Abstract
We have performed large-scale molecular dynamics simulations on hammerhead RNA in water and observed disparity in the dynamical properties between water and RNA. The simulations are carried out above the dynamical transition temperature of RNA and is varied from below freezing to ambient temperature. Using this model, we observed different types of relaxation dynamics for water and RNA. While RNA shows a single stretched exponential decay, the water molecules show a double-exponential decay. Both water and RNA dynamics show temperature and spatial dependence on relaxation times. The RNA relaxations are many orders of magnitude slower compared to water for all temperature and spatial length scales. RNA relaxations show predominantly heterogeneous dynamics. Water dynamics in the hydration shell show a combination of interfacial water and bulk-like water properties and the water dynamics are decoupled from the RNA dynamics. These results explain the dynamics of water in the hydration shell and that of RNA.
Original language | English |
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Article number | 062407 |
Journal | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics |
Volume | 98 |
Issue number | 6 |
DOIs | |
State | Published - Dec 14 2018 |
Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. NAMD simulations were performed using resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the Office of Science of the U.S. DOE under Contract No. DE-AC05-00OR22725. Part of this research was conducted at the Center for Nanophase Materials Sciences (CNMS), which is a DOE Office of Science User Facility.