University of New Hampshire
Mentor: Dr. Harish Vashisth, Department of Chemical Engineering
Computational studies of RNA structure and dynamics
Evidence from experimental characterization of structures of nucleic acids such as RNA suggests that nucleic acids are highly flexible similar to proteins, and can undergo large-scale conformational rearrangements due to motions encoded in their structure or due to binding of triggering factors such as small metabolites or proteins. These observations warrant a detailed understanding of the dynamics of RNA molecules, yet it is not possible to capture all transiently populated conformations of biomolecules using experimental methods alone. Proposed in this work is the development and application of a temperature-based enhanced sampling simulation methodology that has proven successful in the study of conformational changes in proteins. Extending this methodology for application to nucleic acids will increase its scope not only for understanding RNA dynamics, but also for understanding RNA-protein complexes. The technique will be tested on four small RNA molecules that are known to undergo large-scale conformational transitions. A better understanding of variables that can be accelerated in molecular dynamics (MD) simulations will help in the development of improved simulation algorithms and methodologies to characterize structural flexibility of RNA.