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.

The adsorption and subsequent decomposition of CH{sub 3}OH on Pd(111) has been examined with X-ray photoelectron spectroscopy and secondary ion mass spectrometry (SIMS) over the temperature range 110-600 K. The authors find that the thermal decomposition reaction pathway after adsorption at 110 K is strongly dependent on the initial CH{sub 3}OH exposure. Below the saturation CH{sub 3}OH exposure of 1.5 langmuirs the primary decomposition products are observed to be CH{sub 3ads}, OCH{sub 3ads}, and H{sub 2}O{sub ads}. This chemistry suggests that the methanolic C-O bond is activated at the metal surface. These products are observed to form at temperatures as low as 125 K. For exposures above 1.5 langmuirs this decomposition pathway is no longer observed, possibly due to a site blocking effect, and molecular desorption occurs with trace decomposition. Interestingly, they find no evidence that CH{sub 3}OH adsorbed at 110 K with initial exposures below 1.5 langmuirs decomposes to CO at any temperature below the thermal desorption temperature of CO at 490 K. finally, the SIMS ion observed at m/e 15 (CH{sub 3ads}) and associated with the decomposition of CH{sub 3}OH is found to persist over the rather wide temperature range 125-400 K. The unusual stability of CH{sub 3ads}more » suggested by these findings may be related to the effectiveness of Pd-based catalysts to produce CH{sub 3}OH.« less

Thermal decomposition of methanol absorbed on palladium{111}. A new reaction pathway involving methyl formation

Osteoblast adhesion on poly(L-lactic acid)/polystyrene demixed thin film blends: effect of nanotopography, surface chemistry, and wettability.

The mechanism for the formation of small metal clusters ejected from an ion bombarded metal surface is examined in detail. The analysis is performed by classical trajectory methods which determine the positions and momenta of all particles in a model microcrystallite as a function of time. The calculation utilizes pair potentials for Cu derived from elastic constants of the solid and is performed for 600 eV Ar+ ion at normal incidence to the crystal. The results show that cluster species do not leave the surface as intact parts of the solid but form in a region above the surface. A trajectory for Cu5 formation is traced in detail showing a typical mechanism which is valid for Cun formation where n?7.

Formation of small metal clusters by ion bombardment of single crystal surfaces

The chemisorption of oxygen on clean polycrystalline indium surfaces is investigated by the combined techniques of x‐ray photoelectron spectroscopy (XPS) and the static mode of secondary ion mass spectroscopy (SIMS). Oxygen uptake is characterized by a moderately rapid formation of In2O3, with no preoxidation adsorbed O2 phase discernable in the XPS spectra. A high binding energy O (1s) peak becomes prominent after one monolayer of In2O3 has formed, which we ascribe to adsorbed oxygen on the oxide. Formation of In2O3 continues into the bulk either via migration of the adsorbed oxygen through the oxide layer to the metal‐In2O3 interface or by the outward migration of indium cations to the surface. Both the formation of oxide and the onset of adsorption are reflected in the secondary ion yield ratios InO−2/InO− and O−2/O−. The behavior of SIMS molecular cluster ion yields with oxygen exposure are consistent with recent theoretical calculations of the cluster formation process, in which considerable local atomic order of the surface is present in the cluster.

Nicholas Winograd

Papers

Thermal decomposition of methanol absorbed on palladium{111}. A new reaction pathway involving methyl formation

Osteoblast adhesion on poly(L-lactic acid)/polystyrene demixed thin film blends: effect of nanotopography, surface chemistry, and wettability.

Formation of small metal clusters by ion bombardment of single crystal surfaces

Oxidation of polycrystalline indium studied by x‐ray photoelectron spectroscopy and static secondary ion mass spectroscopy

Cationization of organic molecules in secondary ion mass spectrometry