(4cw) Molecular Simulation Investigation Into Nucleation and Growth of Complex Structures

Self-assembly of molecules in water results in the formation of materials involving various complex structures. These materials have found applications in various fields like medicine, energy and environment. The pillars upon which these complex structures can be designed and engineered include an understanding of both the thermodynamics and kinetics of their formation. In general, because the thermodynamic properties are related to the equilibrium state they are studied more in experiments, theory and simulations. The challenge faced in experimental studies of the kinetics is the time resolution of present experimental techniques. Although many ingenious methods have been developed to address this, nanoscopic timescales are still inaccessible in most experimental techniques. Molecular simulations are particularly helpful in this scenario in which the molecular motions of atoms are followed at nanometer length- and nanosecond time- scales. However, several computational challenges are encountered in studying the kinetics of complex structures formation. Specifically, most of these complex structures have large lengthscales and therefore the system sizes are computationally prohibitive. Considerable effort has been directed to develop different reduced models leading to coarse-grained force fields that remove the ?less important? degrees of freedom. These approaches have focused mostly on the structure and stability of the system of interest. In addition, most of them are designed with treating water as a continuum. With kinetics perspective, several interesting questions can be raised: (1) Can we use the coarse-grained models developed using structure and stability to model kinetics? (2) What governs the nucleation and growth of these structures? (3) What is the role of water in the nucleation and growth of these complex structures? How can water be incorporated explicitly and efficiently into these simulations? I am interested in exploring these questions in my future research work. Viruses provide a perfect system for this study. They are complex assemblies composed of a multi-protein shell that encloses the genetic material of the virus. They vary in shape, composition and size which can range from tens to hundreds of nanometers. Due to their large sizes, atomically detailed simulations of viruses in explicit water are computationally prohibitive and therefore, several coarse-grained models have been developed to make computational simulations of viruses feasible. Most of these models are however based on the structure and stability of the viral capsids. Therefore they provide an excellent case study for the questions raised above. I will discuss strategies to address these questions for the virus systems. These strategies can be easily extended to other complex structures such as amyloids fibrils and self-assembled colloidal or nano-particles.