Biomedical subjects

I K Snook

Publications and source records attributed to I K Snook.

11 recordsLinked to original sources

PubMed2006

Quantum Monte Carlo calculations of the dissociation energy of the water dimer.

We report diffusion quantum Monte Carlo (DMC) calculations of the equilibrium dissociation energy D(e) of the water dimer. The dissociation energy measured experimentally, D(0), can be estimated from D(e) by adding a correction for vibrational effects. Using the measured dissociation energy and the modern value of the vibrational energy Mas et al., [J. Chem. Phys. 113, 6687 (2000)] leads to D(e)=5.00+/-0.7 kcal mol(-1), although the result Curtiss et al., [J. Chem. Phys. 71, 2703 (1979)] D(e)=5.44+/-0.7 kcal mol(-1), which uses an earlier estimate of the vibrational energy, has been widely quoted. High-level coupled cluster calculations Klopper et al., [Phys. Chem. Chem. Phys. 2, 2227 (2000)] have yielded D(e)=5.02+/-0.05 kcal mol(-1). In an attempt to shed new light on this old problem, we have performed all-electron DMC calculations on the water monomer and dimer using Slater-Jastrow wave functions with both Hartree-Fock approximation (HF) and B3LYP density functional theory single-particle orbitals. We obtain equilibrium dissociation energies for the dimer of 5.02+/-0.18 kcal mol(-1) (HF orbitals) and 5.21+/-0.18 kcal mol(-1) (B3LYP orbitals), in good agreement with the coupled cluster results.

Journal Article↗

PubMed2005

First-principles modeling of dopants in C29 and C29H24 nanodiamonds.

Presented here is our continuing first-principles density functional theory study of the structural stability of a select group of dopants in diamond nanocrystals. On the basis of the work of others concerning dopants in diamond and endohedral atoms in fullerenes, the dopants selected for use here are oxygen, aluminum, silicon, phosphorus, and sulfur. These atoms were included substitutionally in the center of a 29-carbon-atom nanodiamond crystal, and each structure was relaxed using the Vienna Ab Initio Simulation Package. We describe the bonding and structure of the relaxed doped nanocrystals via examination of the electron charge density and point group symmetry. In combination with our previously reported results, it is anticipated that these results will assist in providing a better understanding of the mechanical stability of doped nanodiamonds for use in diamond nanodevices.

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PubMed2005

Application of numerical basis sets to hydrogen bonded systems: a density functional theory study.

We have investigated and compared the ability of numerical and Gaussian-type basis sets to accurately describe the geometries and binding energies of a selection of hydrogen bonded systems that are well studied theoretically and experimentally. The numerical basis sets produced accurate results for geometric parameters but tended to overestimate binding energies. However, a comparison of the time taken to optimize phosphinic acid dimer, the largest complex considered in this study, shows that calculations using numerical basis sets offer a definitive advantage where geometry optimization of large systems is required.

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PubMed2005

Refinements in the collection of energy filtered diffraction patterns from disordered materials.

In this paper a method for collecting electron diffraction patterns using a Gatan imaging filter is presented. The method enables high-quality diffraction data to be measured at scattering angles comparable to those that can be obtained using X-ray and neutron diffraction. In addition, the method offers the capability for examining small regions of sample in, for example, thin films and nano-structures. Using X-ray, neutron and electron diffraction data collected from the same sample, we demonstrate quantitative agreement between all three. We also present a novel method for obtaining the single scattering contribution to the total diffracted intensity by collecting data at various electron wavelengths. This approach allows pair distribution functions to be determined from electron diffraction in cases where there exists significant multiple scattering.

Journal Article↗

PubMed2005

Simulation and bonding of dopants in nanocrystalline diamond.

The doping of the wide-band gap semiconductor diamond has led to the invention of many electronic and optoelectronic devices. Impurities can be introduced into diamond during chemical vapor deposition or high pressure-high temperature growth, resulting in materials with unusual physical and chemical properties. For electronic applications one of the main objectives in the doping of diamond is the production of p-type and n-type semiconductors materials; however, the study of dopants in diamond nanoparticles is considered important for use in nanodevices, or as qubits for quantum computing. Such devices require that bonding of dopants in nanodiamond must be positioned substitutionally at a lattice site, and must exhibit minimal or no possibility of diffusion to the nanocrystallite surface. In light of these requirements, a number of computational studies have been undertaken to examine the stability of various dopants in various forms of nanocrystalline diamond. Presented here is a review of some such studies, undertaken using quantum mechanical based simulation methods, to provide an overview of the crystal stability of doped nanodiamond for use in diamondoid nanodevices.

Binding Sites↗

PubMed2004

Phase stability of nanocarbon in one dimension: nanotubes versus diamond nanowires.

Since their discovery in 1990, the study of sp2 bonded carbon nanotubes has grown into a field of research in it's own right; however the development of the sp3 analog, diamond nanowires, has been slow. A number of theoretical models have been proposed to compare the relative stability of diamond and graphite at the nanoscale; and more recently, to compare nanodiamonds and fullerenes. Presented here is a study of the phase stability of nanocarbon in one-dimension. The structural energies of carbon nanotubes and diamond nanowires have been calculated using density functional theory within the generalized gradient approximation, and used to determine the atomic heat of formation as a function of size.

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PubMed2002

How hard is a colloidal "hard-sphere" interaction?

Poly-12-hydroxystearic acid (PHSA) is widely used as a coating on colloidal spheres to provide a "hard-sphere-type" interaction. These hard spheres have been widely used in fundamental studies of nucleation, crystallization, and glass formation. Most authors describe the interaction as "nearly" hard sphere. In this paper we directly measure this interaction, using layers of PHSA adsorbed onto mica sheets in a surfaces force apparatus. We find that the layers, in appropriate solvents, have no long-range interaction. When the solvent is decahydronaphthalene (decalin), the repulsion rises from zero to the maximum measurable over a distance range of 15-20 nm. The data is converted to equivalent forces between spheres of different diameters, and modeled using a hard core potential. Using zeroth-order perturbation theory and computer simulation, we demonstrate that the equation of state does not deviate from that of a perfect hard-sphere system under any relevant experimental conditions.

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PubMed2002

The pore structure in processed Victorian Brown coal.

Changes in the pore structure of Victorian Brown coal when upgraded with heated gases under pressure are investigated. We show that the results obtained from ultra-small-angle neutron scattering (USANS) measurements agree with previous results using small-angle X-ray scattering results but that USANS may also be used to investigate the meso porosity. Findings from small-angle scattering are confirmed using electron microscopy. We also show evidence from electron diffraction that thermal conditions within the brown coals during the upgrade procedure may be far more extreme than previously thought.

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PubMed2001

Molecular dynamics study of the stability of the hard sphere glass.

Glassy states have been observed in hard-spherelike colloidal suspensions; however, some recent work suggests that a stable, one-component hard-sphere glass doesn't exist. A possible resolution of this dilemma is that colloidal glass formation results from a small degree of particle polydispersity. In order to investigate this further, we used the molecular-dynamics method to explore the phase behavior of both one- and two-component hard-sphere systems. It was found that the metastable fluid branch of the one-component system ceased to exist at a volume fraction marginally above melting, instead this system always crystallized within a relatively short period of time. Binary systems with a size ratio gamma=0.9 were then used as the simplest approximation to model a polydisperse hard-sphere colloidal system. Here the crystallization process was slowed down dramatically for all volume fractions and the fluid state was maintained for many relaxation times. Indeed, at the lowest volume fraction straight phi=0.55 no sign of crystallization was seen on the simulation time scale. The systems at intermediate volume fractions did eventually crystallize but at the highest volume fraction of straight phi=0.58, a dramatic slowing down in the crystallization process was observed. This is qualitatively in agreement with the experimental results on colloidal suspensions. Using the insight gained from this paper, the reasons behind a polydisperse system forming a stable glass, in contrast to the one-component system, are elucidated.

Journal Article↗

PubMed2001

Long-time behavior of the velocity autocorrelation function for moderately dense, soft-repulsive, and Lennard-Jones fluids.

The long-time behavior of the velocity autocorrelation function (VAF), for hard disk and sphere systems, has been extensively explored. Its behavior for systems interacting via a soft repulsive or attractive potential is less well known. We explore the conditions under which the nonexponential, long-time tail in the velocity autocorrelation function of a tagged atom, in soft-repulsive sphere (Weeks-Chandler-Andersen) and Lennard-Jones atomic fluids, may be readily observed by the molecular dynamics method. The effect of changing the system size, the fluid density, the form of the interatomic force and the mass of the tagged atoms are investigated. We were able to observe this long-time tail only for systems of moderate density. At low density the effect, if it exists, is at longer times than we can currently simulate owing to limitations of system size and at higher densities these tails were not observed possibly due to other effects dominating the behavior of the VAF and masking this behavior. Under the physical conditions that are simulated here attractive forces have very little effect on the behavior of the VAF. However, as the mass of the tagged particles is increased the time at which the long-time tail commences is lengthened and its magnitude is significantly increased. This later effect suggests that by increasing the mass of the tagged particles one may be able to study more readily the behavior, nature and physical origin of long-time behavior of the VAF both by computational and by experimental techniques.

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PubMedDate not supplied

Bucky-wires and the instability of diamond (111) surfaces in one-dimension.

Recent advances in the fabrication and characterization of semiconductor and metallic nanowires are meeting the high expectations of nanotechnolgists. Although diamond has remarkable electronic and chemical properties, development of diamond nanowires has been slow, while the development of carbon nanotube-based technologies continues at a furious pace. Recently, the theoretical and experimental observation of the transformation of nanodiamonds into carbon-onions (and vice versa) has led to a new intermediate phase of carbon, denoted "bucky diamond", with a diamond core encased in an carbon onion-like shell. These findings lead to the question of whether a similar transformation occurs in diamond nanowires. We used ab initio techniques to determine the relaxed structure of diamond nanowires with octahedral surface facets, with results exhibiting delamination of octahedral surfaces, and indicating the formation of "bucky-wires". The effects of surface hydrogenation upon this transition also is examined.

Anisotropy↗