Monte-Carlo Simulations of Soft Matter Using SIMONA: A Review of Recent Applications

Molecular simulations such as Molecular Dynamics (MD) and Monte Carlo (MC) have gained increasing importance in the explanation of various physicochemical and biochemical phenomena in soft matter and help elucidate processes that often cannot be understood by experimental techniques alone. While there is a large number of computational studies and developments in MD, MC simulations are less widely used, but they offer a powerful alternative approach to explore the potential energy surface of complex systems in a way that is not feasible for atomistic MD, which still remains fundamentally constrained by the femtosecond timestep, limiting investigations of many essential processes. This paper provides a review of the current developments of a MC based code, SIMONA, which is an efficient and versatile tool to perform large-scale conformational sampling of different kinds of (macro)molecules. We provide an overview of the approach, and an application to soft-matter problems, such as protocols for protein and polymer folding, physical vapor deposition of functional organic molecules and complex oligomer modeling. SIMONA offers solutions to different levels of programming expertise (basic, expert and developer level) through the usage of a designed Graphical Interface pre-processor, a convenient coding environment using XML and the development of new algorithms using Python/C++. We believe that the development of versatile codes which can be used in different fields, along with related protocols and data analysis, paves the way for wider use of MC methods

Graphitizability of Polymer Thin Films: An In Situ TEM Study of Thickness Effects on Nanocrystalline Graphene/Glassy Carbon Formation

Polymer pyrolysis has emerged as a versatile method to synthesize graphenoid (graphene like) materials with varying thickness and properties. The morphology of the thin film, especially the thickness, greatly affects the graphitizability and the properties of the graphenoid material. Using in situ current annealing inside a transmission electron microscope (TEM), the thickness-dependent structural evolution of the polymer film with a special focus on thickness effects is followed. At high temperatures, thin samples form large graphene layers oriented parallel to the substrate, whereas in thick samples multi-walled cage-like structures are formed. Moleclar Dynamics (MD) simulations reveal a film thickness of 40 Å below which, the carbonized layers align parallel to the surface. For thicker samples, the orientation of the layers becomes increasingly misoriented starting from the surface to the center. This structural change can be attributed to the formation of bonded multi-layers from the initially unsaturated activated edges. The resulting cage-like structures are stable even during simulated annealing at temperatures as high as 3500 K. An atomistic understanding of the formation of these structures is presented. The results clearly indicate the critical effect of thickness on the graphitizability of polymers and provide a new understanding of the structural evolution during pyrolysis

Graphitizability of Polymer Thin Films: An In Situ TEM Study of Thickness Effects on Nanocrystalline Graphene/Glassy Carbon Formation

Polymer pyrolysis has emerged as a versatile method to synthesize graphenoid (graphene like) materials with varying thickness and properties. The morphology of the thin film, especially the thickness, greatly affects the graphitizability and the properties of the graphenoid material. Using in situ current annealing inside a transmission electron microscope (TEM), the thickness‐dependent structural evolution of the polymer film with a special focus on thickness effects is followed. At high temperatures, thin samples form large graphene layers oriented parallel to the substrate, whereas in thick samples multi‐walled cage‐like structures are formed. Moleclar Dynamics (MD) simulations reveal a film thickness of 40 Å below which, the carbonized layers align parallel to the surface. For thicker samples, the orientation of the layers becomes increasingly misoriented starting from the surface to the center. This structural change can be attributed to the formation of bonded multi‐layers from the initially unsaturated activated edges. The resulting cage‐like structures are stable even during simulated annealing at temperatures as high as 3500 K. An atomistic understanding of the formation of these structures is presented. The results clearly indicate the critical effect of thickness on the graphitizability of polymers and provide a new understanding of the structural evolution during pyrolysis