0-value analysis molecular dynamics simulation

In an oligonucleotide-drug hydrate complex, the appearance of a clathrate hydrate-like water structure prompt a molecular dynamics simulation (40). Again the results were only partially successful, prompting the statement, "The predictive value of simulation for use in analysis and interpretation of crystal hydrates remains to be established." However, recent molecular dynamics calculations have been more successful in simulating the water structure in Ae host lattice of a-cyclodextrin and P-cyclodextrin in the crystal structures of these hydrates (41.42). 

Clearly flow aligning behavior of the director is present and do increases linearly with the tilt angle, do. Above a threshold in the Spain rate, y 0.011, undulations in vorticity direction set in. In Fig. 14 the results of simulations for y 0.015 are shown. In Fig. 15 we have plotted the undulation amplitude obtained as a function of the shear rate. The dashed line indicates a square root behavior corresponding to a forward bifurcation near the onset of undulations. This is, indeed, what is expected, when a weakly nonlinear analysis based on the underlying macroscopic equations is performed [54], In Fig. 16 we have plotted an example for the dynamic behavior obtained from molecular dynamics simulations. It shows the time evolution after a step-type start for two shear rates below the onset of undulations. The two solid lines correspond to a fit to the data using the solutions of the averaged linearized form of (27). The shear approaches its stationary value for small tilt angle (implied by the use of the linearized equation) with a characteristic time scale t = fi/Bi. 

Aliev et al. have applied NMR spectroscopy, molecular dynamic simulations, and quantum mechanical calculations for full structural characterization in solution of some cyclic compounds (Fig. 5). The authors have performed calculations of J(H,H) couplings for the most stable conformers of the compounds studied. The analysis of the calculated J values and the comparison with experimental ones allowed establishing the population of conformers in the solution. The calculations were performed at the B3LYP/6-311+G(2d,p) theory level. 

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