Variational Implicit Solvation of Biomolecules
Bo Li
Department of Mathematics
University of California-San Diego
The structure and dynamics of biomolecules such as DNA and proteins determine the functions of underlying biological systems. Modeling biomolecules is, however, extremely challenging due to their enormous complexity. Recent years have seen the initial success of variational implicit-solvent models (VISM), implemented by the level-set method for biomolecules. Central in VISM is an effective free-energy functional of all possible solute-solvent interfaces, coupling together the solute surface energy, solute-solvent van der Waals interactions, and electrostatic contributions. The level-set relaxation of such a functional determines numerically biomolecular equilibrium conformations and minimum free energies. Comparisons with experiments and molecular dynamics simulations demonstrate that level-set VISM can capture the hydrophobic hydration, dry-wet fluctuation, and many other important salvation properties. This talk begins with a review of the level-set VISM and continues to present new developments around the VISM. These include: (1) the coupling of solute molecular mechanical interactions in the VISM; (2) the effective dielectric boundary forces; and (3) the solvent fluid fluctuations. Mathematical theory and numerical methods are discussed and applications are presented.
This is joint work with J. Andrew McCammon, Li-Tien Cheng, Joachim Dzubiella, Jianwei Che, Zhongming Wang, and many others.