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

Not all nanopores are created equal. By definition, nanopores have characteristic diameters or conduit widths between ∼1 and 100 nm. However, the narrowest of such pores, perhaps best called Single...

Critical Knowledge Gaps in Mass Transport through Single-Digit Nanopores: A Review and Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.

The flow of water in carbon nanochannels has defied understanding thus far1, with accumulating experimental evidence for ultra-low friction, exceptionally high water flow rates and curvature-dependent hydrodynamic slippage2-5. In particular, the mechanism of water-carbon friction remains unknown6, with neither current theories7 nor classical8,9 or ab initio molecular dynamics simulations10 providing satisfactory rationalization for its singular behaviour. Here we develop a quantum theory of the solid-liquid interface, which reveals a new contribution to friction, due to the coupling of charge fluctuations in the liquid to electronic excitations in the solid. We expect that this quantum friction, which is absent in Born-Oppenheimer molecular dynamics, is the dominant friction mechanism for water on carbon-based materials. As a key result, we demonstrate a marked difference in quantum friction between the water-graphene and water-graphite interface, due to the coupling of water Debye collective modes with a thermally excited plasmon specific to graphite. This suggests an explanation for the radius-dependent slippage of water in carbon nanotubes4, in terms of the electronic excitations of the nanotubes. Our findings open the way for quantum engineering of hydrodynamic flows through the electronic properties of the confining wall. 

Fluctuation-induced quantum friction in nanoscale water flows

The transport of fluid and ions in nano/molecular confinements is the governing physics of a myriad of embodiments in nature and technology including human physiology, plants, energy modules, water collection and treatment systems, chemical processes, materials synthesis, and medicine. At nano/molecular scales, the confinement dimension approaches the molecular size and the transport characteristics deviates significantly from that at macro/micro scales. A thorough understanding of physics of transport at these scales and associated fluid properties is undoubtedly critical for future technologies. This compressive review provides an elaborate picture on the promising future applications of nano/molecular transport, highlights experimental and simulation metrologies to probe and comprehend this transport phenomenon, discusses the physics of fluid transport, tunable flow by orders of magnitude, and gating mechanisms at these scales, and lists the advancement in the fabrication methodologies to turn these transport concepts into reality. Properties such as chain-like liquid transport, confined gas transport, surface charge-driven ion transport, physical/chemical ion gates, and ion diodes will provide avenues to devise technologies with enhanced performance inaccessible through macro/micro systems. This review aims to provide a consolidated body of knowledge to accelerate innovation and breakthrough in the above fields.

Transport Phenomena in Nano/Molecular Confinements.

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.

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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.

We introduce an analytical method to predict the slip length (L s) in cylindrical nanopores using equilibrium molecular dynamics (EMD) simulations, following the approach proposed by Sokhan and Quirke for planar channels [39] Using this approach, we determined the slip length of water in carbon nanotubes (CNTs) of various diameters The slip length predicted from our method shows excellent agreement with the results obtained from nonequilibrium molecular dynamics (NEMD) simulations The data show a monotonically decreasing slip length with an increasing nanotube diameter The proposed EMD method can be used to precisely estimate slip length in high slip cylindrical systems, whereas, L s calculated from NEMD is highly sensitive to the velocity profile and may cause large statistical errors due to large velocity slip at the channel surface We also demonstrated the validity of the EMD method in a BNNT-water system, where the slip length is very small compared to that in a CNT pore of similar diameter The developed method enables us to calculate the interfacial friction coefficient directly from EMD simulations, while friction can be estimated using NEMD by performing simulations at various external driving forces, thereby increasing the overall computational time The EMD analysis revealed a curvature dependence in the friction coefficient, which induces the slip length dependency on the tube diameter Conversely, in flat graphene nanopores, both L s and friction coefficient show no strong dependency on the channel width

/pdf/prediction-of-fluid-slip-in-cylindrical-nanopores-using-2p2r2pd7iw.pdf

Prediction of fluid slip in cylindrical nanopores using equilibrium molecular simulations.

The intriguing mass transport properties of carbon nanotubes (CNTs) have received widespread attention, especially the rapid transport of water through CNTs due to their atomically smooth wall interiors. Extensive research has been dedicated to the comprehension of various aspects of water flow in contact with CNTs, the most prominent ones being the studies on slip and flow rates. Experimental and computational studies have confirmed an enhanced water flow rate through this graphitic nanoconfinement. However, a quantitative agreement has not yet been attained. These disparities coupled with incomplete knowledge of the mechanisms of water transport at nanoscale regimes are hindering the possibilities to integrate CNTs in numerous nanofluidic applications. In the present review, we focus on the slip and flow rates of water through CNTs and the factors influencing them. We discuss the key sources of discrepancies in water flow rate and suggest directions for future study.

/pdf/fast-transport-of-water-in-carbon-nanotubes-a-review-of-4u6s5jk31i.pdf

Fast transport of water in carbon nanotubes : a review of current accomplishments and challenges

This work presents results towards the bridging of nano- and macroscale acoustics of porous solids. We use molecular dynamics (MD) simulations to estimate the mechanical parameters of a nanoporous solid. These simulations consist in applying tensile and shear deformation to a zeolite
 material and calculate the mechanical properties from the linear regime of the stress-strain curve. The specific outcome of the simulations are phase velocities and mechanical parameters that can be used as inputs in meso/macroscopic models. To further exemplify the proposed nano-macroscale
 modelling strategy, wave propagation in a tube with an array of zeolite-made plates is studied, thereby providing a novel approach to the acoustic modelling of multiscale metamaterials.

Alan Sam

Papers

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

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

Prediction of fluid slip in cylindrical nanopores using equilibrium molecular simulations.

Fast transport of water in carbon nanotubes : a review of current accomplishments and challenges

Towards bridging nano- and macroscale acoustics of porous solids