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.

Molecular dynamics simulation of the microscopic mechanisms of the dissolution, diffusion and aggregation processes for waxy crystals in crude oil mixtures

Comprehensive review of the interfacial behavior of water/oil/surfactant systems using dissipative particle dynamics simulation

Adhesive contacts between graphene sheet (GS) and corrugated substrates made of an ordered array of atomic pillars with variable geometries were investigated by molecular dynamics simulations. Depending on the height and interval distance of the pillars, GS can conformably coat the surface, partially adhere, or remain flat on top of the pillars. The relationship between the geometries of the pillar and the final adhesion configurations of GS was partially established. A critical adsorption energy was determined to achieve stable adsorption configuration of GS on corrugated substrates made of ordered pillar arrays. Besides the geometries of pillars, the effects of initial coating angle of GS were also considered as an important factor that affects the final adsorption configuration. We observed two interesting morphologies of GS, ‘I shape’ and ‘L shape’, which were determined by the initial coating angles.

Interfacial adhesion properties of graphene sheet on nanoscale corrugated surface: a molecular dynamics simulation study

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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Interfacial adhesion properties of graphene sheet on nanoscale corrugated surface: a molecular dynamics simulation study

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.