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.

https://www.osapublishing.org/viewmedia.cfm?URI=IQEC-1987-WCC1

Surface studies using particle-beam-induced desorption and multiphoton resonance ionization

A novel approach to elucidate the ionization mechanism for the [M + H]+ molecular ion of organic molecules is investigated by molecular depth profiling of isotopically enriched thin films. Using a model bi-layer film of phenylalanine (PHE) and PHE-D8, the results show formation of an [M + D]+ molecular ion for the non-enriched PHE molecule attributed to rearrangements of chemical damage due to successive primary ion impacts. The [M + D]+ ion is observed at the interface for 19.9 nm in the enriched-on-top system and 9.9 nm for the enriched-on-bottom system. This ion formation is direct evidence for dynamically created pre-formed ions as a result of chemical damage rearrangement induced by previous primary ion bombardment events. Copyright © 2012 John Wiley & Sons, Ltd.

/pdf/evidence-for-the-formation-of-dynamically-created-pre-formed-3c7of3lzbu.pdf

Evidence for the formation of dynamically created pre-formed ions at the interface of isotopically enriched thin films.

Molecular depth profiling of multilayer organic films is now an established protocol for cluster secondary ion mass spectrometry (SIMS). This unique capability is exploited here to study the ionization mechanism associated with matrix-enhanced SIMS and possibly matrix assisted laser desorption/ionization (MALDI). Successful depth profiling experiments were performed on model bi-layer systems using 2,5-dihydroxybenzoic acid (DHB) as the matrix with dipalmitoylphosphatidylcholine (DPPC) or phenylalanine (PHE). The interaction between the matrix and organic analyte is monitored at the interface of the films. Tri-layer films with D2O as a thin-film sandwiched between the matrix and organic layers are also investigated to determine what role, if any, water plays during ionization. The results show successful depth profiles when taken at 90K. Mixing is observed at the interfaces of the films due to primary ion bombardment, but this mixing does not recreate the conditions necessary for ionization enhancement.

/pdf/investigations-into-the-interactions-of-a-maldi-matrix-with-54nmeaxcao.pdf

Investigations Into the Interactions of a MALDI Matrix with Organic Thin Films Using C60+ SIMS Depth Profiling.

Depth profiles yielding both information on oxidation state and elemental composition have been obtained for model nichrome films by using X-ray Photo-electron Spectroscopy and argon ion sputtering. Evidence is presented showing the formation of thin insulating films at the interface between two metals caused by solid state reactions occuring between metals and metal oxides.

Nichrome Resistor Failures as Studied by X-ray Photoelectron Spectroscopy (XPS or ESCA)

It is known that high molecular weight, thermally labile molecules can be desorbed intact using keY ion beams. This knowledgehas led to numerous applications of fast atom bombardment (FAB) and secondary ion mass spectrometry (SIMS) by mass spec-trometric detection of the desorbed ions. Here we show that these measurements can be significantly enhanced by using reso-nanceenhancedlaser ionization to softly ionize the neutral component ofthe desorbed flux. This experimental configuration canproduce sensitivity improvements of several orders of magnitude over SIMS while adding a certain degree of selectivity to theionization process itself. Examples of this perfonnance will be presented using a wide variety of molecules including aromatichydrocarbons, a number ofbiologically relevant compounds and organic polymer substrates. In some cases, detection limits inthe attomole range can be achieved. 1. INTRODUCTION The application ofenergetic ion bombardment to the analysis ofnonvolatile, thermally labile compounds is a rapidly expandingresearch field. Akey to this expansion began with the discovery thatthermally labile molecules can be desorbed directly from thesolid state using energetic particles (1,2). The ion bombardment approach offers several unique advantages when compared toother related methods. In particular, ion beam desorption, as opposed to laser or thermal desorption, is extremely efficient atselectively removing material from only the top layer of a solid (3). This characteristic means that the signals are specific to thesurface concentration of the analyte. The molecules can be ionized by collisions during the desorption event or subsequentlyusing electron impact, chemical ionization or laser excitation (4). The separation of the desorption event from the ionizationevent is important to improve sensitivity since most of the desorbed flux consists of neutral particles (5).Moreover,matrixionization effects are not nearly as severe when using postionization techniques (6).Our efforts have been focused on utilizing multiphoton resonance ionization (MPRI) spectroscopy to ionize particles desorbedfrom surfaces using keY ion beams (7). MPRI detection offers selective ionization using relatively low power pulsed lasers (8).The low power requirement allows the use of a large ionization volume. This aspect of the technique results in more efficientsampling than ionization schemes based on electron impact or focused lasers. Next, the pulsed nature of the radiation adds an-other dimension ofselectivity provided by the built—in availability ofa time-of—flight (TOF) mass spectrometer detector. Thesedetectors exhibit inherently very high transmission efficiency (9). Finally, MPRI can be an extremely efficient means of produc-ing ions. For the case ofatomic species, we have already demonstrated ionization efficiencies of several percent, yielding detec-tion limits ofjust a few hundreds atoms spread over a 1 cm2 surface (8).Special problems arise when attempting to utilize this technology for the detection of molecules on surfaces using ion beaminduced desorption. Computer simulations (10) as well as a limited number of experimental studies (1 1,12) suggest that themolecules desorb in a variety of highly excited vibrational and rotational states, with the largest population remaining in theground state electronic manifold. Two approaches have been successfully pursued in connection with other desorption schemeswhich will likely have relevance to the ion beam induced desorption technique. In one scheme, the molecules are first entrainedand cooled by a supersonicjet ofa noble gas (13). The advantage ofthis step is that the target molecules are cooled into a singlespectroscopic state. The MPRI process can then be highly selective and efficient. A disadvantage is that only a very smallfraction of the molecules can be trapped into thejet, dramatically reducing sensitivity. In a second approach, the molecules areionized directly by a laser tuned to a wavelength associated with an electronic transition of the molecule. Since there are a highdensity ofoccupied vibrational androtational states in the ground state manifold and since each ofthese states can connect with areal level in the excited state manifold, a degree of selectivity is lost. This simplifl&l scheme, however, offers major advantagesin sensitivity due to the increased sampling efficiency.2

Nicholas Winograd

Papers

Surface studies using particle-beam-induced desorption and multiphoton resonance ionization

Evidence for the formation of dynamically created pre-formed ions at the interface of isotopically enriched thin films.

Investigations Into the Interactions of a MALDI Matrix with Organic Thin Films Using C60+ SIMS Depth Profiling.

Nichrome Resistor Failures as Studied by X-ray Photoelectron Spectroscopy (XPS or ESCA)

Multiphoton resonance ionization of molecules desorbed from surfaces by ion beams