Beaded elastic rods to simulate the diffusive dynamics of biofilament deformations

Abstract

The twisting and bending dynamics of bio-filaments such as DNA are crucial to their biological functions. The nature and time-scales of these deformations are not only influenced by the structural elasticity of the bio-filament but also by their diffusion mechanics. While the elastic rod theory is still evolving to model the structural elasticity with rigorous descriptions of contituive laws, beaded chain models have been very successful to simulate the diffusion mechanics. This paper presents a framework that merges the strengths of beaded chain models with an elastic rod model to simulate the diffusive deformations (twisting and bending) of stiff bio-filemants.