During the past few decades molecular dynamics has been a widely applied tool to simulate fluid confined in micro/nano geometries. What makes interfacial fluids fundamentally different from the bulk fluid is the fact that their density varies considerably over microscopic distances. A class of such strongly inhomogeneous fluids are fluids confined in very narrow channels by solid boundaries. In...

The ground states of Lennard-Jones (LJ) clusters are estimated by finding the Gaussian wave packets that minimize the energy functional. A "phase diagram" for LJ_{n} as a function of size (n=31,...,45) and de Boer quantum delocalization length (Lambdain[0;0.3]) is constructed, showing the stability ranges for the two competing structural motifs, the Mackay and anti-Mackay icosahedra. An increas...

We report results of calculations of the second through sixth virial coefficients for four prototype Lennard-Jones (LJ) mixtures that have been the subject of previous studies in the literature. Values are reported for temperatures ranging from T=0.6 to T=10.0, where here the temperature is given units of the LJ energy parameter of one of the components. Thermodynamic stability of the mixtures ...

Quark clustering, rather than color super-conducting, could occur in cold quark matter because of the strongly coupling between quarks at realistic baryon densities of compact stars. Although one may still not be able to calculate this conjectured matter from first principles, the inter-cluster interaction might be analogized to the interaction between inert molecules. Cold quark matter would t...

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechani...

In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95% efforts are spent on the Lennard-Jones potential o...

We show that a number of model liquids at fixed volume exhibit strong correlations between equilibrium fluctuations of the configurational parts of (instantaneous) pressure and energy. We present detailed results for 13 systems, showing in which systems these correlations are significant. These include Lennard-Jones liquids (both single- and two-component) and several other simple liquids, neit...

Quark clustering could occur in cold quark matter because of the strong coupling between quarks at realistic baryon densities of compact stars. Although one may still not be able to calculate this conjectured matter from first principles, the inter-cluster interaction might be analogized to the interaction between inert molecules. Cold quark matter would then crystallize in a solid state if the...

A set of Lindemann measures, based on positional deviations or return distances, defined with respect to mechanically stable inherent structure configurations, is applied to understand the solid-liquid phase transition in a Lennard-Jones-type system. The key quantity is shown to be the single-particle return distance-squared distribution. The first moment of this distribution is related to the ...

We study the transfer of two-dimensional Lennard-Jones solutes into the two-dimensional Lennard-Jones solvent. Thermodynamic quantities associated with this process are calculated. For this purpose the Monte Carlo method in two different ensembles, reflecting different thermodynamic restrictions, is utilized. The excess free enthalpy, excess enthalpy (p,T), and excess free energy and excess int...