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

Logic gates were fabricated from an array of configurable switches, each consisting of a monolayer of redox-active rotaxanes sandwiched between metal electrodes. The switches were read by monitoring current flow at reducing voltages. In the “closed” state, current flow was dominated by resonant tunneling through the electronic states of the molecules. The switches were irreversibly opened by applying an oxidizing voltage across the device. Several devices were configured together to produce AND and OR logic gates. The high and low current levels of those gates were separated by factors of 15 and 30, respectively, which is a significant enhancement over that expected for wired-logic gates.

http://science.sciencemag.org/content/sci/285/5426/391.full.pdf

Electronically Configurable Molecular-Based Logic Gates

(1976). Nuclear Tracks in Solids (Principles and Applications) Nuclear Technology: Vol. 30, No. 1, pp. 91-92.

Nuclear Tracks in Solids (Principles and Applications)

Teramac is a massively parallel experimental computer built at Hewlett-Packard Laboratories to investigate a wide range of different computational architectures. This machine contains about 220,000 hardware defects, any one of which could prove fatal to a conventional computer, and yet it operated 100 times faster than a high-end single-processor workstation for some of its configurations. The defect-tolerant architecture of Teramac, which incorporates a high communication bandwith that enables it to easily route around defects, has significant implications for any future nanometer-scale computational paradigm. It may be feasible to chemically synthesize individual electronic components with less than a 100 percent yield, assemble them into systems with appreciable uncertainty in their connectivity, and still create a powerful and reliable data communications network. Future nanoscale computers may consist of extremely large-configuration memories that are programmed for specific tasks by a tutor that locates and tags the defects in the system.

/pdf/a-defect-tolerant-computer-architecture-opportunities-for-5e41e3e5n5.pdf

A Defect-Tolerant Computer Architecture: Opportunities for Nanotechnology

Structural materials challenges for advanced reactor systems

Amorphous metallic Fe85B15 alloy has been irradiated at low temperature with Ar, Kr and Xe ions of initial energies of 1.8, 2.7 and 3.0 GeV, respectively. Electrical resistance was measured in situ on samples piled up along the beam direction. It is shown that above a given electronic stopping power threshold the electronic losses play a crucial role in radiation-induced damage.

High-energy heavy-ion irradiations of Fe85B15 amorphous alloy: evidence for electronic energy loss effect

Silicon carbide single crystals were irradiated at room temperature with low energy I ions and high energy Pb ions. It is found that the damaged layer formed by the elastic collisions generated during low energy I ion irradiation can readily be removed by the electronic excitations induced by swift Pb ions. This effect occurs at a temperature quite below that at which the conventional ion-beam induced crystallization process is generally achieved by nuclear energy loss. This finding is interesting both from a fundamental point of view for the understanding of the interaction of swift heavy ions with solids and for a large number of technological applications.

Athermal crystallization induced by electronic excitations in ion-irradiated silicon carbide

Crystalline ${\mathrm{Ni}}_{3}$B ribbons have been irradiated at low temperature with GeV heavy ions (Kr,Xe,U) in order to study the disordering process induced in this material by ion electronic energy loss. The atomic rearrangements produced by irradiation were monitored in situ via electrical resistance measurements and characterized after annealing at room temperature by electron diffraction. The results show a huge electrical resistivity increase above an electronic-energy-loss threshold, which can be ascribed to partial amorphization of the irradiated alloy.

Evidence for amorphization of a metallic alloy by ion electronic energy loss.

The pyrochlore oxides (A2B2O7) exhibit a remarkable range of structural, physical, and magnetic properties related to their various chemical compositions. This article reports the phase transformations induced by high electronic excitation in pyrochlores of the Gd2(ZrxTi1−x)2O7 family irradiated with swift ions. The structural changes, investigated by using several analytical techniques (x-ray diffraction, Raman spectroscopy, and transmission electron microscopy), strongly depend on the chemical composition. The high electronic excitation along the ion trajectory results in the amorphization of ion tracks for Gd2Ti2O7 and Gd2TiZrO7, whereas a defective fluorite structure is formed in Gd2Zr2O7. Moreover, the results underline the existence of an electronic stopping power threshold of 6 keV/nm for amorphizable compounds and 10 keV/nm for Gd2Zr2O7, below which phase transformations do not occur. Finally, the study of the thermal recovery of irradiated pyrochlores provides the recrystallization temperature fo...

Lionel Thomé

Papers

High-energy heavy-ion irradiations of Fe85B15 amorphous alloy: evidence for electronic energy loss effect

Athermal crystallization induced by electronic excitations in ion-irradiated silicon carbide

Evidence for amorphization of a metallic alloy by ion electronic energy loss.

Phase transformations induced by high electronic excitation in ion-irradiated Gd2(ZrxTi1−x)2O7 pyrochlores

Structural evolution of zirconium carbide under ion irradiation