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

Thermal transpiration through carbon nanotubes (CNTs) and graphene channels is studied using molecular dynamics (MD) simulations. The system consists of two reservoirs connected by a CNT. It is observed that a flow is developed inside the CNT from the low temperature reservoir to the high temperature reservoir when the two reservoirs are maintained at different temperatures. The influence of channel size and temperature gradient on the mean velocity is analysed by varying the CNT diameter and the temperature of one of the reservoirs. Larger flow rate is observed in the smaller diameter CNTs showing an increase in the mean velocity with increase in the temperature gradient. For the flow developed inside the CNTs, slip boundaries occur and the slip length is calculated using the velocity profile. We examine the effect of fluid-wall interaction strength (e(fw)), diffusivity (D), and viscosity of the fluid (μ) on the temperature induced fluid transport through the CNTs. Similar investigations are also carried out by replacing the CNT with a graphene channel. Results show that the mean velocity of the fluid atoms in the graphene channel is lower than that through the CNTs. This can be attributed to the higher degree of confinement observed in the CNTs.

Thermal transpiration through single walled carbon nanotubes and graphene channels

Highly efficient water desalination through hourglass shaped carbon nanopores

Calculation of thermo-physical properties of Poiseuille flow in a nano-channel

Heat transfer across fluid-solid interfaces in nanoconfinement has received significant attention due to its relevance in nanoscale systems. In this study, we investigate the Kapitza resistance at the water-graphene interface with the help of classical molecular dynamics simulation techniques in conjunction with our recently proposed equilibrium molecular dynamics (EMD) method [S. Alosious et al., J. Chem. Phys. 151, 194502 (2019)]. The size effect of the Kapitza resistance on different factors such as the number of graphene layers, the cross-sectional area, and the width of the water block was studied. The Kapitza resistance decreases slightly with an increase in the number of layers, while the influence of the cross-sectional area and the width of the water block is negligible. The variation in the Kapitza resistance as a function of the number of graphene layers is attributed to the large phonon mean free path along the graphene cross-plane. An optimum water-graphene system, which is independent of size effects, was selected, and the same was used to determine the Kapitza resistance using the predicted EMD method. The values obtained from both the EMD and the non-equilibrium molecular dynamics (NEMD) methods were compared for different potentials and water models, and the results are shown to be in good agreement. Our method allows us to compute the Kapitza resistance using EMD simulations, which obviates the need to create a large temperature gradient required for the NEMD method.

Kapitza resistance at water–graphene interfaces

We propose a new design for thermally induced water pumping through carbon nanotubes by imposing a thermal gradient along the length of a carbon nanotube (CNT), which connects two water-filled reservoirs. We analyse the flow parameters by varying the imposed thermal gradient (4.62 to 20.98 K nm-1), the radius (0.81 to 1.89 nm) and the length (5 to 50 nm) of the CNT. Using molecular dynamics simulations, we compute the volumetric flow rate of the pump, velocity profiles of flow and thermophoretic forces acting on water molecules for various thermal gradients. The directed motion of water molecules is induced by the spatial variations of CNT-water energy interactions at the interface and the variations in the oscillation of the carbon atoms from hot to cold ends. The net flow and average velocity of water molecules are found to increase linearly with the applied thermal gradient, as well as with an increase in the radius and length of the CNT. We observe that nano-pumps with an increase in the radius and length of the CNT connecting the reservoirs perform better and also achieved higher efficiency levels. The analysis of the results indicates that the present design leads to a realistic system capable of providing continuous transportation of water leading to interesting practical applications in nanoscale devices.

Sarith P. Sathian

Papers

Thermal transpiration through single walled carbon nanotubes and graphene channels

Highly efficient water desalination through hourglass shaped carbon nanopores

Calculation of thermo-physical properties of Poiseuille flow in a nano-channel

Kapitza resistance at water–graphene interfaces

Analysing thermophoretic transport of water for designing nanoscale-pumps.