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Dynamical disparity between hydration shell water and RNA in a hydrated RNA system...

by Debsindhu Bhowmik, Panchapakesan Ganesh, Bobby G Sumpter, Monojoy Goswami
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Physical Review E
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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.