John Brady

John Brady is a Professor in the Department of Food Science at the Ithaca campus. He received a BS in Chemistry from the University of North Carolina at Chapel Hill in 1975, and a PhD in Chemistry from the State University of New York at Stony Brook in 1980. During much of his graduate studies he was a visiting staff member at the Los Alamos National Laboratory in New Mexico. He received his postdoctoral training in Chemistry at Harvard University working with Prof. Martin Karplus. He joined the Cornell faculty in 1983.

Research Focus

Our research primarily involves the dynamics and hydration of biopolymers, and of the relationship between structure, conformation, and function in biological systems. Specific examples includes the solution behavior of biopolymers, the factors which determine secondary and tertiary structure in polymers, enzymatic reaction mechanisms, rational drug design, the effects of point mutations in proteins, and the possibility of engineering desirable modifications in the function of wild-type proteins. In our work we use the techniques of computational theoretical chemistry to numerically model the properties of biopolymers and solutions. These techniques, often called Molecular Mechanics, include computer graphics-based molecular docking, energy minimization and conformational energy calculations, and molecular dynamics simulations.

Teaching Focus

My teaching activities focus on food chemistry and the chemistry of carbohydrates in foods and in other biological systems. I teach the department's required main course in food chemistry and supervise the course in commodity food chemistry.

Areas Of Expertise

• Aqueous Solvation Of Biomolecules
• Biomass Conversion
• Biophysics
• Cellulases And Cellulose Cellulose Hydrolysis
• Cellulose Degradation
• Computer Modeling Of Carbohydrates
• Computer Simulations Of Biological Molecules
• Food Chemistry
• Food Functional Properties
• Molecular Dynamics Simulations
• Neutron Diffraction With Isotopic Substitution
• Theoretical Chemistry
• Trehalose And Cryoprotectants

Graduate Fields

• Biophysics
• Food Science and Technology

Selected Publications

Journal Publications

• Tavagnacco, L., Engström, O., Schnupf, U., Saboungi, M. L., Himmel, M., Widmalm, G., Cesàro, A., & Brady, J. W. (2012). Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study. The Journal of Physical Chemistry B. 116:11701-11711.
• Mason, P. E., Lerbret, A., Saboungi, M., Neilson, G. W., Dempsey , C. E., & Brady, J. W. (2011). The Interactions of Glucose with a Model Peptide. Proteins: Structure, Function, and Bioinformatics. 79:2224-2232.
• Wohlert, J., Schnupf, U. E., & Brady, J. W. (2010). Free Energy Surfaces for the Interaction of D-Glucose with Planar Aromatic Groups in Aqueous Solution. The Journal of Chemical Physics. 1133:155103.
• Bergenstråhle, M., Wohlert, J., Himmel, M., & Brady, J. W. (2010). Simulation Studies of the Insolubility of Cellulose. Carbohydrate Research. 345:2060-2066.
• Mason, P. E., Dempsey, C. E., Neilson, G. W., & Brady, J. W. (2009). Preferential Interactions of Guanidinium Ions with Aromatic Groups over Aliphatic Groups. JACS: Journal of the American Chemical Society. 131:16689-16696.
• Mason, P. E., Neilson, G. W., Enderby, J. E., Saboungi, M., Cuello, G., & Brady, J. W. (2006). Neutron Diffraction and Simulation Studies of the Exocyclic Hydroxymethyl Conformation of Glucose. The Journal of Chemical Physics. 125:9 pages.
• Mason, P. E., Dempsey, C. E., Neilson, G. W., & Brady, J. W. (2005). Nanometer-Scale Ion Aggregates in Aqueous Electrolyte Solutions: Guanidinium Sulfate and Guanidinium Thiocyanate. The Journal of Physical Chemistry B. 109:24185-24196.
• Mason, P. E., Neilson, G. W., Enderby, J. E., Saboungi, M., & Brady, J. W. (2005). Neutron Diffraction and Computer Simulation Studies of D-Xylose. JACS: Journal of the American Chemical Society. 127:10991-10998.
• Mason, P. E., Neilson, G. W., Enderby, J. E., Saboungi, M., Dempsey, C. E., MacKerell, A. D., & Brady, J. W. (2004). The Structure of Aqueous Guanidinium Chloride Solutions. JACS: Journal of the American Chemical Society. 126:11462-11470.