Topical review on irradiation-driven molecular dynamics

July 26, 2021

A review paper on 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 has been published in the European Physical Journal D [1].

Within the IDMD framework [2], 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 molecular dynamics with reactive force fields, in particular with the reactive CHARMM (rCHARMM) force field [3] implemented in MBN Explorer.

The paper [1] 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.

[1] A.V. Verkhovtsev, I.A. Solov’yov, and A.V. Solov’yov, Irradiation-driven molecular dynamics: a review, Eur. Phys. J. D 75 (2021) 213
[2] G.B. Sushko, I.A. Solov'yov, and A.V. Solov’yov, Molecular dynamics for irradiation driven chemistry: application to the FEBID process, Eur. Phys. J. D 70 (2016) 217
[3] G.B. Sushko, I.A. Solov'yov, A.V. Verkhovtsev, S.N. Volkov, and A.V. Solov’yov, Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology, Eur. Phys. J. D 70 (2016) 12