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.

In the present paper, the evolution over time of flat nanowires (NWs) with different widths and at different temperatures is simulated by computer modeling and analyzed. The results can be applied to a wide range of physical systems as the NWs could be parts of nanoelectronic devices or nanosystems, e.g., nanofractals, which can be created during the deposition of nanoparticles on surfaces. The present paper deals with the initial stages of nanowire evolution aiming at the elucidation of the essential features of the fragmentation process. It is demonstrated that the breakup of NWs is driven by the diffusivity of the particles at periphery. The microscopic parameters characterizing the fragmentation are established. The dependence of the time required for the first fragmentation on the nanowire width is presented. The temperature dependence of the nanowire fragmentation is also examined. The dependences of the maximum number of islands created in the fragmentation process on the nanowire width and the temperature are derived. Examination of the temperature dependence of the first fragmentation instant and number of islands as well as the dependence of these quantities on the nanowire width gives the possibility to establish the relationships between experimental observations and microscopic parameters of the system.