Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

Abstract

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system.

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

“…The MBN Explorer program 2 [26,28,29] is an advanced software package for complex biomolecular, nano-and mesoscopic system simulations. It is suitable for classical molecular dynamics, Monte Carlo [30][31][32][33][34] and relativistic dynamics simulations [35][36][37][38] of a large range of molecular systems, such as nano- [39,40] and biological systems, nanostructured materials [41,42], composite/hybrid materials [43][44][45][46], gases, liquids, solids and various interfaces [47,48], with sizes ranging from atomic to mesoscopic. Among applications of MBN Explorer are also the simulations of thermo-mechanical damage in biological systems, e.g.…”

Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion

“…The stochastic motion of MRE11 and NBS1 protein is alternatively simulated by employing the kinetic Monte Carlo approach [ 40 , 41 ] using MBN Explorer [ 42 ], and the first hitting time is measured from the produced trajectories. The kinetic Monte Carlo algorithm works by defining a 3D grid for coarse grained MRE11 and NBS1 particles to move on.…”

Modeling of cellular pearl chain formation using a double photoconductive layer biochip

“…To date, this method is utilized to simulate motion of micro or nanoparticles such as magnetic fluid particles [13], colloidal nanoparticles [14], and silver nanoparticles [15]. Detailed forces related to the applied electric field have been described below.…”