Networks
Brady, John Woodbury
Cornell Faculty Member
Positions
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 Areas
- biochemistry
- biophysics (CALS)
- computational biology
- food science
- molecular biology
- natural resources
- Affiliations
- Research
- Publications
- Teaching
- Service
- Background
- Other
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Affiliations
other Cornell affiliations
Research
research overview
- 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.
research activities
principal investigator on
- MASTER IP MANAGEMENT PLAN: BIOENERGY SCIENCE CENTER (BESC): IP MANAGEMENT PLAN awarded by DEPARTMENT OF ENERGY 2007 - 2012
- MODELING CLOSTRIDIUM THERMOCELLUM CELLULASES awarded by DEPARTMENT OF ENERGY 2008 - 2012
- MODELING THE INTERACTION OF BINDING MODULE FROM CBH I WITH REALISTIC CELLULOSE SUBTRATES awarded by DEPARTMENT OF ENERGY 2008 - 2012
area(s) of concentration/expertise
other area(s) of concentration/expertise
- theoretical chemistry, theoretical biophysics
keywords
- 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
submitted impact statement
- Molecular mechanics simulations of the interaction of cellulases with cellulose
- Molecular Mechanics simulations of the interaction of cellulases with cellulose
- Molecular Mechanics Simulations of the Interaction of Cellulases with Cellulose
- Molecular Mechanics Simulations of the Interaction of Cellulases with Cellulose
Publications
individual publications
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academic article
- Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study. Journal of Physical Chemistry. 116:11701-11711. 2012
- Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields. Journal of Chemical Theory and Computation. 8:735-748. 2012
- Concentration Enrichment of Urea at Cellulose Surfaces – Results from Molecular Dynamics Simulations and NMR Spectroscopy. Cellulose. 19:1-12. 2012
- Free Energy Landscapes of the α-D- and β-D-glucopyranose conformations in both vacuum and aqueous solution.. Molecular Simulation. 38:1186-1197. 2012
- Molecular Dynamics Simulations of the Interaction of Glucose with Imidazole in Aqueous Solution.. Carbohydrate Research. 349:73-77. 2012
- Role of Glucose in Enhancing Stability of Aqueous Silica Gels Against Dehydration.. Journal of Physical Chemistry C. 116:9481-9486. 2012
- Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution. Journal of Physical Chemistry. 115:10957-10957. 2011
- Sugar Binding Sites on the Surface of the Carbohydrate Binding Module of CBH I from Trichoderma reesei. Carbohydrate Research. 346:839-846. 2011
- The High Temperature Behavior of Cellulose I. Journal of Physical Chemistry. 115. 2011
- The Interactions of Glucose with a Model Peptide. Proteins:Structure, Function, and Bioinformatics. 79:2224-2232. 2011
- Water Confined in Cylindrical Pores: A Molecular Dynamics Study. Food Biophysics. 6:233-240. 2011
- Weakly Hydrated Surfaces and the Binding Interactions of Small Biological Solutes. Journal of Biophysics. 41:396-377. 2011
- Free Energy Surfaces for the Interaction of D-Glucose with Planar Aromatic Groups in Aqueous Solution. Journal of Chemical Physics. 1133:155103. 2010
- Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations. Journal of Physical Chemistry. 114:5412-5419. 2010
- Simulation Studies of the Insolubility of Cellulose. Carbohydrate Research. 345:2060-2066. 2010
- The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase is a Flexible, Disordered Protein. Biophysical Journal. 99:3773-3781. 2010
- Water mobility in the dehydration of crystalline trehalose. Food Chemistry. 122:388-393. 2010
- Computational Simulations of the Trichoderma reesei Cellobiohydrolase I Acting on Microcrystalline Cellulose Iβ: The Enzyme-Substrate Complex. Carbohydrate Research. 344:1984-1992. 2009
- Molecular Dynamics Studies of the Conformation of Sorbitol. Carbohydrate Research. 344:2229-2235. 2009
- Preferential Interactions of Guanidinium Ions with Aromatic Groups over Aliphatic Groups. Journal of the American Chemical Society. 131:16689-16696. 2009
- Specificity of Ion-Protein Interactions: Complementary and Competitive Effects of Tetrapropylammonium, Guanidinium, Sulfate, and Chloride Ions. Journal of Physical Chemistry. 113:3227-3234. 2009
- Translational and Rotational Dynamics of Monosaccharide Solutions. Journal of Physical Chemistry. B 113:13079-13085. 2009
- Additive Empirical Force Field for Hexopyranose Monosaccharides. Journal of Computational Chemistry. 28:2543-2564. 2008
- Be2+ Hydration in Concentrated Aqueous Solutions of BeCl2. Journal of Physical Chemistry. 112:1935-1939. 2008
- Interactions of the Complete Cellobiohydrolase I from Trichodera reesei with Microcrystalline Cellulose Iβ. Cellulose. 15:261-273. 2008
- 'Tetrahedrality’ and the Relationship between Collective Structure and Radial Distribution Functions in Liquid Water. Journal of Physical Chemistry B. 111:5669-5679. 2007
- Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production. Science. 315:804-807. 2007
- Dynamics of Trehalose Molecules in Confined Solutions. Journal of Chemical Physics (JCP). 127. 2007
- Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface. Protein Engineering Design and Selection (PEDS). 20:179-187. 2007
- The Interaction of Guanidinium Ions with a Model Peptide. Biophysical Journal. 93. 2007
- The Reversal by Sulfate of the Denaturant Activity of Guanidinium. Journal of the American Chemical Society (JACS). 129. 2007
- Computer simulation studies of microcrystalline cellulose Iβ . Carbohydrate Research. 341:138-152. 2006
- Determination of a Hydroxyl Conformation in Aqueous Xylose Using Neutron Scattering and Molecular Dynamics. Journal of Physical Chemistry B. 110. 2006
- Nanometer-Scale Ion Aggregates in Aqueous Electrolyte Solutions: Guanidinium Carbonate. Journal of Physical Chemistry B. 110:13477-13483. 2006
- Neutron Diffraction and Simulation Studies of CsNO3 and Cs2CO3 Solutions. Journal of the American Chemistry Society (JACS). 128:15136-15144. 2006
- Neutron Diffraction and Simulation Studies of the Exocyclic Hydroxymethyl Conformation of Glucose. Journal of Chemical Physics (JCP). 125. 2006
- Molecular Dynamics of Confined Glucose Solutions. Journal of Chemical Physics (JCP). 122. 2005
- Nanometer-Scale Ion Aggregates in Aqueous Electrolyte Solutions: Guanidinium Sulfate and Guanidinium Thiocyanate. Journal of Physical Chemistry B. 109:24185-24196. 2005
- Neutron Diffraction and Computer Simulation Studies of D-Xylose. Journal of the American Chemical Society (JACS). 127:10991-10998. 2005
- The Structure of Aqueous Glucose Solutions as Determined by Neutron Diffraction with Isotopic Substitution Experiments and MD Calculations. Journal of Physical Chemistry B. 109:13104-13111. 2005
- Dynamics of Water Molecules in Glucose Solutions. Journal of Physical Chemistry B. 108:5120-5126. 2004
- Molecular Dynamics of Glucose in Solution: a Quasi-Elastic Neutron Scattering Study. Journal of Chemical Physics (JCP). 120:3527-3530. 2004
- The Conformational Free Energy Map for Solvated Neocarrabiose. Carbohydrate Research. 339:1953-1960. 2004
- The Structure of Aqueous Guanidinium Chloride Solutions. Journal of the American Chemical Society (JACS). 126:11462-11470. 2004
- Computational and Experimental Studies of the Catalytic Mechanism of Thermobifida fusca Cellulase Cel6A (E2). Protein Engineering. 16:125-134. 2003
- Energetics for Displacing a Single Chain from the Surface of Microcrystalline Cellulose into the Active Site of Acidothermus cellulolyticus Cel5A. Protein Engineering. 16:1005-1015. 2003
- Neutron Diffraction Studies on Aqueous Solutions of Glucose. J. Chem. Phys. 119:3347-3353. 2003
- Carbohydrate Solution Simulations: Producing a Force Field with Experimentally Consistent Primary Alcohol Rotational Frequencies and Populations. Journal of Computational Chemistry. 23:1236-1243. 2002
- Molecular Dynamics Simulation and NMR Study of Aqueous Neocarrabiose 41-Sulfate, a Building Block of κ-Carrageenan. Journal of Physical Chemistry. B 105:8629-8638. 2001
- Reversible Dehydration of Trehalose and Cryptobiosis: From Solution State to an Exotic Glassy-Crystal?. Carbohydr. Res. 334:165-176. 2001
- Calculation of the Potential of Mean Force for the Binding of Glucose to Benzene in Aqueous Solution. Journal of Physical Chemistry. B 104:7228-7234. 2000
- Calculation of the Ramachandran Potential of Mean Force for a Disaccharide in Aqueous Solution. J. Am. Chem. Soc. 121:2244-2252. 1999
- Molecular Dynamics Simulation of a Double Helical ß-Carrageenan Hexamer Fragment in Water. Journal of Physical Chemistry. 102:2749-2758. 1998
- Molecular Dynamics Simulations of Carrabiose. Biopolymers. 41:323-330. 1997
- Molecular Dynamics Simulations of a Glycoprotein: The Lectin from Erythrina corallodendron. Journal of Molecular Structure: THEOCHEM. 395-396:469-475. 1997
- Molecular Dynamics Simulations of the N-Linked Oligosaccharide of the Lectin from Erythrina corallodendron. Protein Engineering. 10:1249-1261. 1997
- Molecular Dynamics Studies of the Hydration of α,α-Trehalose. J. Am. Chem. Soc. 119:7851-7862. 1997
- The Application of Simulated Annealing to the Conformational Analysis of Disaccharides. Chemical Physics. 224:263-273. 1997
- The Model Dependence of the Anisotropic Structuring of Solvent Water Around Sugars in Molecular Dynamics Simulations. Journal of Physical Chemistry. B101:1317-1321. 1997
- Water Structuring Around Complex Solutes: Theoretical Modeling of α-D-Glucopyranose. Chemical Physics. 216:349-363. 1997
- Anisotropic Solvent Structuring in Aqueous Sugar Solutions. J. Am. Chem. Soc. 118:12276-12286. 1996
- Free Energy Simulation Studies of the Binding Specificity of Mannose-Binding Protein. Journal of Physical Chemistry. 100:2528-2534. 1996
- The Anomeric Equilibrium in D-Xylose: Free Energy and the Role of Solvent Structuring. J. Am. Chem. Soc. 118:541-546. 1996
- The Effect of Hydration Upon the Conformation and Dynamics of Neocarrabiose, A Repeat Unit of ß-Carrageenan. Biopolymers. 38:461-469. 1996
- Binding of an Antifreeze Polypeptide to an Ice/Water Interface via Computer Simulation. AIChE J. 41:959-973. 1995
- Conformational Modeling of Substrate Binding to Endocellulase E2 From Thermomonospora fusca. Protein Engineering. 8:1145-1152. 1995
- Use of Umbrella Sampling in the Calculation of the Potential of Mean Force for Maltose in Vacuum From Molecular Dynamics Simulations. Journal of Physical Chemistry. 99:11339-11343. 1995
- Computer Modeling Studies of the Interaction of Water with Carbohydrates. Journal of Food Engineering. 22:43-57. 1994
- Computer Simulations of Cyclic and Acyclic Cholinergic Agonists: Conformational Search and Molecular Dynamics Simulations. Biophysical Journal. 66:314-324. 1994
- Design improvements of β-lactoglobulin. Trend. Food Sci. 5:261-265. 1994
- Simulations of the Aqueous Solvation of Trilaurin. Journal of Agricultural and Food Chemistry. 42:2099-2107. 1994
- Thermostable variants of bovine β-lactoglobulin. Prot. Eng. 7:263-270. 1994
- Molecular Dynamics Simulations of a Winter Flounder 'Antifreeze' Polypeptide in Aqueous Solution. Biopolymers. 33:1481-1503. 1993
- Observations Concerning the Treatment of Long-Range Interactions in Molecular Dynamics Simulations. Journal of Computational Chemistry. 14:278-284. 1993
- The Role of Hydrogen Bonding in Carbohydrates: Molecular Dynamics Simulations of Maltose in Aqueous Solution. Journal of Physical Chemistry. 97:958-966. 1993
- Molecular Dynamics Simulations of the Whey Protein ß-Lactoglobulin. Protein Engineering. 5:17-27. 1992
- Solvent Effect on the Anomeric Equilibrium in D-Glucose: A Free Energy Simulation Analysis. J. Am. Chem. Soc. 113:1553-1557. 1991
- Theoretical Studies of Oligosaccharide Structure and Conformational Dynamics. Curr. Opin. Struct. Biol. 1:711-715. 1991
- Disaccharide Conformational Flexibility. I. An Adiabatic Potential Energy Map for Sucrose. Biopolymers. 29:961-976. 1990
- Disaccharide Conformational Flexibility. II. Molecular Dynamics Simulations of Sucrose. Biopolymers. 29:977-997. 1990
- Molecular Dynamics Simulations of α-D-Glucose in Aqueous Solution. J. Am. Chem. Soc. 111:5155-5165. 1989
- A Revised Potential Energy Surface for Molecular Mechanics Studies of Carbohydrates. Carbohyd. Res. 180:207-221. 1988
- Conformational Analysis and Molecular Dynamics Simulations of Maltose. Biopolymers. 27:1927-1952. 1988
- Molecular Dynamics Simulations of Carbohydrates. Chem. Design Automation News. 3:1. 1988
- Vasopressin Conformational Fluctuations: A Molecular Dynamics Study. Biopolymers. 27:939-956. 1988
- Intramolecular Vibrational Relaxation of CH Stretch Overtones in Benzene. J. Chem. Phys. 86:4411-4417. 1987
- Molecular Dynamics Simulations of ß-D-Glucopyranose. Carbohyd. Res. 165:306-312. 1987
- Classical Dynamics Study of Intramolecular Energy Flow in Benzene. J. Chem. Phys. 85:1848-1853. 1986
- Influence of Anharmonicity of 'Bath' Modes in Intramolecular Energy Transfer From a Local Mode. Chem. Phys. Lett. 131:398-402. 1986
- Molecular Dynamics Simulations of α-D-Glucose. J. Am. Chem. Soc. 108:8153-8160. 1986
- Configurational Entropy of the Alanine Dipeptide in Vacuum and in Solution: A Molecular Dynamics Study. J. Am. Chem. Soc. 107:6103-6105. 1985
- The Structure of Proteins with Single Site Mutations: A Minimum Perturbation Approach. Proceedings at the National Academy of Science USA. 82:1697-1700. 1985
- Cluster Dynamics: A Classical Trajectory Study of . J. Chem. Phys. 74:1026-1028. 1981
- A Classical Trajectory Study of Xenon Atom-Chlorine Dimer Collisions. J. Chem. Phys. 73:292-296. 1980
- Cluster Dynamics: Further Trajectory Study of . J. Chem. Phys. 73:2767-2772. 1980
- Cluster Dynamics: A Classical Trajectory Study of . J. Chem. Phys. 71:2467-2472. 1979
- Velocity Dependence of Angular Distributions in Gas/Solid-Surface Collisions: Relationship to the Interaction Potential. J. Chem. Phys. 69:3458-3461. 1978
- Identification of Essential Arginyl Residues in Cytoplasmic Malate Dehydrogenase with Butanedione. Journal of Biological Chemistry. 250:6222-6227. 1975
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article
-
chapter
- Overview of Computer Modeling of Cellulose. Biomass Conversion: Methods and Protocols. 11-21. 2012
- The Determination of Specific Ion Structure by Neutron Diffraction and Computer Simulation. Specific Ion Effects. 2010
- Structures of Plant Cell Wall Celluloses. Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production. 188-212. 2008
- Molecular Dynamics and Neutron Diffraction Studies of the Structuring of Water by Carbohydrates and Other Solutes. Modelling Molecular Structure and Reactivity in Biological Systems. 2006
- Oligosaccharide Geometry and Dynamics. Carbohydrates: Structures, Synthesis and Dynamics. 228-257. 1999
- Molecular Dynamics Simulations of Carbohydrate Solvation. Methods in Multidimensional Molecular Dynamics. 384-400. 1998
- Computer Modeling of Oligosaccharides. Trichoderma reesei Cellulases and Other Hydrolases. 1993
- The Use of Computer Modeling to Study the Physical Properties of Food Molecules. Advances in Food Engineering. 1992
- Molecular Dynamics Simulation of the Aqueous Solvation of Sugars. Water Relationships in Food: Advances in the 1980's and Trends for the 1990's. 1991
- The Development of Molecular Mechanics Parameters for Carbohydrates. Proteins: Structure, Dynamics and Design. 1991
- Molecular Dynamics Simulations of Carbohydrates. Advances in Biophysical Chemistry. 1990
- The Role of Dynamics and Solvation in Protein Structure and Function. Food Proteins. 1-18. 1989
- Entropy of Macromolecules. Molecular Dynamics and Protein Structure. 1985
- Classical Trajectory Studies of the Formation and Unimolecular Decay of Rare Gas Clusters. Potential Energy Surfaces and Dynamics Calculations. 1981
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conference paper
- Molecular Mechanics Studies of Cellulases. Glycosyl Hydrolases for Biomass Conversion, ACS Symposium Series. 112-130. 2001
- Computer Modeling of Carbohydrate Molecules. ACS Symposium Series No. 430. 1990
- Conformational Analysis of Oligosaccharides: Reconciliation of Theory with Experiment. Computer Modeling of Carbohydrate Molecules, ACS Symposium Series No. 430. 266-280. 1990
- Conformational Flexibility of Sucrose: Static and Dynamic Modeling. Computer Modeling of Carbohydrate Molecules, ACS Symposium Series No. 430. 1990
- Design and modification of protein functionality. Proceedings of the International Bio Symposium 90 Nagoya. 69-73. 1990
- Molecular Dynamics Simulations of Carbohydrates and Their Solvation. Computer Modeling of Carbohydrate Molecules. 1990
- The Solvation of Complex Species 2007
- Computer Modeling of Carbohydrate Solvation 1998
- Molecular Mechanics: Computer Modeling of Functional Properties 1991
speaker at Cornell event
Teaching
teaching overview
- 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.
teaching activities
- FDSC-4170: Food Chemistry I - Spring 2013
- FDSC-5000: Master of Professional Studies (Agriculture) Project - Spring 2013
- FDSC-6000: Seminar in Food Science - Spring 2013
- FDSC-6960: Graduate Internship in Food Science - Spring 2013
- FDSC-6980: Graduate Teaching Experience - Spring 2013
- FDSC-8900: Master's Level Thesis Research - Spring 2013
- FDSC-9900: Doctoral-Level Thesis Research - Spring 2013
- FDSC-4180: Food Chemistry II - Fall 2012
- FDSC-5000: Master of Professional Studies (Agriculture) Project - Fall 2012
- FDSC-6960: Graduate Internship in Food Science - Fall 2012
- FDSC-6980: Graduate Teaching Experience - Fall 2012
- FDSC-8900: Master's Level Thesis Research - Fall 2012
- FDSC-9900: Doctoral-Level Thesis Research - Fall 2012
- FDSC-4170: Food Chemistry I - Spring 2012
- FDSC-5000: Master of Professional Studies (Agriculture) Project - Spring 2012
- FDSC-6960: Graduate Internship in Food Science - Spring 2012
- FDSC-6980: Graduate Teaching Experience - Spring 2012
- FDSC-8900: Master's Level Thesis Research - Spring 2012
- FDSC-9900: Doctoral-Level Thesis Research - Spring 2012
- FDSC-4180: Food Chemistry II - Fall 2011
- FDSC-5000: Master of Professional Studies (Agriculture) Project - Fall 2011
- FDSC-6960: Graduate Internship in Food Science - Fall 2011
- FDSC-6980: Graduate Teaching Experience - Fall 2011
- FDSC-8900: Masters-Level Thesis Research - Fall 2011
- FDSC-9900: Doctoral-Level Thesis Research - Fall 2011
Service
service to the profession
- AMERICAN CHEMICAL SOCIETY Member 1980 -
- International Symposia on Properties of Water Advisory Committee Member 1992 - 1997
reviewer or editor for
Background
education and training
- Ph.D. in Chemistry, State University of New York at Stony Brook 1980
- University of North Carolina at Chapel Hill 1975
Other
alternate name
- J. Brady
college
- CALS
research keyword
- 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
name prefix
- Professor