Search for: All records

The kinetostatic compliance method (KCM) models protein molecules as nanomechanisms consisting of numerous rigid peptide plane linkages. These linkages articulate with respect to each other through changes in the molecule dihedral angles, resulting in a kinematic mechanism with hyper degrees of freedom. Within the KCM framework, nonlinear interatomic forces drive protein folding by guiding the molecule’s dihedral angle vector towards its lowest energy state in a kinetostatic manner. This paper proposes a numerical integrator that is well suited to KCM-based protein folding and overcomes the limitations of traditional explicit Euler methods with fixed step size. Our proposed integration scheme is based on pseudo-transient continuation with an adaptive step size updating rule that can efficiently compute protein folding pathways, namely, the transient three-dimensional configurations of protein molecules during folding. Numerical simulations utilizing the KCM approach on protein backbones confirm the effectiveness of the proposed integrator. 

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.