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

The principal aim of this work is to study the thermophysical aspects of gas interaction on the walls of nano-channels using a three dimensional Molecular Dynamics (MD) model. The complete physics of gas-surface interaction in micro/nano channels in the non continuum regime is yet to be understood. The important parameters that are relevant to such interactions include energy and momentum accommodation coefficients. The study reported in this paper aims at implementing a relatively simple methodology for calculating different accommodation coefficients. Energy accommodation coefficient (EAC) and normal momentum accommodation coefficient (NMAC) are the main focus of the study. The accommodation coefficients for the different equilibrium states are calculated. Instead of tracking individual collision, a collection of collisions are considered for the calculations. The EAC and NMAC reported here are found to be influenced by gas-wall temperature difference and Knudsen number in the transition regime.

A Molecular Dynamics Study of Energy and Momentum Accommodation Coefficients in the Transitional Knudsen Numbers

Thermal transport in MoS2 and 2-D Black Phosphorous

The effects of interfacial molecular mobility on the thermal boundary conductance (TBC) across graphene-water and graphene-perfluorohexane interfaces were investigated using non-equilibrium molecular dynamics simulations. The molecular mobility was varied by equilibrating nanoconfined water and perfluorohexane at different temperatures. The long-chain molecules of perfluorohexane exhibited a prominent layered structure, indicating a low molecular mobility, over a wide temperature range between 200 and 450 K. Alternatively, water increased its mobility at high temperatures, resulting in an enhanced molecular diffusion that significantly contributed to the interfacial thermal transport, in addition to the increasing vibrational carrier population at high temperatures. Furthermore, the TBC across the graphene-water interface exhibited a quadratic relationship with the rise in temperature, whereas for the graphene-perfluorohexane interface, a linear relationship was observed. The high rate of diffusion in interfacial water facilitated additional low-frequency modes, and a spectral decomposition of the TBC also indicated an enhancement in the same frequency range. Thus, the enhanced spectral transmission and higher molecular mobility of water with respect to perfluorohexane explained the difference in the thermal transport across the interfaces considered herein.

Effects of interfacial molecular mobility on thermal boundary conductance at solid-liquid interface.

Study of interfacial thermal resistance in boron nitride nanotube (BNNT)-water interface

In this study, we investigate the effect of uniaxial strain on the thermal conductivity of zigzag graphene (ZG) and armchair graphene (AG). It is observed that the thermal conductivity reduces with strain in ZG and AG. For a given strain, the maximum reduction in thermal conductivity is observed in AG. The tensile strain causes a larger deformation of bonds in AG whereas a minor variation in bond angles is observed. This causes a high reduction of thermal conductivity in AG. DOS (Density of States) and Spectral Energy Density (SED) curves are calculated to study the phonon transport in graphene. It is found that due to strain, high frequency phonon modes undergo a red shift whereas blue shift is observed in the out-of-plane phonon modes. The phonon group velocity and lifetimes of in-plane acoustic modes get reduced because of strain and hence their contribution to the thermal conductivity reduces. But in the ZA modes, strain increases the phonon group velocities and phonon lifetimes. For unstrained graphene, in-plane acoustic modes contribute nearly 60-70% of thermal conductivity in ZG and AG. However, when graphene is strained their contribution sharply reduces and the contribution by ZA mode increases and is nearly 40-60% of the thermal conductivity. But the contribution by TA modes to the thermal conductivity is unaffected by strain. Phonon Mean Free Path (MFP) calculations indicate that MFP of phonon in strained graphene increases due to increase in the wavelength of low frequency ZA phonons. The MFP of phonons is found to be higher in AG than in ZG in both strained and unstrained conditions.

/pdf/effect-of-uniaxial-strain-on-thermal-conductivity-of-d1dct1rk1b.pdf

Sarith P. Sathian

Papers

A Molecular Dynamics Study of Energy and Momentum Accommodation Coefficients in the Transitional Knudsen Numbers

Thermal transport in MoS2 and 2-D Black Phosphorous

Effects of interfacial molecular mobility on thermal boundary conductance at solid-liquid interface.

Study of interfacial thermal resistance in boron nitride nanotube (BNNT)-water interface

Effect of Uniaxial Strain on Thermal Conductivity of Graphene