Multibody minimum-energy trajectory with applications to protein folding

TL;DR

This paper develops a method to compute minimum-energy trajectories for multibody systems, specifically applied to protein folding, by integrating optimal control with elastic band techniques and solving the equations of motion with augmented Lagrangian methods.

Contribution

It introduces a novel approach combining discrete optimal control, elastic band methods, and augmented Lagrangian techniques for multibody systems, with specific application to protein folding.

Findings

Successfully computes minimum-energy folding trajectories for proteins.

Demonstrates the effectiveness of the elastic band approach in controlling system conformation.

Provides a framework for analyzing energy landscapes in multibody systems.

Abstract

This work addresses the optimal control of multibody systems being actuated with control forces in order to find a dynamically feasible minimum-energy trajectory of the system. The optimal control problem and its constraints are integrated in a discrete version of the equation of motion allowing the minimization of system energy with respect to a discrete state and control trajectory. The work is centred on a specific type of open-chain multibody system, with strong local propensity, where the overall system kinematics is described essentially by the torsion around the links that connect rigid bodies. The coupling between the rigid body motion, and the optimal conformation is described as an elastic band of replicas of the original system with different conformations. The band forces are used to control system's motion directly, reflecting the influence of the system energy field on its conformation, using for that the Nudged-Elastic Band method. Here the equation of motion of the multibody grid are solved by using the augmented Lagrangean method. In this context, if a feasible minimum-energy trajectory of the original system exists it is a stationary state of the extended system. This approach is applied to the folding of a single chain protein.