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

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

A second-generation potential energy function for solid carbon and hydrocarbon molecules that is based on an empirical bond order formalism is presented. This potential allows for covalent bond breaking and forming with associated changes in atomic hybridization within a classical potential, producing a powerful method for modelling complex chemistry in large many-atom systems. This revised potential contains improved analytic functions and an extended database relative to an earlier version (Brenner D W 1990 Phys. Rev. B 42 9458). These lead to a significantly better description of bond energies, lengths, and force constants for hydrocarbon molecules, as well as elastic properties, interstitial defect energies, and surface energies for diamond.

/pdf/a-second-generation-reactive-empirical-bond-order-rebo-3nq9vxvup4.pdf

A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons

A new method of desorption ionization is described and applied to the ionization of various compounds, including peptides and proteins present on metal, polymer, and mineral surfaces. Desorption electrospray ionization (DESI) is carried out by directing electrosprayed charged droplets and ions of solvent onto the surface to be analyzed. The impact of the charged particles on the surface produces gaseous ions of material originally present on the surface. The resulting mass spectra are similar to normal ESI mass spectra in that they show mainly singly or multiply charged molecular ions of the analytes. The DESI phenomenon was observed both in the case of conductive and insulator surfaces and for compounds ranging from nonpolar small molecules such as lycopene, the alkaloid coniceine, and small drugs, through polar compounds such as peptides and proteins. Changes in the solution that is sprayed can be used to selectively ionize particular compounds, including those in biological matrices. In vivo analysis is demonstrated.

https://science.sciencemag.org/content/sci/306/5695/471.full.pdf

Mass Spectrometry Sampling Under Ambient Conditions with Desorption Electrospray Ionization

3.6.1. Polishing and Cleaning 2663 3.6.2. Vacuum and Heat Treatments 2664 3.6.3. Carbon Electrode Activation 2665 3.7. Summary and Generalizations 2666 4. Advanced Carbon Electrode Materials 2666 4.1. Microfabricated Carbon Thin Films 2666 4.2. Boron-Doped Diamond for Electrochemistry 2668 4.3. Fibers and Nanotubes 2669 4.4. Carbon Composite Electrodes 2674 5. Carbon Surface Modification 2675 5.1. Diazonium Ion Reduction 2675 5.2. Thermal and Photochemical Modifications 2679 5.3. Amine and Carboxylate Oxidation 2680 5.4. Modification by “Click” Chemistry 2681 6. Synopsis and Outlook 2681 7. Acknowledgments 2682 8. References 2682

/pdf/advanced-carbon-electrode-materials-for-molecular-2y6b22van0.pdf

Advanced carbon electrode materials for molecular electrochemistry.

Esca studies of metal and metal electrode surfaces.

Correction to Measuring Compositions in Organic Depth Profiling: Results from a VAMAS Interlaboratory Study.

Resultats de mesures des spectres de masse d'ions secondaires d'une serie de couches monomoleculaires de composes organiques (benzene et pyridine) adsorbes sur la facette 111 d'argent en vue d'eclaircir le mecanisme fondamental d'ejection des agregats moleculaires

Angle-resolved sims studies of organic monolayers on the silver (111) surface

The adsorption of NO and HCN on Rh surfaces can be monitored using the Rh2NO+ or RhHCN+ molecular cluster ions formed in static SIMS. From parallel XPS studies, for example, we find that NO adsorbs molecularly at 300K on Rh(111) but dissociates significantly on the Rh(331) surface. This dissociation is accompanied by a decrease in the Rh2NO+ ion yield and an increase in the Rh2N+ and Rh2O+ ion intensities. This type of chemical specificity illustrates that SIMS studies are possible on more complex systems which are difficult to monitor using XPS alone.

Nicholas Winograd

Papers

Esca studies of metal and metal electrode surfaces.

Correction to Measuring Compositions in Organic Depth Profiling: Results from a VAMAS Interlaboratory Study.

Angle-resolved sims studies of organic monolayers on the silver (111) surface

SIMS/XPS Studies of Surface Reactions on Rh(111) and Rh(331)

Direct SIMS Obervation of Methylidyne, Methylene, and Methyl Intermediates on a Ni(III) Methanation Catalyst (SIMS: secondary ion mass spectrometry).