The research in my group is focused on the following major areas:
Development and application of novel methods for ab initio electronic structure calculations, including mixed quantum mechanics/molecular mechanics (QM/MM) methods;
Development of a new generation of molecular mechanics force fields, including explicit incorporation of polarizability;
Investigation and improvement of continuum treatments of aqueous solvation;
Computational models and algorithms for protein structure prediction;
Modeling of protein-active site chemistry using quantum chemical and QM/MM methods;
Electron transfer theory; and
Quantum chemical modeling of the interactions of small molecules with surfaces and nanostructures.
Projects typically include a combination of analytical theory, algorithm and software development, and applications of new methods to biology or materials science.
Some highlights of our recent research are as follows:
Ko, Chaehyuk, David K. Malick, Dale A. Braden, Richard A. Friesner and Todd J. Martinez, Pseudospectral time-dependent density functional theory, J. Chem. Phys., 128, 10, 104103, (2008).
Knight, Jennifer L., Zhiyong Zhou, Emilio Gallicchio, Daniel M. Himmel, Richard A. Friesner, Eddy Arnold, and Ronald M. Levy, Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling, Acta Crystallographica Sect. D, Biological Crystallography, 64, 4, 383-396 (2008).
Sellers, Benjamin D., Kai Zhu, Suwen Zhao, Richard A. Friesner, Matthew P. Jacobson, Towards better refinement of comparative models: Predicting loops in inexact environments, Proteins, Structure, Function and Bioinformatics, 72, 3, 959-971 (2008).
Maragakis, Paul, Kresten Lindorff-larsen, Michael P. Eastwood, Ron O. Drorr, John L. Klepeis, Isaiah T. Arkin, Morten O. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arther G. Palmer III, and David E. Shaw, Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins, J. Phys. Chem. B, 112, 19, 6156-6158 (2008).
Trbovic, Nikola, Byungchan Kim, Richard A. Friesner, and Arthur G. Palmer, III, Structural Analysis of Protein Dynamics by MD Simulations and NMR Spin Relaxation, Proteins, Structure, Function, and Bioinformatics, 71, 2, 684-694 (2008).
Felts, Anthony, K., Emilio Gallicchio, Dmitriy Chekmarev, Kristina A. Paris, Richard A. Friesner, and Ronald M. Levy, Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling, J. Chem. Theo. Comput., 4, 5, 855-868 (2008).
Rinaldo, David, Li Tian, Jeremy N. Harvey, and Richard A. Friesner, Density Functional Localized Orbital Corrections for Transition Metals, J. Chem. Phys., 129, 164108-164123 (2008).
Goldfeld, Dahlia A., Arteum D. Bochevarov, and Richard A. Friesner, Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions, J. Chem. Phys., 129, 21, 214105 (2008).