A Numerical Integrator for Forward Dynamics Simulations of Folding Process for Protein Molecules Modeled as Hyper-Redundant Robots

Overview & Synopsis

This paper investigates development of an efficient numerical integrator for forward dynamics simulation of the protein folding process, where protein molecules are modeled as robotic mechanisms consisting of rigid nano-linkages with many degrees-of-freedom. To address the computational burden associated with fixed step-size explicit Euler methods, we develop a fast numerical scheme with an adaptive step-size strategy for computing the folding pathway of protein molecules.