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Research Abstracts Online
January 2008 - March 2009

University of Minnesota Twin Cities
Institute of Technology
Department of Chemistry

PI: Darrin M. York, Fellow

Multiscale Quantum Models for RNA Catalysis

This project involves concurrent development and application of theoretical methods to model the molecular mechanisms of RNA catalysis. The particular focus of the project is on five main areas that integrate method development and application. These include: development of linear-scaling electrostatic and solvent boundary methods for molecular simulation; construction of a database of quantum calculations for RNA catalysis; design of new semiempirical Hamiltonian models for phosphoryl transfer reactions; development of new linear-scaling electronic structure and multiscale quantum methods; and application of multiscale quantum models to RNA analysis.

The application focus of this project is on the study of four ribozyme systems: the hammerhead, hairpin, and hepatitis delta virus ribozymes and L-1-ligase. The researchers hope to elucidate catalytic features that are conserved and what aspects can exhibit variations that can be exploited for ribozyme engineering.

Group Members

Elena Formoso Estensoro, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
George Giambasu, Graduate Student
Timothy Giese, Research Associate
Francesca Guerra, Research Associate
Ming Huang, Graduate Student
Tai-Sung Lee, Research Associate
Yun Liu, Graduate Student
Xabier Lopez, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
Xiaoying Lu, Graduate Student
Adam Moser, Graduate Student
Maria Nagan, Department of Chemistry, Truman State University, Kirksville, Missouri
Olalla Nieto Faza, Research Associate
Carlos Silva Lopez, Supercomputing Institute Research Scholar
Brian Skjerven, Graduate Student