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

Silica is one of the most widely used inorganic materials in experiments and applications involving aqueous solutions of biomolecules, nanoparticles, etc. In this paper, we construct a detailed atomistic model of a silica interface that captures the essential experimentally known properties of a silica interface. We then perform all-atom molecular dynamics simulations of a silica nanochannel subjected to either an external pressure or an electric field and provide an atomistic description of ionic transport and both electro-osmotic flow and streaming currents for a solution of monovalent (0.4 M NaCl) as well as divalent (0.2 and 1.0 M CaCl{sub 2}) salts. Our results allow a detailed investigation of {zeta}-potentials, Stern layer conductance, charge inversion, ionic mobilities, as well as continuum theories and Onsager relations. We conclude with a discussion on the implications of our results for silica nanopore experiments and micro- and nanofluidic devices.

Molecular Dynamics of Ionic Transport and Electrokinetic Effects in Realistic Silica Channels

We study the thermophoretic motion of water nanodroplets confined inside carbon nanotubes using molecular dynamics simulations. We find that the nanodroplets move in the direction opposite the imposed thermal gradient with a terminal velocity that is linearly proportional to the gradient. The translational motion is associated with a solid body rotation of the water nanodroplet coinciding with the helical symmetry of the carbon nanotube. The thermal diffusion displays a weak dependence on the wetting of the water−carbon nanotube interface. We introduce the use of the moment scaling spectrum (MSS) in order to determine the characteristics of the motion of the nanoparticles inside the carbon nanotube. The MSS indicates that affinity of the nanodroplet with the walls of the carbon nanotubes is important for the isothermal diffusion and hence for the Soret coefficient of the system.

Thermophoretic Motion of Water Nanodroplets confined inside Carbon Nanotubes

At an electrified interface of metal and electrolyte, ion concentration in the diffuse layer is different from the bulk and is impacted by metal charge. The double-layer structure can significantly enhance local ionic conductivity. Understanding the conductivity enhancement with conventional electrochemical measurements is challenging; however, electrokinetic experiments can be more useful in probing local ionic conductivities. We used streaming-current experiments for a range of pH values to measure ζ-potential at metal–electrolyte interfaces. We extend the method by incorporating a three-electrode electrochemical cell where the potential of the metal can be varied. By using a range of applied potentials between −200 and 800 mV (vs standard hydrogen electrode), we explored how surface charging of Au electrode affects ζ-potential. An inflection point is observed on the plot of ζ-potential against applied potential, and this point is believed to be a potential of zero charge of the electrode. Using the Gouy–Chapman–Stern–Grahame model, we correlate measured ζ-potential values to metal surface charge and calculate ionic distribution and conductivity within the microchannel. Finally, ionic conductivity is calculated as a function of metal surface charge, and as expected, Gouy–Chapman theory shows a parabolic relationship.

Electrokinetic Streaming-Current Methods to Probe the Electrode–Electrolyte Interface under Applied Potentials

Electrostatic interactions in nanoscale systems can influence the heat transfer mechanism and interfacial properties. This study uses molecular dynamics simulations to investigate the impact of various electrostatic interactions on the Kapitza resistance (Rk) on a hexagonal boron nitride-water system. The Kapitza resistance at hexagonal boron nitride nanotube (hBNNT)-water interface reduces with an increase in diameter of the nanotube due to more aggregation of water molecules per unit surface area. An increase in the partial charges on boron and nitride caused the reduction in Rk. With the increase in partial charge, a better hydrogen bonding between hBNNT and water was observed, whereas the structure and order of the water molecules remain the same. Nevertheless, the addition of NaCl salt into water does not have any influence on interfacial thermal transport. Rk remains unchanged with electrolyte concentration because the cumulative Coulombic interaction between the ions and the hBNNT is significantly less when compared with water molecules. Furthermore, the effect of electric field strength on interfacial heat transfer is also investigated by providing uniform positive and negative surface charges on the outermost hBN layers. Rk is nearly independent of the practical range of applied electric fields and decreases with an increasing electric field for extreme field strengths until the electrofreezing phenomenon occurs. The ordering of water molecules toward the charged surface leads to an increase in the layering effect, causing the reduction in Rk in the presence of an electric field.

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Effects of Electrostatic Interactions on Kapitza Resistance in Hexagonal Boron Nitride-Water Interfaces.

Electrokinetic flows are generally analyzed, assuming isothermal conditions even though such situations are hard to be achieved in practice. In this paper, the flow of a symmetric electrolyte in a charged nanochannel subjected to an axial temperature gradient is investigated using molecular dynamics simulations. We analyze the relative contribution of the Soret effect, the thermoelectric effect, and the double layer potential in the electrical double layer for various surface charges and temperature gradients. We find the flow driven by thermal gradient analogous to electroosmotic flow. The thermophoretic motion of the electrolyte is significant for negative surface charge than the positive surface charge. The vibrational spectrum of graphene is calculated to delineate the effect of the surface charge polarity on the observed thermophoretic motion of the electrolyte. A unique structure of interfacial water layer is observed for the positive and negative surface charges. We attribute the presence of these structures to the differences in water-carbon interactions existing for various surface charge polarity. For an applied thermal gradient in the range 2.6 K/nm to 8 K/nm, we observe a continuous net flow with average velocities reaching up to 9.4 m/s inside the channel for a negative surface charge of -0.101 C/m2. The results indicate that in a charged graphene-based nanochannel, temperature gradients can be employed to induce streaming current, depending on the relative influence of the Soret effect and the double layer potential.

Kiran Prakash

Papers

Non-isothermal flow of an electrolyte in a charged nanochannel.

Flow-induced electrohydrodynamics in a nanochannel with finite temperature gradient