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Research Abstracts Online
January 2009 - March 2010

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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. Simulations of RNA catalysis represent a grand challenge for advanced computing research due to the extremes in spatial extent and time domain required to model catalysis in these systems. The highly charged nature of RNA requires consideration of large amounts of solvent molecules and counter and co-ions, whereas the high degree of conformational variation exhibited by these systems necessitates long-time simulation and specialized sampling techniques on the quantum energy surface.

These researchers focus on four project areas that integrate method development and application. These include: construction of a database of quantum calculations for RNA catalysis; development of new, parallel linear-scaling methods for RNA catalysis; application of multiscale quantum models to study the mechanisms of RNA catalysis; and large-scale molecular dynamics simulations of conformational transitions in RNA.

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

Brian Radak, Graduate Student
Thakshila D. Dissanayake Rallage, Graduate Student
Elena Formoso Estensoro, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
George Giambasu, Graduate Student
Timothy Giese, Research Associate
Brent Gregersen, Graduate Student
Francesca Guerra, Research Associate
Hugh Heldenbrand, Graduate Student
Ming Huang, Graduate Student
Erich R. Keuchler, Graduate Student
Tai-Sung Lee, Research Associate
Yun Liu, Graduate Student
Violeta Lopez, Collaborator
Xabier Lopez, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
Xiaoying Lu, Graduate Student
Evelyn Mayaan, Graduate Student
Adam Moser, Graduate Student
Maria Nagan, Department of Chemistry, Truman State University, Kirksville, Missouri
Kwangho Nam, Graduate Student
Olalla Nieto Faza, Research Associate
Kevin Range, Graduate Student
Carlos Silva Lopez, Research Associate
Brian Skjerven, Graduate Student
Simael Tejero-Villagrasa, Visiting Researcher
Ross Walker, Visiting Researcher
Kin-Yiu Wong, Graduate Student
Curtis Wray, Undergraduate Student