The structure of ST2 water around a pair of spherical nonpolar (Lennard-Jones) particles. A}-A2' is studied as a function of pair separation. r, using a force-bias Monte Carlo technique with importance sampling. The change in the water structure (or equivalently the hydrophobic hydration) is correlated with the potential of mean force, WAA (r), determined in a previous study. It is found that t...

Methods for efficient and accurate prediction of RNA structure are increasingly valuable, given the current rapid advances in understanding the diverse functions of RNA molecules in the cell. To enhance the accuracy of secondary structure predictions, we developed and refined optimization techniques for the estimation of energy parameters. We build on two previous approaches to RNA free-energy ...

We conduct a numerical investigation of structural order in the shifted-force Lennard-Jones system by calculating metrics of translational and bond-orientational order along various paths in the phase diagram covering equilibrium solid, liquid, and vapor states. A series of nonequilibrium configurations generated through isochoric quenches, isothermal compressions, and energy minimizations are ...

the effect of sds (0.03-0.07 m) and brij-35(0-0.003 m) concentrations and temperature on retention parameters of 30 solutes in micellar reversed- phase liquid chromatography systems were studied using solvation parameter model. the system constants were determined by multiple linear regression analysis from experimental values of the retention factors with known descriptors by computer using th...

This article presents the results obtained using an unbiased Population Based Search (PBS) for optimizing Lennard-Jones clusters. PBS is able to repeatedly obtain all putative global minima, for Lennard-Jones clusters in the range 2 < or = N < or = 372, as reported in the Cambridge Cluster Database. The PBS algorithm incorporates and extends key techniques that have been developed in other Lenn...

The controversial observation of a minimum in the surface tension of dilute aqueous electrolyte solutions by Jones and Ray in the 1930s is confirmed by new resonance-enhanced second harmonic generation (SHG) experiments demonstrating surface enhancement of simple inorganic anions in the same concentration range. New experiments show that the quadruply charged ferrocyanide, Fe(CN)(6)(4-), anion ...

We apply a recently introduced method for global optimization to determine the ground state energy and configuration for model metallic clusters. The global minimum for a given N–atom cluster is found by following the damped dynamics of the N particle system on an evolving potential energy surface. In this application, the time dependent interatomic potential interpolates adiabatically between ...

In this report we compare the predictions of the collinear parton model and the kT -factorization approach in J/Ψ and D ⋆ meson photoproduction at HERA energies. It is shown that obtained D⋆ meson spectra over pT and η are very similar in the parton model and kT -factorization approach and they underestimate the experimental data. Opposite, the predictions of the both approaches for pT and z-sp...