Biomedical subjects

Paul A Madden

Publications and source records attributed to Paul A Madden.

14 recordsLinked to original sources

PubMed2006

Condensed phase ionic polarizabilities from plane wave density functional theory calculations.

A method is presented to allow the calculation of the dipole polarizabilities of ions and molecules in a condensed-phase coordination environment. These values will be useful for understanding the optical properties of materials and for developing simulation potentials which incorporate polarization effects. The reported values are derived from plane wave density functional theory calculations, though the method itself will apply to first-principles calculations on periodic systems more generally. After reporting results of test calculations on atoms to validate the procedure, values for the polarizabilities of the oxide ion and various cations in a range of materials are reported and compared with experimental information as well as previous theoretical results.

Journal Article↗

PubMed2006

Ionic motion in crystalline cryolite.

The character of the ion dynamics in crystalline cryolite, Na(3)AlF(6), a model double perovskite-structured mineral, has been examined in computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. NMR studies, and conductivity measurements, have indicated a high degree of mobility, in both Na(+) ion diffusion and reorientation of the AlF(6) octahedral units. The simulations reproduce the low-temperature (tilted) crystal structure and the existence of a transition to a cubic structure at elevated temperatures, in agreement with diffraction measurements, though the calculated transition temperature is too low. The reorientational dynamics of the AlF(6) octahedra is shown to consist of a hopping motion between the various tilted positions of the low-temperature form, even above the transition temperature. The rate of reorientation estimated by extrapolation to the temperature régime of the NMR measurements is consistent with the experimental data. In addition, we report a novel cooperative "tilt-swapping" motion of the differently tilted sublattices, just below the transition temperature. The perfect crystals show no Na(+) diffusion, in apparent disagreement with observation. We argue, following previous analyses of the cryolite phase diagram, that the diffusion observed in the experimental studies is a consequence of defects that are intrinsic to the thermodynamically stable form of cryolite. By introducing defects into the simulation cell, we obtain diffusion rates that are consistent with the NMR and conductivity measurements. Finally, we demonstrate a link between diffusion of the Na(+) ions and the reorientation of AlF(6) units, though the correlation between the two is not very strong.

Journal Article↗

PubMed2006

An atomistic MD simulation and pair-distribution-function study of disorder and reactivity of alpha-AlF3 nanoparticles.

Cubic nanoparticles of alpha-AlF(3) containing 864 and 2048 atoms were investigated by using molecular dynamics simulations. Significant structural rearrangements of these particles occurred, primarily at the edges and corners of the particles, and 3 and 5 membered (Al-F-)(n) ring structures were observed in addition to the 4-membered rings seen in bulk alpha-AlF(3). These 3 and 5 membered ring structures are, however, present in other metastable forms of AlF(3), which are formed at low temperatures from high surface area precursors. The surfaces of the nanoparticles were very dynamic on the timescale of the MD run, Al-F bonds being continually broken and formed, resulting in the movement of the low coordinate Lewis acid Al sites on the surfaces of the particles. The Lewis acid sites, which represent the catalytically active sites for F/Cl exchange reactions, are largely present at the corners and edges of the particles. The particles show larger rhombohedral distortions than present in the bulk phase and do not undergo a rhombohedral to cubic phase transition at elevated temperatures. The results are compared with pair distribution function (PDF) analysis results from fluorinated gamma-Al(2)O(3), nanoparticles of AlF(3) prepared by plasma routes and alpha- and beta-AlF(3). Broad peaks between 3.3 and 4.5 A in the PDF plots of the fluorinated Al(2)O(3) and the nanoparticles indicate a distribution of Al-F distances arising from Al and F atoms in connected AlF(6) octahedra; this is consistent with the presence of ring structures other than those found in alpha-AlF(3).

Aluminum Compounds↗

PubMed2006

A first-principles description of liquid BeF2 and its mixtures with LiF: 1. Potential development and pure BeF2.

The construction of an interaction potential for BeF2 and its mixtures with LiF on a purely first-principles basis is described. The quality of the representation of the forces on the ions obtained from ab initio electronic structure calculations by various potentials, which include many-body interaction effects to different extents, are considered. The predictions of the properties of pure BeF2 obtained in simulations with a polarizable potential are then compared with experimental values. In the subsequent paper, a more extensive comparison of the predicted properties of LiF-BeF2 mixtures with experiment is considered.

Journal Article↗

PubMed2006

A first-principles description of liquid BeF2 and its mixtures with LiF: 2. Network formation in LiF-BeF2.

A polarizable ionic interaction potential, constructed from first-principles calculations, is used to examine the structure, vibrational spectra, and transport properties of molten mixtures of LiF and BeF2 across a range of compositions. The simulations reproduce the experimentally measured vibrational frequencies of the fluoroberyllate (BeF4(2-)) ions, which form in the melt, as well as conductivity and viscosity values across the composition range. Examination of the structures of the melts reveals the emergence of a slowly relaxing network of BeF4 units as the concentration of BeF2 is increased. The relationship between the appearance of the network and the composition dependence of the transport properties is explored.

Journal Article↗

PubMed2006

Simulation of the pressure-driven wurtzite to rock salt phase transition in nanocrystals.

Nanocrystals in the size range 12-21 nm of a model binary ionic material in the wurtzite (B4) structure were constructed with morphologies which minimize the surface energy. These were then embedded in a pressurization medium, consisting of a binary Lennard-Jones-type fluid and progressively pressurized in "constant pressure" molecular dynamics simulation runs. Phase transitions to the rocksalt (B1) phase were confirmed by examining calculated powder diffraction patterns, which show the same changes in features as seen for experimental systems. By directly observing the atomic trajectories throughout the duration of the transition the local mechanism has been identified. The transition proceeds via a trigonal bipyramidal intermediate, denoted as the h-MgO structure. It is initiated by a single nucleation event at a [1120]B4 surface with subsequent growth of the B1 region throughout the remainder of the nanocrystal. The consequences of this mechanism for the particle shape of the product phase are detailed and contrasted with those previously found for initially zincblende (B3) structured nanoparticles, using the same interaction potential. The observed transition pressures are elevated relative to the thermodynamically predicted pressure for the bulk, but there is no observable system size effect on the transition pressure across the size range of nanocrystals investigated.

Computer Simulation↗

PubMed2006

Raman spectra of ionic liquids: a simulation study of AlF3 and its mixtures with NaF.

Theoretical Raman spectra of the melts of NaF/AlF3 mixtures have been obtained from computer simulations in order to examine how the Raman spectra reflect the coordination structure around the Al3+ ions. The Raman spectra, both polarized and depolarized, are calculated from a model for the dependence of the polarizability of the system on the ionic coordinates which was inspired by electronic structure calculations of the polarizabilities of ions in a condensed-phase environment. The shapes of the spectra and their evolution with composition in the mixtures conform remarkably well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn(3-n) coordination complexes which are found in the melts. Finally, we calculate quantities which relate to the degree of cross-linking between these coordination complexes and their lifetimes.

Journal Article↗

PubMed2005

Diffusion coefficients in ionic liquids: relationship to the viscosity.

The relationship between the diffusion coefficient and the viscosity has been examined in computer simulations for a number of ions diffusing in a molten salt (alkali halide) solvent. The comparison gives a measure of a hydrodynamic radius for the diffusing ions which is then compared with the bare ionic radius and a characteristic radius of the coordination complex formed by halide ions around polyvalent cations. K(+) and Cl(-) ions appear to diffuse as isolated spherical particles, whereas the trivalent cations Sc(3+), Y(3+), and La(3+) diffuse as if with an intact coordination shell. These different behaviors can be related to the time scale for the relaxation of the coordination shell, compared to the structural relaxation time of the solvent.

Journal Article↗

PubMed2005

New insights into the melting behavior of MgO from molecular dynamics simulations: the importance of premelting effects.

We provide a plausible resolution of a long-standing controversy relevant to the geophysics community, namely, that the experimental slope of the melting curve Tm(P) of MgO at low pressures is about 3 times smaller than that obtained from computer simulation of the melting of the normal rock-salt-structured crystal. With increasing temperature at zero pressure, our simulations predict a solid-solid phase transition (from a rock salt to a wurtzite crystalline lattice) to occur just before melting. The coexistence of wurtzite and liquid phases at low pressures is found to be described by a Clapeyron slope which is in much better agreement with the experimental results of Zerr and Boehler [Nature (London) 371, 506 (1994)] than the calculated melting line for the rock salt structure. We also show that the existence of a certain concentration of lattice defects in the rock salt phase cannot provide an alternative explanation.

Journal Article↗

PubMed2005

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

Comment↗

PubMed2004

Raman spectra of ionic liquids: a simulation study of LaCl3 and its mixtures with alkali chlorides.

Theoretical Raman spectra of the elpasolite-structured crystal Cs2NaLaCl6 and of molten mixtures of LaCl6 with NaCl and CsCl have been obtained from computer simulations in order to examine how the Raman spectra reflect the coordination structure around the La3+ ions. This system is a model for many other trivalent metal halides and for examining how the network structure of the pure melts is broken down by the addition of alkali halides with different structure-breaking powers. The results suggest a way of reconciling the conclusions of Raman studies about the structures of the melts with those of neutron and x-ray-diffraction studies, which have already been examined with the same simulation methods. The Raman spectra, both polarized and depolarized, are calculated from a model for the dependence of the polarizability of the system on the ionic coordinates which was inspired by electronic structure calculations of the polarizabilities of ions in a condensed phase environment. Some results on the lifetimes of the coordination complexes responsible for the appearance of the discrete Raman bands are discussed.

Journal Article↗

PubMed2004

Raman spectra of ionic liquids: interpretation via computer simulation.

Theoretical Raman spectra of the complex-forming ionic liquids LaCl3 and ScCl3, derived from molecular dynamics computer simulations, are presented. These simulations, which use polarizable ion interaction models, have previously been shown to predict structural properties in excellent agreement with diffraction experiments. The dependence of the polarizability of the melt on the ionic positions, which determines the Raman spectrum through the time dependence of the polarizability correlation function, is modeled on the basis of ab initio electronic structure calculations carried out on alkali chlorides. New simulation techniques are introduced in order to allow the spectrum to be calculated with acceptable statistics. The calculated spectra are in semiquantitative agreement with experimental data. The distinctive bands which appear in the spectra of such complex melts are linked to the vibrations of the transient coordination complexes which form in these melts and new interpretations for the origin of several well-known features are proposed. The simulations thus enable a link between the structure of a melt as perceived through Raman spectroscopy and through diffraction experiments to be made.

Journal Article↗

PubMed2004

Ion mobilities and microscopic dynamics in liquid (Li,K)Cl.

The dynamical properties of ionic melts formed from mixtures of LiCl and KCl have been studied across the full composition range in computer simulations of sufficient length to enable reliable values for such collective transport coefficients as the viscosity, conductivity, and internal mobilities to be determined reliably. Interest centers on the nontrivial concentration dependence exhibited by these transport coefficients, which agrees well with that observed experimentally, and in relating this to the strength of the association between an ion and its first coordination shell. The relationships between the various transport coefficients, such as those between the diffusion coefficient and the viscosity (Stokes-Einstein) and the conductivity (Nernst-Einstein) also exhibit composition dependences that reflect this association. The connection between the internal mobility and two measures of the coordination shell dynamics (the cage relaxation time and the self-exchange velocity) is explored; it is shown that the self-exchange velocity follows the composition and temperature dependence of the internal mobility very well. Finally, it is shown that allowing for anion polarization in the interaction model increases the mobility of all species without changing the structure of the melt discernibly, with the largest effect being found for the Li(+) ion.

Journal Article↗

PubMed2003

Multipoles and interaction potentials in ionic materials from planewave-DFT calculations.

Oxide potentials which transfer well between different materials have to account explicitly for many-body contributions to the interaction potentials between the ions. These include dipole and quadrupole polarization effects and the compression and deformation of an oxide ion by its immediate coordination environment. Such complex potentials necessarily involve many parameters. We examine how the results of ab initio electronic structure calculations, based upon planewave DFT methods, on general configurations of ions derived from simulations at finite temperature, may be used to parameterize an "aspherical ion method" (AIM) potential (A. J. Rowley, P. Jemmer, M. Wilson and P. A. Madden, J Chem. Phys., 1998, 108, 10209). Dipoles and quadrupoles on the individual ions are obtained via a transformation of the Kohn Sham orbitals to localized orbitals on each ion, which enables a distorted charge density for each ion to be obtained. The dipoles and quadrupoles appearing in polarization parts of the AIM potential are fit to those obtained from the ab initio ionic charge densities obtained in this way. The remaining parts of the potential, describing short-range repulsive interactions between ions with compressed and deformed charge densities, are fit to the ab initio forces and the stress tensor. By using a sufficiently large and varied set of configurations on which to carry out this optimization, an excellent transferable potential is obtained.

Journal Article↗