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Advanced Simulations of RNA-based Biological Nanostructures

Authors:
Shyam Badu
Roderick Melnik
Sanjay Prabhakar

Keywords: Coarse-Graining Algorithms; Ribonucleic Acid Nanostructures; Molecular Dynamics; Scaffolding; Medical Biology; High Performance Computing

Abstract:
We present a methodology and the results of numerical simulations of complex biological polymeric molecular nanostructures, whose major components consist of ribonucleic acids (RNAs). The case where such nanostructures are considered in fluids, e.g. physiological solutions, is also reported. The developed methodology is based on molecular dynamics and our efficient coarse graining algorithms applied to such structures. We discuss such important characteristics as the radius of gyration, root mean square deviation, and radial distribution function in the application to RNA nanotubes, consisting of a number nanorings, studied in the previous works. Among other things, we provide insight into typical distributions of various ions around the RNA nanotubes as a function of time within a distance of a few angstroms from their surface.

Pages: 56 to 58

Copyright: Copyright (c) IARIA, 2016

Publication date: May 22, 2016

Published in: conference

ISSN: 2308-3484

ISBN: 978-1-61208-478-7

Location: Valencia, Spain

Dates: from May 22, 2016 to May 26, 2016