Paper Citing NAMD - Abstract
Badu, S. R.; Melnik, R.; Paliy, M.; Prabhakar, S.; Sebetci, A.; Shapiro, B. A.
Modeling of RNA nanotubes using molecular dynamics simulation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 43:555-564, NOV 2014
In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.
