Prof. Rakwoo Chang, Department of Chemistry, Kwangwoon University, Seoul 01897, South Korea

Speech Title: Applying polymer concepts to biological systems

Abstract:Recent applications of polymer-based molecular simulations to biological systems are presented. The first application is Monte Carlo (MC) simulation studies of neurofilament (NF) brushes. NF is a cytoskeletal filament that is expressed almost exclusively in neuronal cells and assembled from three distinct molecular weight proteins: NF-L, NF-M, and NF-H. The exact nature of the assembly of NF as well as the precise mechanism by which NF regulates axonal diameter and maintain distinctive cytoskeletal organization is not well understood. We try to understand the structural behavior of NF qualitatively using a primitive model of NF. The molecular model of NF systems consists of three primitive models representing NF backbone (rigid rod), side arms (freely-jointed hard-spherical chains), and small ions (hard spheres). We discuss the structural properties such as density profile, mean-square radius of gyration of each type of side arms and also the effects of Ca2+ ions or ionic strength. The second application is to predict the conformation of DNA in nano-scale channels using MC simulations of a primitive DNA model. In this model, the DNA molecule is represented as a linear chain of charged spherical monomers and the rectangular nanochannel is represented as hard walls having the same dimensions as those employed in experiments. Despite its simplicity, our model shows an excellent agreement with experiments and provides molecular details of DNA conformation in nanochannels. In the last application, a lattice model of cellulose fibers is briefly discussed. In this model, each cellobiose unit of a cellulose chain is modeled as rectangular cubes in a lattice and the cellulose fibril is represented by 36 cellulose chains. By choosing proper parameters, our model reproduces the structural behavior of cellulose fibers and can be applied to enzyme-catalyzed cellulose hydrolysis.