Prof. Douglas J. Tobias

Professor of Chemistry [Ph. D., Chemistry/Biophysics, Carnegie Mellon University] He brings expertise in molecular dynamics simulations of atmospherically relevant systems as well as biological systems to the ORU.

Dr. Tobias uses atomic-scale computer simulation techniques based on classical and quantum mechanics to study the structure and dynamics of biological molecules and interfaces between aqueous solutions—like sea salt—and water that are important in atmospheric chemical processes. His computer simulations are invaluable in interpreting the chemistry of complex systems in the atmosphere, including how air pollutants interact with biological systems like the human lung. A substantial portion of research in the Tobias group is devoted to the development, implementation, and optimization of novel simulation methodology and analysis tools. Current research in the group may be organized into two broad categories: (1) structure and chemical dynamics at aqueous and organic interfaces relevant to heterogeneous atmospheric chemistry; (2) structure, stability, dynamics, and function of membranes and membrane proteins.

In the first area, he uses molecular dynamics simulations to model the air-solution interfaces of salt solutions, with and without organic coatings. The simulations are used to predict the compositions of the interfaces, which are often different from the bulk solution, and the reactivity of ions toward atmospheric oxidants (trace gases such as ozone and hydroxyl radical). An essential aspect of his simulations of the interfaces of aqueous ionic solutions is the use of empirical force fields that explicitly account for electronic polarization. His group invests considerable effort developing and validating polarizable force fields. With the use of polarizable force fields, they have predicted that certain anions adsorb to the air-water interface. Their predictions are tested in collaborations with experimentalists using surface-sensitive spectroscopic techniques. The presence of ions at the air/solution interface opens the door for potentially novel chemistry.

They are exploring the mechanisms of reactions occurring on the surface of aqueous solutions using so-called “ab initio molecular dynamics” simulations, in which the forces are computed from electronic structure, and ground and excited state high- level electronic structure calculations on configurations extracted from their simulations. They are also modeling the effects of organic coatings on the surfaces of aerosol particles, the uptake and transport of atmospheric gases in organic thin films, and the interactions of particulate matter with biological membrane-mimetic systems. In the second area, the Tobias group is studying lipid monolayers and bilayer membranes, and membrane proteins using large-scale, atomistic molecular dynamics simulations.

Current subjects under investigation in this area are: the role of lipid-protein interactions in determining the specificity of the binding of peripheral membrane proteins, including peptide toxins and signaling proteins; the motion of charges through membranes in the context of voltage sensing by voltage gated ion channels; predicting conformational changes that occur in a proton-coupled sugar transporter protein; recognition of peptide sequences by the membrane-bound translocon complex, which either secretes peptides into the lumen of the cell or inserts them into membranes; the role of protein- lipid-water dynamical coupling in the dynamics and function of membrane proteins. In addition, they are using multi-scale quantum mechanical/molecular mechanical

(QM/MM) approaches to study proton transport across membrane by proton channel proteins, and they are developing normal mode analyses of elastic network models for the prediction of large-scale conformational cha nges in membrane proteins.