Urea-induced denaturation of PreQ1-riboswitch

Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive all atom molecular dynamics (MD) simulations to determine the molecular underpinnings of urea-induced RNA denaturation. Urea displays its denaturing power in both secondary and tertiary motifs of the riboswitch (RS) structure. Our simulations reveal that the denaturation of RNA structures is mainly driven by the hydrogen bonds and stacking interactions of urea with the bases. Through detailed studies of the simulation trajectories, we found that geminate pairs between urea and bases due to hydrogen bonds and stacks persist only ~ (0.1-1) ns, which suggests that urea-base interaction is highly dynamic. Most importantly, the early stage of base pair disruption is triggered by penetration of water molecules into the hydrophobic domain between the RNA bases. The infiltration of water into the narrow space between base pairs is critical in increasing the accessibility of urea to transiently disrupted bases, thus allowing urea to displace inter base hydrogen bonds. This mechanism, water-induced disruption of base-pairs resulting in the formation of a "wet" destabilized RNA followed by solvation by urea, is the exact opposite of the two-stage denaturation of proteins by urea. In the latter case, initial urea penetration creates a dry-globule, which is subsequently solvated by water penetration leading to global protein unfolding. Our work shows that the ability to interact with both water and polar, non-polar components of nucleotides makes urea a powerful chemical denaturant for nucleic acids.Comment: 41 pages, 18 figure

A Study on Verification of the Dynamic Modeling for a Submerged Body Based on Numerical Simulation

This study proposed a procedure to identify maneuvering coefficients that brought about abnormal motions in the simulation of a submerged body. The first step in responding to abnormal motions was conducting stability analysis to determine whether the submerged body could be simulated. If doing so was feasible, sensitivity analysis was then performed to determine maneuvering coefficients that caused the abnormal motion in the simulation. Finally, we analyzed the order of maneuvering coefficients identified by the sensitivity analysis. We also compared it with empirical formulas and other results obtained from model tests. The dynamics model targeting a high-speed submerged body was indirectly verified by the above procedure. In this study, the effectiveness of the dynamic model was verified, and parameters causing the abnormal motion were identified in accordance with the developed procedure

Pulsed Laser Deposition of Rocksalt Magnetic Binary Oxides

Here we systematically explore the use of pulsed laser deposition technique (PLD) to grow three basic oxides that have rocksalt structure but different chemical stability in the ambient atmosphere: NiO (stable), MnO (metastable) and EuO (unstable). By tuning laser fluence, an epitaxial single-phase nickel oxide thin-film growth can be achieved in a wide range of temperatures from 10 to 750 {\deg}C. At the lowest growth temperature, the out-of-plane strain raises to 1.5%, which is five times bigger than that in a NiO film grown at 750 {\deg}C. MnO thin films that had long-range ordered were successfully deposited on the MgO substrates after appropriate tuning of deposition parameters. The growth of MnO phase was strongly influenced by substrate temperature and laser fluence. EuO films with satisfactory quality were deposited by PLD after oxygen availability had been minimized. Synthesis of EuO thin films at rather low growth temperature prevented thermally-driven lattice relaxation and allowed growth of strained films. Overall, PLD was a quick and reliable method to grow binary oxides with rocksalt structure in high quality that can satisfy requirements for applications and for basic research