- Series
- Mathematical Biology Seminar
- Time
- Wednesday, February 8, 2012 - 2:00pm for 1 hour (actually 50 minutes)
- Location
- Skiles 005
- Speaker
- Nathan Baker – Pacific Northwest National Laboratory – http://kdi.pnnl.gov/bios/baker.stm
- Organizer
- Christine Heitsch
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. **Please note nonstandard time and room.**