Molecular Dynamics Simulations of Collagen and S-layer Assemblies
Cristian V. Ciobanu
Fibrillar collagens are common tissue scaffolds, and are known to assemble into ordered arrays in matrices such as bones, tendon, and cartilage. The collagen molecules and other biomolecules like lipids, viruses, and S-layers have been found to assemble in-vitro on inorganic surfaces. Such directed organization of functional biomolecular materials provides an artificial platform for exploiting membrane protein function, building bionanoelectronic structures, and exploring the electronic and transport properties of these assemblies. These resulting bio-nanostructures have potential applications in molecular recognition, specific ion-transport, environmental sensing, light harvesting, high surface area electrodes and drug delivery. The variety of self-assembled collagen structures, often hierarchical, can lead to a variety of applications and to fundamental understanding of the assembly processes. Such processes can be highly complex, and can benefit from even the most basic models that capture the essential interactions between collagen molecules in solution, which leads to assembly. In this project, we focus on developing a coarse-grained model in which the collagen strands are treated as strings of beads connected via springs, with well-defined interactions between beads that belong to different strings. Molecular dynamics simulations based on this model can provide insights into the complex assembly process in terms of a competition between several forces such as intermolecular, intramolecular, and molecule-surface interactions. In turn, this study will contribute to the design of novel bio-nanostructures that possess specific morphology, and desired electronic, transport, biological properties.