Paper Citing NAMD - Abstract
Badu, Shyam R.; Melnik, Roderik; Paliy, Maxim; Prabhakar, Sanjay; Sebetci, Ali; Shapiro, Bruce A.
High Performance Computing Studies of RNA Nanotubes
PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, 601-607, 2014
Based on the previous studies of RNA nanorings, in this contribution we computationally analyze the structure and properties of RNA nanotubes, where we focus on nanotubes consisting of up to five nanorings of around 20nm in diameter. We have developed a molecular dynamics (MD) method and implemented it by using the NAMD and VMD packages in a high-performance computing environment to study the structural and thermal properties of the nanotube in physiological solutions. In particular, we have analyzed such characteristics as the Root Mean Square Deviation (RMSD), the radius of gyration, the number of hydrogen bonds per base pairs, and the radial distribution function for the different nanoclusters in nanotubes of various sizes. Due to flexibility of RNA molecules, we can build various motifs which are essential in bionanotechnological applications such as scaffolding and drug delivery systems.
