Preface

MesoBioNano (MBN) Explorer is a multi-purpose software package for advanced multiscale simulations of complex molecular structure and dynamics. It has many unique features and a wide range of applications in physics, chemistry, biology, materials science, and related industries. A variety of algorithms and interatomic potentials implemented in the program allow for the simulation of the structure and dynamics of a broad range of systems with the sizes from the atomic up to the mesoscopic scales. This provides the necessary molecular level quantitative details for the construction of the multiscale approaches in many areas of modern research. MBN EXPLORER is equipped with a special multi-task toolkit—the MBN STUDIO, which enables construction of input files, simple start of simulations, as well as visualization and analysis of the results obtained. The systematic description of the capabilities of these universal and powerful software packages and their applications in numerous areas of research are discussed in the book chapters. This book attempts to present the state-of-the-art understanding of the mechanisms of clustering, self-organization, growth and structure formation in complex MBN systems on the basis of modern theoretical and computational physics approaches. Due to the large diversity of the systems and processes, the book does not even consider touching many of them. Instead, it is focused on the description of the key research methodologies that proved to be successful and led to the better understanding of some of the above-mentioned problems. These methodologies often rely on novel computational approaches, algorithms and high-performance computing, which are introduced and discussed via the exemplar case studies of clustering, self-organization and structure formation in various MBN systems. The material is arranged as follows. In the introductory chapter we describe the field of MBN science, introduce main concepts and computation approaches related to the field, explain the basic features of MBN EXPLORER and MBN STUDIO. Chapter 2 presents a summary of main theoretical methods on which MBN EXPLORER is based, elaborates the key algorithms implemented in the package, outlines the basic ideas towards the multiscale description of MBN systems by means of kinetic Monte Carlo approach and the irradiation driven molecular dynamics. Chapter 3 introduces general aspects of the computational approach based on MBN EXPLORER,