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

Understanding and controlling the flow of water confined in nanopores has tremendous implications in theoretical studies and industrial applications. Here, we propose a simple model for the confined water flow based on the concept of effective slip, which is a linear sum of true slip, depending on a contact angle, and apparent slip, caused by a spatial variation of the confined water viscosity as a function of wettability as well as the nanopore dimension. Results from this model show that the flow capacity of confined water is 10 −1 ∼10 7 times that calculated by the no-slip Hagen–Poiseuille equation for nanopores with various contact angles and dimensions, in agreement with the majority of 53 different study cases from the literature. This work further sheds light on a controversy over an increase or decrease in flow capacity from molecular dynamics simulations and experiments.

https://www.pnas.org/content/pnas/114/13/3358.full.pdf

Wettability effect on nanoconfined water flow

We report high magnetic field scanning tunneling microscopy and Landau level spectroscopy of twisted graphene layers grown by chemical vapor deposition. For twist angles exceeding ~3° the low energy carriers exhibit Landau level spectra characteristic of massless Dirac fermions. Above 20° the layers effectively decouple and the electronic properties are indistinguishable from those in single-layer graphene, while for smaller angles we observe a slowdown of the carrier velocity which is strongly angle dependent. At the smallest angles the spectra are dominated by twist-induced van Hove singularities and the Dirac fermions eventually become localized. An unexpected electron-hole asymmetry is observed which is substantially larger than the asymmetry in either single or untwisted bilayer graphene.

Single-Layer Behavior and Its Breakdown in Twisted Graphene Layers

Hydrodynamic and hydromagnetic stability

Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show that there is a range of polymer lengths in which the system is approximately translationally invariant, and we develop a coarse-grained description of this regime. From this description, general features of the distribution of times for the polymer to pass through the pore may be deduced. We also introduce a more microscopic model. This model provides a physically reasonable scenario in which, as in experiments, the polymer's speed depends sensitively on its chemical composition, and even on its orientation in the channel. Finally, we point out that the experimental distribution of times for the polymer to pass through the pore is much broader than expected from simple estimates, and speculate on why this might be.

Driven Polymer Translocation Through a Narrow Pore

Molecular dynamics simulations are carried out to study the pressure driven fluid flow of water through single walled carbon nanotubes. A method for the calculation of viscosity of the confined fluid based on the Eyring theory of reaction rates is proposed. The method involves the calculation of the activation energy directly from the molecular dynamics trajectory information. Computations are performed using this method to study the effect of surface curvature on the confined fluid viscosity. The results indicate that the viscosity varies nonlinearly with the carbon nanotube diameter. It is concluded that the reason behind the observed enhancement in the rate of fluid flow through carbon nanotubes could be the nonlinear variation of viscosity.

The role of activation energy and reduced viscosity on the enhancement of water flow through carbon nanotubes

Although the importance of temperature control in nonequilibrium molecular dynamics simulations is widely accepted, the consequences of the thermostatting approach in the case of strongly confined fluids are underappreciated. We show the strong influence of the thermostatting method on the water transport in carbon nanotubes (CNTs) by considering simulations in which the system temperature is controlled via the walls or via the fluid. Streaming velocities and mass flow rates are found to depend on the tube flexibility and on the thermostatting algorithm, with flow rates up to 20% larger when the walls are flexible. The larger flow rates in flexible CNTs are explained by a lower friction coefficient between water and the wall. Despite the lower friction, a larger solid-fluid interaction energy is found for flexible CNTs than for rigid ones. Furthermore, a comparison of thermostat schemes has shown that the Berendsen and Nose-Hoover thermostats result in very similar transport rates, while lower flow rates are found under the influence of the Langevin thermostat. These findings illustrate the significant influence of the thermostatting methods on the simulated confined fluid transport.

/pdf/water-flow-in-carbon-nanotubes-the-effect-of-tube-l4psa6t0a1.pdf

Water flow in carbon nanotubes: The effect of tube flexibility and thermostat.

We investigated the effects of the chirality of carbon nanotubes (CNTs) on water transport using molecular dynamics simulations. For the study, we considered CNTs with similar diameter and varying chiralities, obtained by altering the chiral indices (n,m) of the nanotubes. The tubes with an armchair (n = m) structure show the maximum streaming velocity, flux, flow rate enhancement and slip length, whereas the corresponding values are lower for chiral (n≠m) tubes, and are the lowest in zigzag (m = 0) CNTs. The difference in flow rates with varying tube structures can be primarily attributed to the alteration in potential energy landscape experienced by the water molecules, leading to changes in the friction coefficient at the fluid-solid interface. The water molecules experienced the least resistance to flow in an armchair tube, while the force exerted by the CNT surface on the water molecules increased monotonically with the change in the CNT type to chiral and then to zigzag. The chirality effects on water transport are, however, found to decrease with an increase in tube diameter. Furthermore, an analysis of the influence of the CNT type on ion (Na+ or Cl-) transport in water-filled CNTs showed the interaction energy of ions with water to be much higher than that with the CNT surface, demonstrating minimal dependence of ion transport on the chiral structure. Hence, the tube chirality should be considered an ineludible factor in controlling the water transport through CNTs and in the designing of novel devices in nanotechnology.

Water flow in carbon nanotubes: the role of tube chirality.

The dielectric constant for water is reduced under confinement. Although this phenomenon is well known, the underlying physical mechanism for the reduction is still in debate. In this work, we investigate the effect of the orientation of hydrogen bonds on the dielectric properties of confined water using molecular dynamics simulations. We find a reduced rotational diffusion coefficient for water molecules close to the solid surface. The reduced rotational diffusion arises due to the hindered rotation away from the plane parallel to the channel walls. The suppressed rotation in turn affects the orientational polarization of water, leading to a low value for the dielectric constant at the interface. We attribute the constrained out-of-plane rotation to originate from a higher density of planar hydrogen bonds formed by the interfacial water molecules.

/pdf/effect-of-hydrogen-bonds-on-the-dielectric-properties-of-43srr43d8c.pdf

Effect of Hydrogen Bonds on the Dielectric Properties of Interfacial Water.

We report a molecular-dynamics study of flow of Lennard-Jones fluid through a nanochannel where size effects predominate. The momentum and energy accommodation coefficients, which determine the amount of slip and temperature jumps, are calculated for a three-dimensional Poiseuille flow through a nano-sized channel. Accommodation coefficients are calculated by considering a " gravity"- (acceleration field) driven Poiseuille flow between two infinite parallel walls that are maintained at a fixed temperature. The Knudsen number (Kn) dependency of the accommodation coefficients, slip length, and velocity profiles is investigated. The system is also studied by varying the strength of gravity. The accommodation coefficients are found to approach a limiting value with an increase in gravity and Kn. For low values of Kn (<0.15), the slip length obtained from the velocity profiles is found to match closely the results obtained from the linear slip model. Using the calculated values of accommodation coefficients, the first- and second-order slip models are validated in the early transition regime. The study demonstrates the applicability of the Navier-Stokes equation with the second-order slip model in the early transition regime.

Sarith P. Sathian

Papers

The role of activation energy and reduced viscosity on the enhancement of water flow through carbon nanotubes

Water flow in carbon nanotubes: The effect of tube flexibility and thermostat.

Water flow in carbon nanotubes: the role of tube chirality.

Effect of Hydrogen Bonds on the Dielectric Properties of Interfacial Water.

Molecular-dynamics study of Poiseuille flow in a nanochannel and calculation of energy and momentum accommodation coefficients.