John W. Brady, Jr.
Professor of Food Science

John W. Brady, Jr.




Department of Food Science
103 Stocking Hall
Cornell University
Ithaca, NY 14853-2703


Web Sites

Department Profile


B.S. in Chemistry, University of North Carolina at Chapel Hill, 1975
Ph.D. in Chemistry, SUNY at Stony Brook, 1980 (Classical Trajectory Studies of Two van der Waals Systems: I. Homogeneous Nucleation of Rare Gases and II. Inelastic Collisions of Xenon with Chlorine Dimers)
Postdoctoral Fellow with Professor Martin Karplus, Harvard University, Department of Chemistry, 1980-1983
Assistant Professor, Department of Food Science, Cornell University, 1983-1989
Associate Professor, Department of Food Science, Cornell University, 1989-1999
Professor, Department of Food Science, Cornell University, 1999-present

Research Description

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.


“Molecular Dynamics Simulations of Water Confined in Model Cylindrical Pores” by A. Lerbret, G. Lelong, P.E. Mason, M.-L. Saboungi, and J.W. Brady, in preparation.

 “The Interactions of Glucose with a Model Peptide” by P.E. Mason, A. Lerbret, M.-L. Saboungi, G.W. Neilson, C.E. Dempsey, and J.W. Brady, in preparation.

 “Free Energy Surfaces for the Interaction of Glucose with Planar Aromatic Groups in Aqueous Solution” by J. Wohlert, U. Schnupf, and J.W. Brady, submitted to Biophysical J.

 “Simulation Studies of the Insolubility of Cellulose”, by M. Bergenstråhle, J. Wohlert, M.E. Himmel, and J.W. Brady, submitted to Carbohydr. Res.

 “Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations”, by P.E. Mason, G.W. Neilson, C.E. Dempsey, D.L. Price, M.-L. Saboungi, and J.W. Brady, J. Phys. Chem. B., 114, 5412-5419 (2010).

 “The Determination of Specific Ion structure by Neutron Diffraction and Computer Simulation”, by G.W. Neilson, P.E. Mason, and J.W. Brady, in Specific Ion Effects, W. Kunz, ed. (World Scientific Publishing, 2010).

 “Water Mobility in the Dehydration of Crystalline Trehalose”, by F. Sussich, C. Skopec, J. Brady, and A. Cesàro, Food Chemistry, 122, 388-393 (2010).

 “Preferential Interactions of Guanidinium Ions with Aromatic Groups over Aliphatic Groups”, by. P.E. Mason, C.E. Dempsey, G.W. Neilson, S.R. Kline, and J.W. Brady, J. Am. Chem. Soc., 131, 16689-16696 (2009).

 “Specificity of Ion-Protein Interactions: Complementary and Competitive Effects of Tetrapropylammonium, Guanidinium, Sulfate, and Chloride Ions”, by P.E. Mason, C.E. Dempsey, L. Vrbka, J. Heyda, J.W. Brady, P. Jungwirth, J. Phys. Chem. B, 113, 3227-
3234 (2009).

 “Translational and Rotational Dynamics of Monosaccharide Solutions”, by G. Lelong, W.S. Howells, J.W. Brady, C. Talon, D.L. Price, and M.-L. Saboungi, J. Phys. Chem. B, 113, 13079-13085 (2009).

 “Molecular Dynamics Studies of the Conformation of Sorbitol” by A. Lerbret, P.E. Mason, R.M. Venable, A. Cesàro, M.-L. Saboungi, R.W. Pastor, and J.W. Brady, Carbohydr. Res., 344, 2229-2235 (2009).

 “Computational Simulations of the Trichoderma reesei Cellobiohydrolase I Acting on Microcrystalline Cellulose Iβ: The Enzyme-Substrate Complex", by L. Zhong, J.F. Matthews, P.I. Hansen, M.F. Crowley, J.M. Cleary, R.C. Walker, M.R. Nimlos, C.L. Brooks III, W.S. Adney, M.E. Himmel, and J.W. Brady, Carbohydr. Res. 344, 1984-1992 (2009).

 “Additive Empirical Force Field for Hexopyranose Monosaccharides”, by O. Guvench, S.N. Greene, G. Kamath, J.W. Brady, R.M. Venable, R.W. Pastor, and A.D. Mackerell, J. Comput. Chem. 29, 2543-2564 (2008).

 “Interactions of the Complete Cellobiohydrolase I from Trichodera reesei with Microcrystalline Cellulose Iβ”, by L. Zhong, J.F. Matthews, M.F. Crowley, T. Rignall, C. Talón, J.M. Cleary, R.C. Walker, G. Chukkapalli, C. McCabe, M.R. Nimlos, C.L. Brooks III, M.E. Himmel, and J.W. Brady, Cellulose, 15, 261-273 (2008).

 “Be2+ Hydration in Concentrated Aqueous Solutions of BeCl2”, by P.E. Mason, S. Ansell, G.W. Neilson, J.W. Brady, J. Phys. Chem. B, 112, 1935-1939 (2008).

 “Structures of Plant Cell Wall Celluloses”, by R.H. Atalla, J.W. Brady, J.F. Matthews, S.-Y. Ding, M.E. Himmel, in Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy, M.E. Himmel, ed. (Blackwell, Oxford, 2008).

 “The Reversal by Sulfate of the Denaturant Activity of Guanidinium”, by C.E. Dempsey, P.E. Mason, J.W. Brady, G.W. Neilson, J. Am. Chem. Soc., 129, 15895-15902 (2007).

 “Dynamics of Trehalose Molecules in Confined Solutions”, by G. Lelong, D.L. Price, J.W. Brady, M.-L. Saboungi, J. Chem. Phys., 2007, 127(6), Art. No. 065102.

 “The Solvation of Complex Species”, by P.E. Mason, J.W. Brady, G.W. Neilson, J.E. Enderby, M.-L. Saboungi, G.J. Cuello, 2006 Annual Report, Institute Laue-Langevin (ILL, Grenoble, 2007).

 “Molecular Modeling Suggests Induced Fit of Family I Carbohydrate Binding Modules with a Broken Chain Cellulose Surface”, by M.R. Nimlos, J.F. Matthews, M.F. Crowley, R.C. Walker, G. Chukkapalli, J.W. Brady, W.S. Adney, J.M. Cleary. L. Zhong, and M.E. Himmel, Protein Engineering, Design & Selection 20, 179-187 (2007).

 “The Interaction of Guanidinium Ions with a Model Peptide”, by P.E. Mason, J.W. Brady, G.W. Neilson, and C.E. Dempsey, Biophysical Journal 93, L04-L06 (2007).

 “’Tetrahedrality’ and the Relationship between Collective Structure and Radial Distribution Functions in Liquid Water”, by P.E. Mason and J.W. Brady, J. Phys. Chem. B. 111, 5669-5679 (2007).

“Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production”, by M.E. Himmel, S.-Y. Ding, D.K. Johnson, W.S. Adney, M.R. Nimlos, J.W. Brady, and T.D. Foust, Science 315, 804-807 (2007).