Department of Chemistry, University of Minnesota

Darrin M. York

Darrin York e-mail: york [at] umn.edu
Office:328 Smith Hall
Phone: (612)624-8042
Fax:(612)626-2006

B.S. Chemistry/Honors - UNC Chapel Hill
Ph.D. Physical Chemistry - UNC Chapel Hill (Advisor: Lee G. Pedersen)

NSF Postdoctoral Fellow in Computational Science and Engineering - Duke University
NIH Postdoctoral Fellow in Chemistry - Harvard University
EMBO Postdoctoral Fellow - Universite Louis Pasteur, Strasbourg, FRANCE

The focus of my research is on the development and application of theoretical methods to study biological macromolecules in solution. My group designs linear-scaling semiempirical and density-functional electronic structure methods, hydrid quantum mechanical/molecular mechanical (QM/MM) potentials, new molecular simulation techniques, many-body force fields and solvation models. The extension of quantum mechanical methods to complicated biological systems in realistic environments is an immensely important and challenging area. These methods being developed in my lab provide a quantum electronic structure description of biological systems in solvated environments with greatly increased accuracy and efficiency.

Accurate quantum mechanical simulations can provide detailed insight into the molecular mechanisms of biocatalysis, assist in the interpretation of experimental results, and guide the development of new pharmaceutical drugs or biotechnology. Quantum effects are particularly important in the study of RNA enzymes, or ribozymes. These are highly charged polynucleic acid systems that interact strongly with metal ions and solvent, and often exhibit a high degree of conformational variation. To attack this problem, we design multi-scale quantum models: the integration of a hierarchy of theoretical levels that work synchronously to model complicated chemical events, such ribozyme catalysis, that span a broad range of spatial domains and time scales.

The main application area of my lab involves the study of nucleic acid structure and the molecular mechanisms of RNA catalysis. Two systems are a focus of current research: the hammerhead ribozyme and the hairpin ribozyme. The unraveling of the mechanistic details of these prototype ribozymes would provide a tremendous step toward the understanding of RNA catalysis at the atomic level.