Biomedical subjects

Ian K Snook

Publications and source records attributed to Ian K Snook.

11 recordsLinked to original sources

PubMed2006

Density functional theory study of hydrogen bonding in ionic molecular materials.

Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.

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PubMed2006

Topological characterization of crystallization of gold nanoclusters.

In this study we use a new topological structure measure to analyze the local environment of 923 atom gold clusters quenched from the melt, at various quench rates, by molecular dynamics. The crystallization and geometrical rearrangements of the core atoms upon freezing can be clearly observed using our structure measure which is based on planar graphs. Our results support the hypothesis that crystallization is initiated from the surface and proceeds into the cluster core.

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PubMed2006

Dynamical signatures of freezing: stable fluids, metastable fluids, and crystals.

Mean squared displacements and velocity auto correlation functions are calculated using molecular dynamics for hard spheres under a range of conditions (i) for the equilibrium fluid below freezing; (ii) for the metastable fluid above freezing; and (iii) for the hard sphere crystal, both in the metastable region between freezing and melting, and in the stable region above melting. In addition, simulations are carried out for a metastable Lennard-Jones system. The results confirm recent studies that indicated the disappearance of the classical Alder long-time tail, and show that they apply to systems other than the metastable hard sphere fluid. The implications of these results for our understanding of crystallization and the glass transition are discussed.

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PubMed2006

Viscosity of a binary mixture: approach to the hydrodynamic limit.

We have used equilibrium and nonequilibrium molecular dynamics simulations to study the solute self-diffusion coefficient and the shear rate dependence of the solution viscosity in solutions of model nanocolloidal particles that range in mass ratio from mu=1 up to mu=50 and size ratio from s=1 up to s=4.03 at various concentrations. The zero shear rate viscosities and the initial rates of shear thinning were determined from data in the shear rate region in which the suspension is strongly shear thinning while the solvent remains Newtonian or is weakly shear thinning. The rate of shear thinning increased dramatically with solute volume fraction, regardless of whether the increase was due to increasing solute size or increasing the solute concentration. In a series of simulations in which the mass ratio was varied while keeping the size ratio fixed at s=1, we found that the approach of the viscosities and self-diffusion coefficients to their limiting mass ratio independent values was well described by a rather simple exponential dependence on mass ratio. The concentration dependence of the limiting infinite mass ratio values of the self-diffusion coefficients and zero shear rate viscosities were determined, and used to compute the hydrodynamic radius RH of the solute particles by various methods. The values of RH that were obtained by the different methods were reasonably consistent with each other, and indicated that the radius at which the slip boundary condition holds is slightly smaller than the cross-interaction radius between the solute and solvent particles.

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PubMed2006

Effect of S arrangement on Fe(110) properties at 1/3 monolayer coverage: a DFT study.

Using density functional theory calculations, we compare the relative stabilities and properties of different arrangements of S on Fe(110) at a 1/3 monolayer coverage, including two observed experimentally. For all studied arrangements, S is adsorbed in the three high-symmetry adsorption sites: 4-fold hollow, 3-fold hollow, bridge, and atop sites. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are determined and compared. The most stable overlayer arrangement corresponds to the overlayer seen by experiment after dissociative adsorption of H2S and has S adsorbed in 4-fold hollow sites. In the other arrangements, the S atoms are located closer to each other on the surface reducing the stability of the overlayer. S causes a minor adsorbate-induced reconstruction of the Fe surface and quenches the magnetic moment of the Fe atoms it bonds to directly. It adsorbs as an electropositive species, causing a positive work function change and forms polar covalent bonds to the surface.

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PubMed2005

On fitting a gold embedded atom method potential using the force matching method.

We fit a new gold embedded atom method (EAM) potential using an improved force matching methodology which included fitting to high-temperature solid lattice constants and liquid densities. The new potential shows a good overall improvement in agreement to the experimental lattice constants, elastic constants, stacking fault energy, radial distribution function, and fcc/hcp/bcc lattice energy differences over previous potentials by Foiles, Baskes, and Daw (FBD) [Phys. Rev. B 33, 7983 (1986)] Johnson [Phys. Rev. B 37, 3924 (1988)], and the glue model potential by Ercolessi et al. [Philos. Mag. A 50, 213 (1988)]. Surface energy was improved slightly as compared to potentials by FBD and Johnson but as a result vacancy formation energy is slightly inferior as compared to the same potentials. The results obtained here for gold suggest for other metal species that further overall improvements in potentials may still be possible within the EAM framework with an improved fitting methodology. On the other hand, we also explore the limitations of the EAM framework by attempting a brute force fit to all properties exactly which was found to be unsuccessful. The main conflict in such a brute force fit was between the surface energy and the liquid lattice constant where both could not be fitted identically. By intentionally using a very large number of spline sections for the pair potential, electron-density function, and embedding energy function, we eliminated a lack of functional freedom as a possible cause of this conflict and hence can conclude that it must result from a fundamental limitation in the EAM framework.

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PubMed2005

Effect of sulfur coverage on Fe(110) adhesion: a DFT study.

The effect of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in match and mismatch is examined using density functional theory (DFT). S is adsorbed in atop, bridge, and 4-fold hollow sites on one side of the interface in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 and 1 monolayer, respectively. The calculated adhesion energy values at different interfacial separations are fitted to the universal binding energy relation, and the effect of the S coverages on the adhesive strength is analyzed. The effect of relaxation of the interfaces at equilibrium is also investigated, and the resulting interfacial structures and related magnetic and charge density properties are compared.

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PubMed2005

Coverage-dependent adsorption of atomic sulfur on Fe(110): a DFT study.

Adsorption of atomic sulfur at different coverages on the Fe(110) surface is examined using density functional theory (DFT) in order to investigate the effect that adsorbate-adsorbate interactions may have on the surface properties. S is adsorbed in the high-symmetry adsorption sites: 4-fold hollow, bridge, and atop sites in the following surface arrangements: c(2 x 2) and p(1 x 1) which correspond to coverages of 1/2 and 1 monolayer, respectively. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are examined and compared to our previous study of S adsorbed at 1/4 monolayer coverage and p(2 x 2) arrangement [Spencer et al. Surf. Sci. 2003, 540, 420]. It was found that S forms polar covalent bonds to the surface. The bonding goes from being S-Fe dominated at the low coverages to being S-S dominated at the higher coverages where the S atoms are located closer together on the surface and interact with each other.

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PubMed2005

On the computational calculation of surface free energies for the disordered semihexagonal reconstructed Au(100) surface.

Previously we developed a general method for calculating the free energy of any surface constrained to a distinct surface excess number/density. In this paper we show how to combine a range of such surfaces, whose free energies have been calculated, to produce an ad hoc semigrand canonical ensemble of surfaces from which ensemble surface properties can be calculated, including the ensemble surface free energy. We construct such an ensemble for the disordered Au(100) semihexagonal reconstructed surface using a Glue model potential at 1000 K and calculate the ensemble surface free energy to be 0.088 18 eVA(2). The ensemble average surface lateral density was found to be 1.375 (with respect to the bulk), which is in agreement with previous grand canonical Monte Carlo studies.

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PubMed2005

Application of the constrained fluid lambda-integration path to the calculation of high temperature Au(110) surface free energies.

Recently a method termed constrained fluid lambda-integration was proposed for calculating the free energy difference between bulk solid and liquid reference states via the construction of a reversible thermodynamic integration path; coupling the two states in question. The present work shows how the application of the constrained fluid lambda-integration concept to solid/liquid slab simulation cells makes possible a generally applicable computer simulation methodology for calculating the free energy of any surface and/or surface defect structure, including surfaces requiring variations in surface atom or density number, such as the (1 x 5) Au(100) or (1 x 2) missing row Au(110) reconstructed surfaces or excess adatom/vacancy/step populated surfaces. We evaluate the methodology by calculating the free energy of various disordered high temperature Au(110) embedded atom method surfaces constrained to differing excess surface atom numbers [including those corresponding to the (1 x 2) missing row reconstructed surface] and obtained the interesting result that at 1000 K (as distinct from lower temperatures) the free energy difference between these surfaces is reduced to zero; a result which is consistent with an expected order-disorder phase transition for the Au(110) surface at such high temperatures.

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PubMed2004

"Exact" surface free energies of iron surfaces using a modified embedded atom method potential and lambda integration.

Previously a new universal lambda-integration path and associated methodology was developed for the calculation of "exact" surface and interfacial free energies of solids. Such a method is in principle applicable to any intermolecular potential function, including those based on ab initio methods, but in previous work the method was only tested using a relatively simple embedded atom method iron potential. In this present work we apply the new methodology to the more sophisticated and more accurate modified embedded atom method (MEAM) iron potential, where application of other free- energy methods would be extremely difficult due to the complex many-body nature of the potential. We demonstrate that the new technique simplifies the process of obtaining "exact" surface free energies by calculating the complete set of these properties for the low index surface faces of bcc and fcc solid iron structures. By combining these data with further calculations of liquid surface tensions we obtain the first complete set of exact surface free energies for the solid and liquid phases of a realistic MEAM model system. We compare these predictions to various experimental and theoretical results.

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