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

We demonstrate that a monolayer graphene membrane is impermeable to standard gases including helium. By applying a pressure difference across the membrane, we measure both the elastic constants and the mass of a single layer of graphene. This pressurized graphene membrane is the world's thinnest balloon and provides a unique separation barrier between 2 distinct regions that is only one atom thick.

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Impermeable atomic membranes from graphene sheets.

SINCE the invention of the scanning tunnelling microscope1, the value of establishing a physical connection between the macroscopic world and individual nanometre-scale objects has become increasingly evident, both for probing these objects2–4 and for direct manipulation5–7 and fabrication8–10 at the nanometre scale. While good progress has been made in controlling the position of the macroscopic probe of such devices to sub-angstrom accuracy, and in designing sensitive detection schemes, less has been done to improve the probe tip itself4. Ideally the tip should be as precisely defined as the object under investigation, and should maintain its integrity after repeated use not only in high vacuum but also in air and water. The best tips currently used for scanning probe microscopy do sometimes achieve sub-nanometre resolution, but they seldom survive a 'tip crash' with the surface, and it is rarely clear what the atomic configuration of the tip is during imaging. Here we show that carbon nanotubes11,12 might constitute well defined tips for scanning probe microscopy. We have attached individual nanotubes several micrometres in length to the silicon cantilevers of conventional atomic force microscopes. Because of their flexibility, the tips are resistant to damage from tip crashes, while their slenderness permits imaging of sharp recesses in surface topography. We have also been able to exploit the electrical conductivity of nanotubes by using them for scanning tunnelling microscopy.

Nanotubes as nanoprobes in scanning probe microscopy

The Interaction of Water with Solid Surfaces: Fundamental Aspects Revisited

A concept for molecular electronics exploiting carbon nanotubes as both molecular device elements and molecular wires for reading and writing information was developed. Each device element is based on a suspended, crossed nanotube geometry that leads to bistable, electrostatically switchable ON/OFF states. The device elements are naturally addressable in large arrays by the carbon nanotube molecular wires making up the devices. These reversible, bistable device elements could be used to construct nonvolatile random access memory and logic function tables at an integration level approaching 10 12 elements per square centimeter and an element operation frequency in excess of 100 gigahertz. The viability of this concept is demonstrated by detailed calculations and by the experimental realization of a reversible, bistable nanotube-based bit.

/pdf/carbon-nanotube-based-nonvolatile-random-access-memory-for-2m51guev4k.pdf

Carbon nanotube-based nonvolatile random access memory for molecular computing

Molecular ion detection by a laser induced change in mobility

The interaction of electron and photon beams with insulating materials is of substantial current interest. Alkali halides are the most ionic of the ionic insulators, and they have comparatively simple geometric and electronic structures, thus they are useful prototypes for basic studies. When energetic electrons or photons are incident on alkali halides, particles are desorbed with high efficiency. The flux of particles leaving the bombarded region includes ground-state neutrals, excited-state neutrals, and positive ions. The vast majority of the desorbed particles are ground-state neutral atoms and molecules, which are ejected via bulk-defect mediated processes [l]. The ground-state yields can be remarkably large - for 1 keV electrons incident on NaCl at T=300 C, roughly 5 Na atoms and 5 CI atoms are desorbed per incident electron [2,3]. The desorption mechanisms for the ground-state particles have been qualitatively understood for some time. The initial excitation caused by the incident radiation is electron-hole generation in the bulk. The holes (neutral halogen atoms) are incorporated into stable defects called H centers which can diffuse to the surface, where neutral halogen atom desorption can occur. Neutral alkali atoms can be formed on the surface by re-combination of electrons and alkali ions, and these neutral atoms can then thermally desorb. This process appears to be limited by the diffusion of electrons (as F centers) to the surface [4]. The very large yields of ground state neutrals are related to the fact that the initial excitation results in a stable defect in the bulk, and desorption can occur much later after defect diffusion to the surface. The time delay due to the diffusion of defects to the surface has been directly observed in experiments using pulsed electron beams [4,5].

The Origin of Positive Ions and Excited Neutrals in Electron Stimulated Desorption from Alkali Halides

The interaction of O2(g) with clean Si(s) surfaces at high temperature and low pressure leads to an etching reaction, 1/2 O2(g) + Si(s) → SiO(g), which results in the evolution of SiO molecules from the surface. Above a critical O2 pressure, an oxide film SiO2(s) begins to grow. The evolution of diatomic SiO during the early stages of film growth may provide a mechanism to account for deviations from standard models of oxidation kinetics for thin oxides, and for the results of oxygen isotope tracer studies of oxide formation. In order to monitor the rate of SiO evolution, we have made in-situ measurements of the SiO concentration in the gas phase, using a laser-induced fluorescence technique. With this method, SiO(g) can be monitored in the furnace with good spatial resolution and a sensitivity limit of ~ 106 molecules cm−3. Measurements of SiO evolution and the implications for oxide growth will be discussed.

Robert E. Walkup

Papers

Molecular ion detection by a laser induced change in mobility

The Origin of Positive Ions and Excited Neutrals in Electron Stimulated Desorption from Alkali Halides

The Role of Diatomic SiO in Dry Oxidation of Si