Dynamical averages based on functionals of dynamical trajectories, such as time-correlation functions, play an important role in determining kinetic or transport properties of matter. At temperatures of interest, the expectations of these quantities are often dominated by contributions from rare events, making the precise calculation of these quantities by molecular dynamics simulation difficul...

In 1897 Ostwald formulated his step rule for formation of the most stable crystal state for a system with crystal polymorphism. The rule describes the irreversible way a system converts to the crystal with lowest free energy. But in fact the irreversible way a supercooled gas below the triple point temperature Ttr.p. crystallizes via a liquid droplet is an example of Ostwald's step rule. The ho...

Density dependent, implicit solvent (DDIS) potentials, the generation of which has been described previously [E. C. Allen and G. C. Rutledge, J. Chem. Phys. 128, 154115 (2008); E. C. Allen and G. C. Rutledge, J. Chem. Phys. 130, 034904 (2009)], are used in this work to examine the self-assembly of a model surfactant system. While the measurement of thermodynamic properties in simulations of sol...

The aim of this study was to evaluate hypocholesterolemic potential phytoconstituents ethanolic seed extract cumin (Cuminum cyminum L.) by assessments interaction capabilities with 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMG-CoA) through in vivo and silico along screening the test extract. were identified Gas chromatography-mass spectrometry (GC-MS)/MS examinations. hypercholesterolem...

The composition dependence of thermal transport properties of the (Na,K)Cl rocksalt solid solution is investigated through equilibrium molecular dynamics (EMD) simulations in the entire range of composition and the results are compared with experiments published in recent work [Gheribi et al., J. Chem. phys. 141, 104508 (2014)]. The thermal diffusivity of the (Na,K)Cl solid solution has been me...

This series of papers is devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids with more than 90% correlation between their virial W and potential energy U fluctuations in the NVT ensemble. Paper IV [N. Gnan et al., J. Chem. Phys. 131, 234504 (2009)] showed that strongly correlating liquids have "isomorphs," which are curves in the phase diagram alo...

We design and implement HPMC, a scalable hard particle Monte Carlo simulation toolkit, and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees instead of cell lists on the CPU for fast performance, especially with large particle size disparity, and optimize inner loops with SIMD vector intrinsics on the C...

Combined Metropolis Monte Carlo computer simulation and first-principles quantum mechanical calculations of pyridine in water are performed to analyze the role of thermal disorder in the electronic properties of hydrogen bonds in an aqueous environment. The simulation uses the NVT ensemble and includes one pyridine and 400 water molecules. Using a very efficient geometric-energetic criterion, t...

We present a novel simulation algorithm based on tempering a fraction of relaxation-limiting interactions to accelerate the process of obtaining uncorrelated equilibrium configurations of self-associating polymer solutions. This approach consists of tempering (turning off) the attractive interactions for a fraction of self-associating groups determined by a biasing field h. A number of independ...

In this paper, the separation of binary gas mixture carbon monoxide and hydrogen using single-walled carbon nanotubes (SWNTs) is studied by grand canonical Monte Carlo (GCMC) simulation. All of the particle–particle interactions between hydrogen, carbon monoxide and carbon are modeled with Lennard–Jones potential. Widom test particle method in NVT ensemble is used in determining chemical potent...