Current Research

Computational Chemistry, Biophysics, and Engineering:
A molecular-level understanding of biologically and environmentally-relevant processes is fundamental in order to manipulate and modify such systems to present desired properties and behaviors. Molecular modeling and computational chemistry methods, ranging from the resolution of electrons (quantum chemistry) to classical particles (classical/ Newtonian mechanics) to mescoscopic/ coarse-grained entities, are applied in our lab to study a variety of biologically and environmentally-inspired systems.

Inorganic and Organic Solutes at Aqueous Liquid- Vapor Interfaces (Figure 1):
The study of interfaces is important for understanding physicochemical processes such ion transport across cellular membranes, catalysis, and ozone depletion. Molecular dynamics simulations can provide an accurate atomicallyresolved view of these processes, provided the force field used is capable of describing the physics across such interfaces. Therefore, development of accurate transferable models is important for studying these systems.

Protein-Ligand Binding (Figure 2):

Hen Egg-White Lysozyme-NAG systems. Left: Lysozyme- Nag Dimer complex (pdb id: 1SF4.PDB). Proteins shown as a surface and in cartoon forms; the surface coloring does not reflect any physical properties of the protein.

Molecular recognition processes are integral to biological function. It is this interaction that is exploited in the development of novel pharmaceuticals targeted to specific proteins of known structure and relation to dysfunctional states. Complementing experimental approaches to drug discovery and design, current state-of–the-art computational methodologies strive to expedite the early discovery process by screening for smallmolecules with high binding affinity, specificity, and pharmacological properties. The fundamental quantity of interest is the binding affinity (binding constant), and this is rigorously related to the free energy change (with respect to some standard state) associated with a binding reaction.

Biological Membranes (Lipid Bilayers), Ion Channels, and Integral Membrane Proteins:
Issues related to ion conduction energetics and mechanisms in integral membrane proteins will be targeted; integral membrane proteins are classic, model systems for testing models capable of representing physical systems in strongly anisotropic regions since an accurate description of the process whereby an ion trans-locates from a bulk aqueous environment (external to the cell) through the lipid-like environment of the cell membrane to the cell interior is required to connect atomistic-level information to macroscopic observables.