Irradiation driven molecular dynamics: A review

TL;DR

This review introduces Irradiation Driven Molecular Dynamics (IDMD), a new computational approach that simulates irradiation effects on molecular systems by integrating quantum processes into classical molecular dynamics, demonstrated through case studies.

Contribution

The paper presents the IDMD methodology and the reactive CHARMM force field, enabling atomistic simulations of irradiation-induced transformations in complex molecular systems.

Findings

IDMD effectively models irradiation-driven molecular transformations.

The rCHARMM force field allows reactive simulations under irradiation conditions.

Case studies demonstrate the method's applicability to real systems.

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.