989 resultados para atom surface collisions
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An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally reach the detector. As a result, the detector is illuminated by intensive “showers,” where each event of detection must be weighted according to the actual probability of the atom displacement. The computational cost of such simulation is orders of magnitude lower than in the direct approach, and a comprehensive analysis of multiple and plural scattering effects becomes possible. We use this method for two purposes. First, the accuracy of the approximate approaches, developed mainly for ion-beam structural analysis, is verified. Second, the possibility to reproduce a wide class of experimental conditions is used to analyze some basic features of ion-solid collisions: the role of double violent collisions in low-energy ion scattering; the origin of the “surface peak” in scattering from amorphous samples; the low-energy tail in the energy spectra of scattered medium-energy ions due to plural scattering; and the degradation of blocking patterns in two-dimensional angular distributions with increasing depth of scattering. As an example of simulation for ions of MeV energies, we verify the time reversibility for channeling and blocking of 1-MeV protons in a W crystal. The possibilities of analysis that our approach offers may be very useful for various applications, in particular, for structural analysis with atomic resolution.
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The residue environment in protein structures is studied with respect to the density of carbon (C), oxygen (O), and nitrogen (N) atoms within a certain distance (say 5 Å) of each residue. Two types of environments are evaluated: one based on side-chain atom contacts (abbreviated S-S) and the other based on all atom (side-chain + backbone) contacts (abbreviated A-A). Different atom counts are observed about nine-residue structural categories defined by three solvent accessibility levels and three secondary structure states. Among the structural categories, the S-S atom count ratios generally vary more than the A-A atom count ratios because of the fact that the backbone (O) and (N) atoms contribute equal counts. Secondary structure affects the (C) density for the A-A contacts whereas secondary structure has little influence on the (C) density for the S-S contacts. For S-S contacts, a greater density of (O) over (N) atom neighbors stands out in the environment of most amino acid types. By contrast, for A-A contacts, independent of the solvent accessibility levels, the ratio (O)/(N) is ≈1 in helical states, consistent with the geometry of α-helical residues whose side-chains tilt oppositely to the amino to carboxy α-helical axis. The highest ratio of neighbor (O)/(N) is achieved under solvent exposed conditions. This (O) vs. (N) prevalence is advantageous at the protein surface that generally exhibits an acid excess that helps to enhance protein solubility in the cell and to avoid nonspecific interactions with phosphate groups of DNA, RNA, and other plasma constituents.
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Plasma processing is a standard industrial method for the modification of material surfaces and the deposition of thin films. Polyatomic ions and neutrals larger than a triatomic play a critical role in plasma-induced surface chemistry, especially in the deposition of polymeric films from fluorocarbon plasmas. In this paper, low energy CF3+ and C3F5+ ions are used to modify a polystyrene surface. Experimental and computational studies are combined to quantify the effect of the unique chemistry and structure of the incident ions on the result of ion-polymer collisions. C3F5+ ions are more effective at growing films than CF3+, both at similar energy/atom of ≈6 eV/atom and similar total kinetic energies of 25 and 50 eV. The composition of the films grown experimentally also varies with both the structure and kinetic energy of the incident ion. Both C3F5+ and CF3+ should be thought of as covalently bound polyatomic precursors or fragments that can react and become incorporated within the polystyrene surface, rather than merely donating F atoms. The size and structure of the ions affect polymer film formation via differing chemical structure, reactivity, sticking probabilities, and energy transfer to the surface. The different reactivity of these two ions with the polymer surface supports the argument that larger species contribute to the deposition of polymeric films from fluorocarbon plasmas. These results indicate that complete understanding and accurate computer modeling of plasma–surface modification requires accurate measurement of the identities, number densities, and kinetic energies of higher mass ions and energetic neutrals.
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In this work, the different adsorption properties of H and alkali metal atoms on the basal plane of graphite are studied and compared using a density functional method on the same model chemistry level. The results show that H prefers the on-top site while alkali metals favor the middle hollow site of graphite basal plane due to the unique electronic structures of H, alkali metals, and graphite. H has a higher electronegativity than carbon, preferring to form a covalent bond with C atoms, whereas alkaline metals have lower electronegativity, tending to adsorb on the highest electrostatic potential sites. During adsorption, there are more charges transferred from alkali metal to graphite than from H to graphite.
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The low index Magnesium hydride surfaces, MgH2(001) and MgH2(110), have been studied by ab intio Density Functional Theory (DFT) calculations. It was found that the MgH2(110) surface is more stable than MgH2(001) surface, which is in good agreement with the experimental observation. The H-2 desorption barriers vary depending on the crystalline surfaces that are exposed and also the specific H atom sites involved-they are found to be generally high, due to the thermodynamic stability of the MgH2, system, and are larger for the MgH2(001) surface. The pathway for recombinative desorption of one in-plane and one bridging H atom from the MgH2(110) surface was found to be the lowest energy barrier amongst those computed (172 KJ/mol) and is in good agreement with the experimental estimates. (c) 2006 Elsevier B.V. All rights reserved.
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Ab initio density functional theory (DFT) calculations are performed to explore possible catalytic effects on the dissociative chemisorption of hydrogen on a Mg(0001) surface when carbon is incorporated into Mg materials. The computational results imply that a C atom located initially on a Mg(0001) surface can migrate into the subsurface and occupy an fcc interstitial site, with charge transfer to the C atom from neighboring Mg atoms. The effect of subsurface C on the dissociation of H-2 on the Mg(0001) surface is found to be relatively marginal: a perfect sublayer of interstitial C is calculated to lower the barrier by 0.16 eV compared with that on a pure Mg(0001) surface. Further calculations reveal, however, that sublayer C may have a significant effect in enhancing the diffusion of atomic hydrogen into the sublayers through fcc channels. This contributes new physical understanding toward rationalizing the experimentally observed improvement in absorption kinetics of H2 when graphite or single walled carbon nanotubes (SWCNT) are introduced into the Mg powder during ball milling.
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The edge-to-edge matching model, which was originally developed for predicting crystallographic features in diffusional phase transformations in solids, has been used to understand the formation of in-plane textures in TiSi2 (C49) thin films on Si single crystal (001)si surface. The model predicts all the four previously reported orientation relationships between C49 and Si substrate based on the actual atom matching across the interface and the basic crystallographic data only. The model has strong potential to be used to develop new thin film materials. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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Ab initio density functional theory (DFT) calculations are performed to study the adsorption of H-2 molecules on a Ti-doped Mg(0001) surface. We find that two hydrogen molecules are able to dissociate on top of the Ti atom with very small activation barriers (0.103 and 0.145 eV for the first and second H-2 molecules, respectively). Additionally, a molecular adsorption state of H-2 above the Ti atom is observed for the first time and is attributed to the polarization of the H-2 molecule by the Ti cation. Our results parallel recent findings for H-2 adsorption on Ti-doped carbon nanotubes or fullerenes. They provide new insight into the preliminary stages of hydrogen adsorption onto Ti-incorporated Mg surfaces.
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We describe the production of BECs on a new type of atom chip based on silver foil. Our atom chip is fabricated with thick wires capable of carrying currents of several amperes without overheating. The silver surface is highly reflective to light resonant with optical transitions used for Rb. The pattern on the chip consists of two parallel Z-trap wires, capable of producing two-wire guide, and two additional endcap wires for varying the axial confinement. Condensates are produced in magnetic microtraps formed within 1 mm of surface of the chip. We have observed the fragmentation of cold atom clouds when brought close to the chip surface. This results from a perturbed trapping potential caused by nanometer deviations of the current path through the wires on the chip. We present results of fragmentation of cold clouds at distances below 100 µm from the wires and investigate the origin of the deviating current. The fragmentation has different characteristics to those seen with copper conductors. The dynamics of atoms in these microtraps is also investigated. ©2005 COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
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A new surface analysis technique has been developed which has a number of benefits compared to conventional Low Energy Ion Scattering Spectrometry (LEISS). A major potential advantage arising from the absence of charge exchange complications is the possibility of quantification. The instrumentation that has been developed also offers the possibility of unique studies concerning the interaction between low energy ions and atoms and solid surfaces. From these studies it may also be possible, in principle, to generate sensitivity factors to quantify LEISS data. The instrumentation, which is referred to as a Time-of-Flight Fast Atom Scattering Spectrometer has been developed to investigate these conjecture in practice. The development, involved a number of modifications to an existing instrument, and allowed samples to be bombarded with a monoenergetic pulsed beam of either atoms or ions, and provided the capability to analyse the spectra of scattered atoms and ions separately. Further to this a system was designed and constructed to allow incident, exit and azimuthal angles of the particle beam to be varied independently. The key development was that of a pulsed, and mass filtered atom source; which was developed by a cyclic process of design, modelling and experimentation. Although it was possible to demonstrate the unique capabilities of the instrument, problems relating to surface contamination prevented the measurement of the neutralisation probabilities. However, these problems appear to be technical rather than scientific in nature, and could be readily resolved given the appropriate resources. Experimental spectra obtained from a number of samples demonstrate some fundamental differences between the scattered ion and neutral spectra. For practical non-ordered surfaces the ToF spectra are more complex than their LEISS counterparts. This is particularly true for helium scattering where it appears, in the absence of detailed computer simulation, that quantitative analysis is limited to ordered surfaces. Despite this limitation the ToFFASS instrument opens the way for quantitative analysis of the 'true' surface region to a wider range of surface materials.
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This thesis considers the computer simulation of moist agglomerate collisions using the discrete element method (DEM). The study is confined to pendular state moist agglomerates, at which liquid is presented as either absorbed immobile films or pendular liquid bridges and the interparticle force is modelled as the adhesive contact force and interstitial liquid bridge force. Algorithms used to model the contact force due to surface adhesion, tangential friction and particle deformation have been derived by other researchers and are briefly described in the thesis. A theoretical study of the pendular liquid bridge force between spherical particles has been made and the algorithms for the modelling of the pendular liquid bridge force between spherical particles have been developed and incorporated into the Aston version of the DEM program TRUBAL. It has been found that, for static liquid bridges, the more explicit criterion for specifying the stable solution and critical separation is provided by the total free energy. The critical separation is given by the cube root of liquid bridge volume to a good approximation and the 'gorge method' of evaluation based on the toroidal approximation leads to errors in the calculated force of less than 10%. Three dimensional computer simulations of an agglomerate impacting orthogonally with a wall are reported. The results demonstrate the effectiveness of adding viscous binder to prevent attrition, a common practice in process engineering. Results of simulated agglomerate-agglomerate collisions show that, for colinear agglomerate impacts, there is an optimum velocity which results in a near spherical shape of the coalesced agglomerate and, hence, minimises attrition due to subsequent collisions. The relationship between the optimum impact velocity and the liquid viscosity and surface tension is illustrated. The effect of varying the angle of impact on the coalescence/attrition behaviour is also reported. (DX 187, 340).
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The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein’s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.
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Acknowledgments This research has been enabled by the use of computing resources provided by WestGrid, the Shared Hierarchical Academic Research Computing Network (SHARCNET: www.sharcnet.ca), and Compute/Calcul Canada. O.S. thanks NSERC for an Alexander Graham Bell Canada Graduate Scholarship.
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We calculate elastic scattering of positronium (Ps) by the Xe atom using the recently developed pseudopotential method (Fabrikant and Gribakin 2014 Phys. Rev. A 90 052717) and review general features of Ps scattering from heavier rare-gas atoms: Ar, Kr and Xe. The total scattering cross section is dominated by two contributions: elastic scattering and Ps ionization (break-up). To calculate the Ps ionization cross sections we use the binary-encounter method for Ps collisions with an atomic target. Our results for the ionization cross section agree well with previous calculations carried out in the impulse approximation. Our total Ps–Xe cross section, when plotted as a function of the projectile velocity, exhibits similarity with the electron-Xe cross section for the collision velocities higher than 0.8 a.u., and agrees very well with the measurements at Ps velocities above 0.5 a.u.