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

Two-dimensional (2D) materials such as graphene, molybdenum sulfide, and hexagonal boron nitride are widely studied for separation applications such as water desalination. Desalination across such 2D nanoporous membranes is largely influenced by the bulk transport properties of water, which are, in turn, sensitive to the operating temperature. However, there have been no studies on the effect of temperature on desalination through 2D nanopores. We investigated water desalination through hydrogen functionalized graphene nanopores of varying pore areas at temperatures 275.0 K, 300.0 K, 325.0 K, and 350.0 K. The water flux showed a direct relation with the diffusion coefficient and an inverse relation with the hydrogen-bond lifetime. As a direct consequence, the water flux was found to be related to the temperature as per the Arrhenius equation, similar to an activated process. The results from the present study improve the understanding on water and ion permeation across nanoporous 2D materials at different temperatures. Furthermore, the present investigation suggests a kinetic model, which can predict the water and ion permeation based on the characteristics of the nanopore.

The effect of temperature on water desalination through two-dimensional nanopores.

A Langevin dynamics study of nanojets

The role of thermal fluctuations on the formation and stability of nano-scale drops

The controlled transport of water through nanoscale devices is an important requirement in the design and development of various nanofluidic systems. Molecular dynamics simulations are performed to investigate the phonon coupling induced thermophoretic transport of water through a carbon nanotube (CNT). Phonon coupling is believed to have a significant role in the transport of heat at the liquid-solid interface. The thermally induced vibrational modes of water-filled and empty CNTs are examined at various thermal gradients. The spatial asymmetry along the length of a CNT due to the imposed thermal gradient contributes to the diffusion enhancement of water confined in the CNT, but does not have a strong correlation with the applied thermal gradient. Analysis shows that the vibrational modes present in the center-of-mass oscillations of CNTs do not play any significant role in the development of the thermophoretic force on water. The low-frequency phonon vibrational modes of CNTs are suppressed due to the phonon coupling between water and the CNT. Also, we observed that the spectral heat current across the water-CNT interface dominates at frequencies below 5 THz, which is the same frequency range as radial breathing modes observed in the vibrational spectrum of CNT. This observation leads us to the conclusion that the coupling of radial breathing phonon modes contributes significantly to thermophoresis. This study substantiates the existence of phonon coupling at the water-CNT interface and quantifies the accumulated heat transfer across the interface.

Phonon coupling induced thermophoresis of water confined in a carbon nanotube.

Thermal transport in graphene is strongly influenced by strain. We investigate the influence of biaxial tensile strain on the thermal conductivity of zigzag and armchair graphene (AG and ZG) using non-equilibrium molecular dynamics simulations (NEMD). We observe that the thermal conductivity is significantly reduced under strain with a maximum reduction obtained at equi-biaxial strain. It is interesting to note that the high lateral to longitudinal strain ratios reduce the negative impact of strain on the thermal conductivity of AG and ZG. The in-plane acoustic modes are found to be the major heat carriers in unstrained graphene but are severely softened due to strain, and hence, their contribution to the conductivity drops down significantly. Strain alleviates the out-of-plane fluctuations in graphene and the group velocity of the out-of-plane acoustic mode (ZA) increases due to the linearisation of its dispersion relation. These factors result in the dominance of ZA mode in the thermal transport of strained graphene. Significant increase in the size dependence of the thermal conductivity of strained graphene is observed, which is attributed to the long-wavelength ZA phonons. The discrepancies between the results of BTE studies and NEMD are also discussed. This study suggests that biaxial strain can be an effective method to tune the thermal transport in graphene. Our findings can lead to better phonon engineering of graphene for various nanoscale applications.

https://iopscience.iop.org/article/10.1088/1361-6528/ab9042/pdf

Sarith P. Sathian

Papers

The effect of temperature on water desalination through two-dimensional nanopores.

A Langevin dynamics study of nanojets

The role of thermal fluctuations on the formation and stability of nano-scale drops

Phonon coupling induced thermophoresis of water confined in a carbon nanotube.

Thermal conductivity of graphene under biaxial strain: an analysis of spectral phonon properties.