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.

/pdf/impermeable-atomic-membranes-from-graphene-sheets-xtis5huy2d.pdf

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

This paper examines the communication characteristics of a collection of scientific applications selected from the LLNL's Sequoia suite of benchmarks and the ANL's workload. By using an instrumentation library built on top of MPI we collect and characterize the applications's messaging behavior: the type of communication patterns and primitives used, the amount of time spent for communication, the message sizes, the total amount of data exchanged, and the impact of collective primitives, through communication matrices we visualize the actual communication patterns to highlight symmetries and other relevant peculiarities. Our analysis exposes several similarities between the applications -- namely the utilization of common low-dimensional stencils, and the use of a small set of collective primitives, in particular all-reduces with small vectors. Overall, our study provides a better understanding of the communication characteristics of several important scientific applications and benchmarks.

Characterization of the Communication Patterns of Scientific Applications on Blue Gene/P

Photon- or electron stimulated desorption (PSD or ESD) from solid surfaces results from the excitation of localized surface or adsorbate electronic states. The fundamental issues include the identification of electronic excitations with lead to desorption, the mechanisms for localization of the excitation, and the competition between nuclear motion and quenching of the excited states. We discuss these basic issues and their role in understanding stimulated desorption of molecular adsorbates from metal surfaces, and the desorption processes important in electron or photon bombardment of ionic solids. We focus on simple systems which serve as useful prototypes: CO chemisorbed on metals for adsorbate systems, and alkali-halides tor ionic solids. We review the current understanding of PSD and ESD for these systems, including a variety of very recent results. Finally, we discuss an example of the application of ESD to provide precise control of surface chemistry in the synthesis of electronic materials.

Desorption via electronic transitions: Fundamental mechanisms and applications

We present a simple collision model which describes the vibrational energy distributions and dissociation probability for diatomic molecules that are directly ejected by collisional sputtering. The results show that the probability that molecules survive sputtering without dissociation can be quite high (> 90%), and that monotonically decreasing vibrational distributions can often be expected, with a majority of the molecules in low vibrational levels (n = 0,1,2, 3). The model provides a collisional explanation for the observation of Boltzmann-like vibrational distributions for sputtered molecules. The calculations show that the use of impulsive collision models can reasonably account for the relative yield of sputtered molecules. However, in order to predict vibrational energy distributions which are qualitatively correct, it is necessary to go beyond the impulsive approximation by explicitly allowing for the finite duration of collisions.

Model for direct ejection of diatomic molecules by collisional sputtering

Classical trajectory multiple interaction simulations were used to study the bombardment of a clean, perfect, Cu target by low energy (

Classical trajectory study of atom and molecule ejection during low energy bombardment of copper by oxygen

Optimizing future supercomputing applications will depend on delivering the best performance for a given power budget. To determine the effect on efficiency of application-scaling parameters, this article analyzes system power and performance measurement results for real-world applications exploiting thread- and data-level parallelism on the Blue Gene/L system

Robert E. Walkup

Papers

Characterization of the Communication Patterns of Scientific Applications on Blue Gene/P

Desorption via electronic transitions: Fundamental mechanisms and applications

Model for direct ejection of diatomic molecules by collisional sputtering

Classical trajectory study of atom and molecule ejection during low energy bombardment of copper by oxygen

Exploiting Workload Parallelism for Performance and Power Optimization in Blue Gene