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 interaction of vapor-deposited Al atoms with self-assembled monolayers of HS(CH2)15CO2H chemisorbed at polycrystalline Au(111) surfaces has been studied using time-of-flight secondary-ion mass spectrometry, X-ray photoelectron spectroscopy, and infrared spectroscopy. The Al deposition was performed incrementally at room temperature. The Al atoms do not penetrate into the organic monolayer, but rather they remain at the vacuum interface where they undergo chemical interactions solely with the CO2H groups. Reaction of the CO2H groups continues until slightly more than one atom per reacting group is deposited, on average; thereafter, no further reaction is observed. However, 20−25% of the CO2H groups remain unreacted, regardless of the Al coverage. These results are explained on the basis of a combination of chemical and steric effects.

The interaction of vapor-deposited Al atoms with CO2H groups at the surface of a self-assembled alkanethiolate monolayer on gold

Spectroelectrochemical measurement of chemical reaction rates. First-order catalytic processes

A hybrid quadrupole orthogonal time-of-flight mass spectrometer optimized for matrix-assisted laser desorption ionization (MALDI) and electrospray ionization has been equipped with a C60 cluster ion source. This configuration is shown to exhibit a number of characteristics that improve the performance of traditional time-of-flight secondary ion mass spectrometry (TOF-SIMS) experiments for the analysis of complex organic materials and, potentially, for chemical imaging. Specifically, the primary ion beam is operated as a continuous rather than a pulsed beam, resulting in up to 4 orders of magnitude greater ion fluence on the target. The secondary ions are extracted at very low voltage into 8 mTorr of N2 gas introduced for collisional focusing and cooling purposes. This extraction configuration is shown to yield secondary ions that rapidly lose memory of the mechanism of their birth, yielding tandem mass spectra that are identical for SIMS and MALDI. With implementation of ion trapping, the extraction effic...

/pdf/c60-secondary-ion-mass-spectrometry-with-a-hybrid-quadrupole-3gguz2icxy.pdf

C60 secondary ion mass spectrometry with a hybrid-quadrupole orthogonal time-of-flight mass spectrometer.

Methylidyne, methylene, and methyl fragments have been proposed to be key intermediates in the methanation of CO and H/sub 2/ over Group VIII (groups 8-10) metals, but the direct experimental observation of these species has proven difficult to achieve. Methylidyne and methylene fragments adsorbed on Fe(110) have been observed by electron energy loss spectrometry (EELS) immediately after Fischer-Tropsch synthesis at 1 atm, but on Ru(001) only methylide was detected by EELS after hydrogenation of a predeposited carbide under vacuum conditions. Only methyl fragments have been previously observed by X-ray photoelectron spectroscopy (XPS) after CH/sub 3/Cl decomposition on Ni or Co surfaces between 170 and 200 K. Here static secondary ion mass spectrometry (SIMS) and XPS data on a Ni(111) single crystal immediately after CO + H/sub 2/ reaction at 50-100 torr, 550 K are presented. The data show the formation of all three of the intermediates methyne, methylene, and methyl. 15 references, 1 figure, 1 table.

Nicholas Winograd

Papers

The interaction of vapor-deposited Al atoms with CO2H groups at the surface of a self-assembled alkanethiolate monolayer on gold

Spectroelectrochemical measurement of chemical reaction rates. First-order catalytic processes

C60 secondary ion mass spectrometry with a hybrid-quadrupole orthogonal time-of-flight mass spectrometer.

Direct SIMS Observation of Methylidyne, Methylene, and Methyl Intermediates on a Ni(111) Methanation Catalyst

Spectroscopic studies of methanol decomposition on Pd[lcub]111[rcub]