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 Department of Physics Colloquium:

 

Polyelectrolyte Behavior of RNA

 

Udayan Mohanty

Department of Chemistry, Boston College

 

Host: Paul Whitford

 

 

Thursday, March 9, 2017

114 Dana Research Center

4:00 p.m.

 

 RNA is a highly charged molecule that is exquisitely sensitive to its ionic environment. The basis of how divalent and monovalent metal cations effect RNA stability and dynamics, and the characteristics of ion-RNA interactions are less than well understood. I will discuss a new theoretical and computational approach that combines a coarse grained structure-based molecular dynamics simulation for describing minimally frustrated energy landscape, with heterogeneous, site-dependent, generalization of Manning condensation model, to shed light on the distribution of excess ions near an irregular RNA structure in solution containing Group-I (X+) and Group-II (Y2+) cations, and monovalent anion (Cl-), from added salts. Explicit Y2+ but implicit XCl account for ion-ion correlations. A hypothesis in this work is that dynamic description of XCl condensation is crucial to characterize the dense outer sphere population and connecting the excess number of Y2+ ions with experimental data. Fundamental understanding of the interactions between arbitrary configurations of RNA, the condensed ions, and the screening ions, within native basin, of the characteristics of the dense outer sphere Y2+ population, and of the ionic effects between conformational basins, are the focus of this study.

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