Variational implicit-solvent modeling and the level-set computation of biomolecular structures and interactions

Part II: The level-set method

Professor Li-Tien Cheng
Department of Mathematics
UC San Diego


Understanding biomolecules---their structures, dynamics, and interactions with solvent---is essential to revealing mechanisms and functions of biological systems. While atomistic simulations that treat both solvent and solute molecules explicitly are usually more accurate, implicit or continuum solvent models for biomolecules are far more efficient. With an implicit solvent, the free energy and structure of an underlying solvation system is described through the solute particles and the interface that separates the solutes and solvent.

Dzubiella, Swanson and McCammon [Phys. Rev. Lett.104, 527 (2006) and J. Chem. Phys. 124, 084905 (2006)] developed a class of variational implicit-solvent models. Central in these models is a free-energy functional of all admissible solute-solvent interfaces, coupling both nonpolar and polar contributions of an underlying system. An energy-minimizing interface then defines an equilibrium solute-solvent interface. Cheng et al. [J. Chem. Phys. 127, 084503 (2007)] developed a robust level-set method for numerically capturing such interfaces.

In this talk, I will begin with a brief introduction of the level-set method. I will then give details of the application of this method to the implicit-solvent computation of nonpolar molecules. Finally, I will present some new results on the coupling of the level-set method with molecular mechanics for implicit-solvent modeling of molecules.

This is joint work with Jianwei Che, Joachim Dzubiella, Bo Li, J. Andy McCammon, and Yang Xie.