Variational implicit-solvent modeling and the level-set computation
of biomolecular structures and interactions
Part I: An overview
Professor Bo Li
Department of Mathematics and CTBP
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
In this talk, I will give an overview of the recent
development of variational implicit-solvent approach for solvation systems.
I will point out how various kinds of mathematical concepts and techniques
from differential geometry and partial differential equations can be
applied to this approach.
Joint work with
Jianwei Che, Li-Tien Cheng, Joachim Dzubiella, J. Andy McCammon, and Yang Xie.