Victor Guallar, Ph.D.

DEPARTMENT OF Biochemistry & Molecular Biophysics
Keywords: QM/MM, protein modeling, theoretical enzymology, DNA-protein interactions

The theoretical study of complex biochemical processes requires a complete understanding of the different times scales. The fast motions, often involving a chemical reaction, might require a time-dependent quantum mechanical description of the active site. The slow motions, responsible for conformational changes, require the description of the biological environment (such as protein-protein interaction, solvent, etc.) and various physical properties (such as temperature and pressure). An accurate description of these different time scales bridges the gap between theoretical and experimental studies. Thus, it is essential to explore the chemical responses to local and global configuration changes, which may be achieved by coupling a quantum-mechanical description of the reactive process with advanced sampling techniques. For this purpose, several simulation protocols and algorithms, which combine optimized sampling techniques with hybrid QM/MM methods and semiclassical dynamics corrections, are being studied.

The research is centered in two main areas. First, we place particular importance on the application of such methods, with emphasis on protein-RNA/DNA interactions and protein-substrate interactions. The second area involves the development of new methodological components, centered in obtaining long-time protein dynamics by means of a kinetic Monte Carlo scheme. These two areas provide different venues for students and researchers to explore, based on their strengths and interests.