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

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Large-Scale Fabrication of Boron Nitride Nanosheets and Their Utilization in Polymeric Composites with Improved Thermal and Mechanical Properties

Two dimensional hexagonal boron nitride (2D-hBN), an isomorph of graphene with a very similar layered structure, is uniquely featured by its exotic opto-electrical properties together with mechanical robustness, thermal stability, and chemical inertness. It is thus extensively studied for application in field effect transistors (FETs), tunneling devices, deep UV emitters and detectors, photoelectric devices, and nanofillers. 2D-hBN is considered as one of the most promising materials that can be integrated with other 2D materials, such as graphene and transition metal dichalcogenides (TMDCs), for the next generation microelectronic and other technologies. Although it is by itself an insulator, it can well be tuned by several strategies in terms of properties and functionalities, such as by doping, substitution, functionalization and hybridization, making 2D-hBN a truly versatile type of functional materials for a wide range of applications. In this review, the distinct structural characteristics of 2D-hBN, doping- and defect-induced variations in energy bands and structures, and resultant properties, are presented. There are a wide variety of processing routes that have been developed for 2D-hBN, including also those for doping, substitution, functionalization and combination with other materials to form heterostructures or h-BNC hybrid nanosheets, which are systematically elaborated for novel functions. The comprehensive overview provides the types of the state-of-the-art 2D-hBN made by new synthesis strategies, where the mainstream approaches include exfoliation, chemical vapor deposition, and gas phase epitaxy, together with several other new methods that have been successfully developed in the past few years. On the basis of the extraordinary electrical and functional properties and thermal–mechanical stability, the applications of hBN-based nanosheets as substrates and dielectrics, passivation layers, and nanofillers in nanodevices and nanocomposites are discussed, together with the peculiar optical and wetting characteristics.

Two dimensional hexagonal boron nitride (2D-hBN): synthesis, properties and applications

Graphene and other two-dimensional materials offer a new approach to controlling mass transport at the nanoscale. These materials can sustain nanoscale pores in their rigid lattices and due to their minimum possible material thickness, high mechanical strength and chemical robustness, they could be used to address persistent challenges in membrane separations. Here we discuss theoretical and experimental developments in the emerging field of nanoporous atomically thin membranes, focusing on the fundamental mechanisms of gas- and liquid-phase transport, membrane fabrication techniques and advances towards practical application. We highlight potential functional characteristics of the membranes and discuss applications where they are expected to offer advantages. Finally, we outline the major scientific questions and technological challenges that need to be addressed to bridge the gap from theoretical simulations and proof-of-concept experiments to real-world applications.

Fundamental transport mechanisms, fabrication and potential applications of nanoporous atomically thin membranes

Desalination is a favorable method employed to supply clean water in recent years. Various contaminants entering water resources must be removed from water by novel structures like nanostructure membranes. Accordingly, molecular dynamics simulations were performed to study the ion removal from the water using a graphene nanosheet (GNS) based on the permeability and selectivity of graphene. The studied system consisted of two functionalized GNSs immersed in the aqueous ionic solution of NaCl. The GNSs had one pore each, both being approximately of the same size. For the ion removal from water using these GNSs, an external electric field was applied to the system. For the preferential permeation of cation or anion across the graphene, the pore of the GNS was functionalized by passivating each carbon atom at the edge of the pore by fluoride (F-pore), negatively charged, and hydrogen atoms (H-pore), which were positively charged. The results showed that by using the electric field the F-pore and the H-pore of...

Functionalized Graphene Nanosheet as a Membrane for Water Desalination Using Applied Electric Fields: Insights from Molecular Dynamics Simulations

Improving the performance of water desalination through ultra-permeable functionalized nanoporous graphene oxide membrane

Molecular dynamics simulation of trihalomethanes separation from water by functionalized nanoporous graphene under induced pressure

A computer simulation was performed to investigate the removal of Zn2+ as a heavy metal from aqueous solution using the functionalized pore of a graphene nanosheet and boron nitride nanosheet (BNNS). The simulated systems were comprised of a graphene nanosheet or BNNS with a functionalized pore containing an aqueous ionic solution of zinc chloride. In order to remove heavy metal from an aqueous solution using the functionalized pore of a graphene nanosheet and BNNS, an external voltage was applied along the z-axis of the simulated box. For the selective removal of zinc ions, the pores of graphene and BNNS were functionalized by passivating each atom at the pore edge with appropriate atoms. For complete analysis systems, we calculated the potential of the mean force of ions, the radial distribution function of ion–water, the residence time of ions, the hydrogen bond, and the autocorrelation function of the hydrogen bond.

Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations.

The purpose of the present study was to investigate the removal of copper and mercury using functionalized graphene as a nanostructured membrane. The molecular dynamics simulation method was used to investigate the removal ability of these ions from aqueous solution using functionalized graphene membrane. The studied systems included a functionalized graphene membrane which was placed in the aqueous ionic solution of CuCl2 and HgCl2. An external electrical field was applied along the z axis of the system. The results indicated that the application of electrical field on the system caused the desired ions to pass through the functionalized graphene membrane. The Fluorinated pore (F-pore) terminated graphene selectively conducted Cu2+ and Hg2+ ions. The calculation of the potential of mean force of ions revealed that Cu2+ and Hg2+ ions face a relatively small energy barrier and could not pass through the F-pore graphene unless an external electrical field was applied upon them. In contrast, the energy barrier for the Cl− ion was large and it could not pass through the F-pore graphene. The findings of the study indicate that the permeation of ions across the graphene was a function of applied electrical fields. The findings of the present study are based on the detailed analysis and consideration of potential of mean force and radial distribution function curves.

Jafar Azamat

Papers

Functionalized Graphene Nanosheet as a Membrane for Water Desalination Using Applied Electric Fields: Insights from Molecular Dynamics Simulations

Improving the performance of water desalination through ultra-permeable functionalized nanoporous graphene oxide membrane

Molecular dynamics simulation of trihalomethanes separation from water by functionalized nanoporous graphene under induced pressure

Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations.

Functionalized graphene as a nanostructured membrane for removal of copper and mercury from aqueous solution: a molecular dynamics simulation study.