Coarse-grained and multiscale models <br/><br/>of bulk liquids and macromolecules

Tuesday, November 4, 2008 - 9:15am - 10:00am
EE/CS 3-180
Teresa Head-Gordon (University of California, Berkeley)
I will describe two coarse-grained models and a multiscale
model relevant in the context of molecular or langevin dynamics
of bulk liquids and macromolecules. We have recently achieved a
fundamental result in deriving an analytical solution for
computing the screened electrostatic interaction between
arbitrary numbers of proteins of arbitrarily complex charge
distributions, assuming they are well described by spherical
low dielectric cavities in a higher dielectric salty medium
[1]. Ultimately, smooth and systematic increase or decrease in
spatial resolution back and forth between simple dielectric
cavities and atomic level descriptions will be the centerpiece
of a multiscale scheme [2]. I will also describe a
coarse-grained model of water to investigate
thermodynamic-dynamic relationships [3] as well as a
coarse-grained protein model relevant for lengthscales and
timescales relevant for disease aggregation [4, 5].

[1] I. Lotan & T. Head-Gordon (2006). An analytical
electrostatic model for salt screened interactions between
multiple proteins J. Comp. Theo. Chem. 2, 541-555.

[2] E.-H. Yap & T.Head-Gordon (2008). In progress

[3] M.E. Johnson and T. Head-Gordon (2008). Thermodynamic
theories of liquid dynamics. submitted.

[4] E.-H. Yap, N. Lux Fawzi & T. Head-Gordon (2008). A
coarse-grained a-carbon protein model with anisotropic
hydrogen-bonding. Proteins, Struct. Func.. Bioinf. 70, 626-638.

[5] N. Lux Fawzi, E.-H. Yap, Y. Okabe, K. Kohlstedt, S. P.
Brown & T. Head-Gordon (2008). Contrasting disease and
non-disease protein aggregation. Acc. Chem. Research 41,
MSC Code: