Variational Methods for Biomolecular Modeling

TL;DR

This paper discusses variational methods based on energetic principles to model biomolecular systems, emphasizing interface geometry and phase field techniques for efficient simulation of biomolecular interactions and dynamics.

Contribution

It introduces a unified variational framework incorporating interface curvature into biomolecular modeling and demonstrates its application to electrostatics, membrane microdomains, and protein localization.

Findings

Inclusion of interface curvature improves biomolecular energy models.

Phase field methods reduce computational complexity.

Applications successfully simulate biomolecular phenomena.

Abstract

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.