(1) Development of methods for calculating internal conformational structure
and interpreting conformational equilibria of biomolecules in aqueous
environments.
(2) Stability and thermodynamics of DNA/RNA structures in solution and
on surfaces both dielectric and metallic.
(3) Peptide/Protein folding via solution stability criteria. Theory of
biomolecular solutions.
(4) Structural and thermodynamic description of molecular fluids,
including water, ions, polar biomolecular solutes and other condensed
phase systems via integral equation and density functional methods.
(5) Development of theoretical techniques for the description of the thermodynamics
and structure of biomolecules as anisotropic fluids.
(6) Development of computer simulation methodology for material science
and biotechnology.
The solution environment as well as the sequence are known to determine the
conformation, kinetic and thermodynamic behavior of polymers. It is widely appreciated
for biopolymers that biological activity is usually found within a
narrow range of solvent and salt concentration. Formulating hypotheses
to explain this sensitivity is a unifying goal for the studies in
the laboratory. The physical sensitivity is also reflected in a parameter
sensitivity in theories and simulations of these systems which must
be accounted for in any physical interpretations. Projects in this
laboratory bring theoretical and calculational approaches to bear
to an array of problems.
An area of considerable interest to us is how the presence of a surface,
either, dielectric or metallic, affects the binding affinities between targets
and probes. This is an improtant problem for optimizing DNA chips and Protein-chips.
We have both theoretical and computational work which shows how one can optimize
such surface effects to gain the most sensitivity in a DNA analysis.
