Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Interfacial and molecular interactions between fractions of heavy oil and surfactants in porous media: Comprehensive review.

Recovery of crude oil in rock nanopores plays an important role in the petroleum industry. In this work, we carried out molecular dynamics (MD) simulations to study the process of ionic surfactant solution driven oil-detachment in model silica (SiO2) nanochannels. Our MD simulation results revealed that the oil-detachment induced by the ionic surfactant flooding can be described by a three-stage process including the formation and delivery of surfactant micelles, the surfactant micelle disintegration-spread and migration on the oil-aggregate surface, and oil molecular aggregate deformation-to-detachment. A flooding from rear (FFR) phenomenon is revealed that the surfactant molecules tend to migrate to the rear bottom of the oil molecular aggregate caused by the water flow effect and hydration of polar head groups of surfactants, which facilitate the penetration of water molecules into the oil-rock interface, and the oil molecule detachment occurs at the rear bottom of the oil molecular aggregate. The present MD simulation results also indicate that the dodecyl benzenesulfonate (SDBS) has higher oil-driven efficiency than that of dodecyl trimethylammonium bromide (DTAB). The difference of oil displacement efficiency between the two surfactants is attributed to the hydration property of the polar head groups. Compared with the -N(CH3)3+ headgroup in DTAB, the bare O atom in the -SO3- group has a stronger H bond interaction with the surrounding water molecules. The stronger interaction between the headgroup of SDBS and the adjacent water molecule results in the surfactant migrating to the rear bottom of the oil molecules more quickly, thus accelerating the detachment of oil molecules.

Molecular Dynamics Simulation of Surfactant Flooding Driven Oil-Detachment in Nano-Silica Channels.

Computer simulation studies aimed at elucidating the phase behavior of crude oils inevitably require atomistically detailed models of representative molecules. For the lighter fractions of crudes, ...

/pdf/catalogue-of-plausible-molecular-models-for-the-molecular-2ej5ll40su.pdf

Catalogue of Plausible Molecular Models for the Molecular Dynamics of Asphaltenes and Resins Obtained from Quantitative Molecular Representation

Phase transition mechanisms of paraffin in waxy crude oil in the absence and presence of pour point depressant

The self-organization of five model side-chain decorated polyaromatic asphaltene molecules with or without toluene solvent was investigated by means of atomistic molecular dynamic (MD) simulations. It was found that the organizational structure of polycyclic asphaltene molecules is significantly affected by the position and length of side chains. In the present study, two types of phase-separated stacking configurations, including the phase separated lamellar structure (PSLS) and the phase separated columnar structure (PSCS), were found. The PSLS and PSCS were also maintained in the presence of a small amount of toluene additive (30% wt fraction). When adding excess toluene molecules, the asphaltene molecules formed highly dispersed nanoaggregates. The dynamic properties of the π–π stacking structures in the PSLS and PSCS, as well as the nanoaggregates, were probed. It was found that the number and size of alkyl side chains significantly impacted the size and number of π–π stacking structures in the aggregates. Through tracking the structural evolution of the nanoaggregates, a possible dissociation mechanism of nanoaggregates is also suggested.

/pdf/molecular-dynamics-simulations-of-the-self-organization-of-2v58xbglyk.pdf

Molecular dynamics simulations of the self-organization of side-chain decorated polyaromatic conjugation molecules: phase separated lamellar and columnar structures and dispersion behaviors in toluene solvent

The detachment process of an oil molecular layer situated above a horizontal substrate was often described by a three-stage process. In this mechanism, the penetration and diffusion of water molecules between the oil phase and the substrate was proposed to be a crucial step to aid in removal of oil layer/drops from substrate. In this work, the detachment process of a two-dimensional alkane molecule layer from a silica surface in aqueous surfactant solutions is studied by means of molecular dynamics (MD) simulations. By tuning the polarity of model silica surfaces, as well as considering the different types of surfactant molecules and the water flow effects, more details about the formation of water molecular channel and the expansion processes are elucidated. It is found that for both ionic and nonionic type surfactant solutions, the perturbation of surfactant molecules on the two-dimensional oil molecule layer facilitates the injection and diffusion of water molecules between the oil layer and silica sub...

Molecular Dynamics Simulations of the Oil-Detachment from the Hydroxylated Silica Surface: Effects of Surfactants, Electrostatic Interactions, and Water Flows on the Water Molecular Channel Formation.

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Molecular dynamics simulations of the self-organization of side-chain decorated polyaromatic conjugation molecules: phase separated lamellar and columnar structures and dispersion behaviors in toluene solvent

Molecular Dynamics Simulations of the Oil-Detachment from the Hydroxylated Silica Surface: Effects of Surfactants, Electrostatic Interactions, and Water Flows on the Water Molecular Channel Formation.