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. Graphic abstract

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4

“…Metal clusters containing up to about 30 Pt atoms preserve a spherical shape and tend to rearrange after an elongation caused by the merging of clusters of comparable size (see cycles 1-9). The sequential coalescence of larger clusters containing several tens of Pt atoms results in the formation of randomly oriented branched structures (see cycles [10][11][12][13][14][15][16][17][18][19][20]. The continuation of the irradiation and replenishment processes leads to further growth and interconnection of the branched clusters into a single metal network observed in this simulation at the 27th cycle corresponding to a PE fluence of 9.4 × 10 18 cm −2 (see Figure 5).…”

“…A breakthrough into the atomistic description of FEBID has been achieved recently by means of irradiation-driven molecular dynamics (IDMD) [13], a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems. This approach overcomes the limitations of previously used computational methods and describes FEBID-based nanostructures at the atomistic level by accounting for quantum and chemical transformation of surface-adsorbed molecular systems under focused electron beam irradiation [13][14][15][16].…”

Multiscale modeling of stochastic dynamics processes with MBN Explorer

“…The dynamics of such systems is treated employing the Langevin Equation 44,45 . If molecular systems are exposed to radiation, which may cause their damaging and chemical transformations, their dynamics can be simulated within the framework known as the irradiation driven MD (IDMD), 37,38 or reactive MD 46 . The Monte Carlo simulations of particles transport are based on similar principles, but the medium here is considered as homogeneous and static 47,48 …”

“…The multiscale approaches interlinking different methodologies describing dynamical phenomena on different temporal and spatial scales have been developed relatively recently in various areas of research [15][16][17][18][19][20][21][22][23] and have already become an essential avenue in modern computational physics, chemistry, biology, and material science. Often their development have been driven by the modern computational methods and computational powers.…”

“…[26][27][28][29] Another significant topic in nanoscience concerns the problem of controlled fabrication of nanosystems. [30][31][32][33][34] Exploiting focused photon, electrons or ion beams in the nanofabrication processes opens a wide range of possibilities for the control of these processes, see for example, recent reviews on the focused electron beam induced deposition (FEBID), 21,31,33,[35][36][37][38] nanolithography, 33,39,40 and the focused ion beam induced deposition (FIBID). 32,41 The developed methodology opens numerous possibilities for computational modeling and investigation of such systems.…”