- Mathematical Biology Seminar
- Wednesday, December 7, 2011 - 11:00 for 1 hour (actually 50 minutes)
- Skiles 006
- Nathan Baker – Pacific Northwest National Laboratory
Implicit solvent models are important components of modern biomolecular simulation methodology due to their efficiency and dramatic reduction of dimensionality. However, such models are often constructed in an ad hoc manner with an arbitrary decomposition and specification of the polar and nonpolar components. In this talk, I will review current implicit solvent models and suggest a new free energy functional which combines both polar and nonpolar solvation terms in a common self-consistent framework. Upon variation, this new free energy functional yields the traditional Poisson-Boltzmann equation as well as a new geometric flow equation. These equations are being used to calculate the solvation energies of small polar molecules to assess the performance of this new methodology. Optimization of this solvation model has revealed strong correlation between pressure and surface tension contributions to the nonpolar solvation contributions and suggests new ways in which to parameterize these models.