molecular systems (such as topological changes, 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.

arXiv comment12 pages, 8 figures. Review paper to be published in Eur. Phys. J. D

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• Atomistic simulation of the FEBID-driven growth of iron-based nanostructures
• Irradiation driven molecular dynamics simulation of the FEBID process for Pt(PF${}_3$)${}_4$
• Role of the molecular environment in quenching the irradiation-driven fragmentation of Fe(CO)${}_5$: a reactive molecular dynamics study
• Atomistic modeling of thermal effects in focused electron beam induced deposition of Me${}_2$Au(tfac)