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 role of the location of energy deposition during cluster ion bombardment on the quality of molecular depth profiling was examined by varying the incident angle geometry. Cholesterol films ∼300 nm in thickness deposited onto silicon substrates were eroded using 40-keV C60+ at incident angles ranging from 5° to 73° with respect to the surface normal. The erosion process was evaluated by determining at each incident angle the total sputtering yield of cholesterol molecules, the damage cross section of the cholesterol molecules, the altered layer thickness within the solid, the sputter yield decay in the quasi-steady-state sputter regime, and the interface width between the cholesterol film and the silicon substrate. The results show that the total sputtering yield is largest relative to the product of the damage cross section and the altered layer thickness at 73° incidence, suggesting that the amount of chemical damage accumulated is least when glancing incident geometries are used. Moreover, the signal...

Energy Deposition during Molecular Depth Profiling Experiments with Cluster Ion Beams

We have investigated the merits of fullerene cluster ions as projectiles in time-of-flight secondary neutral mass spectrometry (ToF-SNMS) sputter depth profiling of an Ni:Cr multilayer sample similar to the corresponding NIST depth profiling standard. It is shown that sputter erosion under bombardment with C60+ ions of kinetic energies between 10 and 20 keV provides good depth resolution corresponding to interface widths of several nanometres. This depth resolution is maintained during the complete removal of the multilayer stack with a total thickness of 500 nm. This finding is in contrast to the case where atomic Ga+ projectile ions of comparable kinetic energy are used, demonstrating the unique features of cluster projectiles in sputter depth profiling. Copyright © 2004 John Wiley & Sons, Ltd.

http://www.ilp.physik.uni-essen.de/wucher/Reference%20Manager/Sun%20SIA%2036%202004%201367.pdf

Use of C60 cluster projectiles for sputter depth profiling of polycrystalline metals

Characteristics of the electrode-solution interface under faradaic and non-faradaic conditions as observed by internal reflection spectroscopy

Homogeneous electron-transfer reactions studied by internal reflection spectroelectrochemistry

Coexisting liquid phases of model membrane systems are chemically identified using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS). The systems studied were Langmuir−Blodgett (LB) model membranes of cholesterol (CH) with two different phospholipids, one a major component in the outer plasma membrane bilayer leaflet (dipalmitoylphosphatidylcholine (PC)) and the other a major component in the inner leaflet (dipalmitoylphosphatidylethanolamine (PE)). Binary mixtures of CH with each of the phospholipids were investigated, as well as a ternary system. A single homogeneous phase is evident for PC/CH, whereas both systems containing PE show lateral heterogeneity with phospholipid-rich and CH-rich regions. The interaction between CH and the two phospholipids differs due to the disparity between the phospholipid headgroups. Imaging TOF-SIMS offers a novel opportunity to chemically identify and differentiate the specific membrane locations of CH and phospholipid in membrane regions without the use...

Nicholas Winograd

Papers

Energy Deposition during Molecular Depth Profiling Experiments with Cluster Ion Beams

Use of C60 cluster projectiles for sputter depth profiling of polycrystalline metals

Characteristics of the electrode-solution interface under faradaic and non-faradaic conditions as observed by internal reflection spectroscopy

Homogeneous electron-transfer reactions studied by internal reflection spectroelectrochemistry

Phosphatidylethanolamine-Induced Cholesterol Domains Chemically Identified with Mass Spectrometric Imaging