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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A method of fabricating ultrathin (≈22–53 nm thick) graphene nanofiltration membranes (uGNMs) on microporous substrates is presented for efficient water purification using chemically converted graphene (CCG). The prepared uGNMs show well packed layer structure formed by CCG sheets, as characterized by scanning electron microscopy, atomic force microscopy, and transmission electron microscopy. The performance of the uGNMs for water treatment was evaluated on a dead end filtration device and the pure water flux of uGNMs was high (21.8 L m−2 h−1 bar−1). The uGNMs show high retention (>99%) for organic dyes and moderate retention (≈20–60%) for ion salts. The rejection mechanism of this kind of negatively charged membranes is intensively studied, and the results reveal that physical sieving and electrostatic interaction dominate the rejection process. Because of the ultrathin nature of uGNMs, 34 mg of CCG is sufficient for making a square meter of nanofiltration membrane, indicating that this new generation graphene-based nanofiltration technology would be resource saving and cost-effective. The integration of high performance, low cost, and simple solution-based fabrication process promises uGNMs great potential application in practical water purification.

Ultrathin Graphene Nanofiltration Membrane for Water Purification

We report a novel procedure to synthesize a new type of water separation membrane using graphene oxide (GO) nanosheets such that water can flow through the nanochannels between GO layers while unwanted solutes are rejected by size exclusion and charge effects. The GO membrane was made via layer-by-layer deposition of GO nanosheets, which were cross-linked by 1,3,5-benzenetricarbonyl trichloride, on a polydopamine-coated polysulfone support. The cross-linking not only provided the stacked GO nanosheets with the necessary stability to overcome their inherent dispensability in water environment but also fine-tuned the charges, functionality, and spacing of the GO nanosheets. We then tested the membranes synthesized with different numbers of GO layers to demonstrate their interesting water separation performance. It was found that the GO membrane flux ranged between 80 and 276 LMH/MPa, roughly 4–10 times higher than that of most commercial nanofiltration membranes. Although the GO membrane in the present deve...

Enabling graphene oxide nanosheets as water separation membranes.

Pressure-driven ultrafiltration membranes are important in separation applications. Advanced filtration membranes with high permeance and enhanced rejection must be developed to meet rising worldwide demand. Here we report nanostrand-channelled graphene oxide ultrafiltration membranes with a network of nanochannels with a narrow size distribution (3-5 nm) and superior separation performance. This permeance offers a 10-fold enhancement without sacrificing the rejection rate compared with that of graphene oxide membranes, and is more than 100 times higher than that of commercial ultrafiltration membranes with similar rejection. The flow enhancement is attributed to the porous structure and significantly reduced channel length. An abnormal pressure-dependent separation behaviour is also reported, where the elastic deformation of nanochannels offers tunable permeation and rejection. The water flow through these hydrophilic graphene oxide nanochannels is identified as viscous. This nanostrand-channelling approach is also extendable to other laminate membranes, providing potential for accelerating separation and water-purification processes.

/pdf/ultrafast-viscous-water-flow-through-nanostrand-channelled-1y64fqm2a4.pdf

Ultrafast viscous water flow through nanostrand-channelled graphene oxide membranes

The purpose of this paper is threefold. First, we review the existing literature on flow rates of water in carbon nanotubes. Data for the slip length which characterizes the flow rate are scattered over 5 orders of magnitude for nanotubes of diameter 0.81-10 nm. Second, we precisely compute the slip length using equilibrium molecular dynamics (EMD) simulations, from which the interfacial friction between water and carbon nanotubes can be found, and also via external field driven non-equilibrium molecular dynamics simulations (NEMD). We discuss some of the issues in simulation studies which may be reasons for the large disagreements reported. By using the EMD method friction coefficient to determine the slip length, we overcome the limitations of NEMD simulations. In NEMD simulations, for each tube we apply a range of external fields to check the linear response of the fluid to the field and reliably extrapolate the results for the slip length to values of the field corresponding to experimentally accessible pressure gradients. Finally, we comment on several issues concerning water flow rates in carbon nanotubes which may lead to some future research directions in this area.

https://researchbank.swinburne.edu.au/file/762e6a29-197f-4d24-b1b5-1cc29c6e8cc4/1/PDF (Published version).pdf

How fast does water flow in carbon nanotubes

Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is “not practical, if not impossible” based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.

/pdf/slip-length-of-water-on-graphene-limitations-of-non-4yepvdt2hl.pdf

Slip length of water on graphene: Limitations of non-equilibrium molecular dynamics simulations

We investigate the hydrodynamic boundary condition for simple nanofluidic systems such as argon and methane flowing in graphene nanochannels using equilibrium molecular dynamics simulations (EMD) in conjunction with our recently proposed method [J. S. Hansen, B. D. Todd, and P. J. Daivis, Phys. Rev. E 84, 016313 (2011)10.1103/PhysRevE.84.016313]. We first calculate the fluid-graphene interfacial friction coefficient, from which we can predict the slip length and the average velocity of the first fluid layer close to the wall (referred to as the slip velocity). Using direct nonequilibrium molecular dynamics simulations (NEMD) we then calculate the slip length and slip velocity from the streaming velocity profiles in Poiseuille and Couette flows. The slip lengths and slip velocities from the NEMD simulations are found to be in excellent agreement with our EMD predictions. Our EMD method therefore enables one to directly calculate this intrinsic friction coefficient between fluid and solid and the slip length for a given fluid and solid, which is otherwise tedious to calculate using direct NEMD simulations at low pressure gradients or shear rates. The advantages of the EMD method over the NEMD method to calculate the slip lengths/flow rates for nanofluidic systems are discussed, and we finally examine the dynamic behaviour of slip due to an externally applied field and shear rate.

https://researchbank.swinburne.edu.au/file/5560ab4f-0da3-4dcb-9286-dc75cebb9e8a/1/PDF (Published version).pdf

Slip flow in graphene nanochannels

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.

https://espace.library.uq.edu.au/view/UQ:692308/UQ692308_OA.pdf

Sridhar Kumar Kannam

Papers

How fast does water flow in carbon nanotubes

Slip length of water on graphene: Limitations of non-equilibrium molecular dynamics simulations

Slip flow in graphene nanochannels

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

Hydrogen bonds and twist in cellulose microfibrils