Biomedical subjects

Peter H Poole

Publications and source records attributed to Peter H Poole.

5 recordsLinked to original sources

PubMed2005

Simulated silica.

We review how molecular dynamics computer simulations are providing a comprehensive picture of the behaviour of silica, as modelled by the van Beest-Kramer-van Santen (BKS) potential. We have recently evaluated a number of key properties of this model system: the phase diagram, including melting lines of three crystal phases; the equation of state and free energy of the liquid phase; the dynamical equation of state; the average energy of inherent structures, and configurational entropy, associated with the potential energy landscape of the liquid; and a characterization of the local coordination environments in the supercooled liquid. The results reveal the interplay among a number of phenomena, in particular, the relationship between the energy landscape and the fragile-to-strong crossover of the liquid dynamics; and the relation of both of these to the possibility of a liquid-liquid phase transition in the supercooled liquid.

Computer Simulation↗

PubMed2005

Bulk motion of granular matter in an agitated cylindrical bed.

Experimental results are reported for the bulk motion induced in a bed of granular matter contained in a cylindrical pan with a flat bottom subjected to simultaneous vertical and horizontal vibrations. The motion in space of the moving pan is quantified. A number of distinct bulk dynamical modes are observed in which the particle bed adopts different shapes and motions. At the lowest pan excitation frequency omega , the bed forms a "heap," and rotates about the cylinder axis. As omega is increased, a more complex "toroidal" mode appears in which the bed takes the shape of a torus; in this mode, circulation occurs both about the cylinder axis, and also radially, with particles moving from the outer edge of the pan to the center on the top surface of the bed, and back to the outer edge along the pan bottom. At the highest omega , surface modulations ("surface waves" and "sectors") of the toroidal mode occur. The origin of this family of behavior in terms of the pan motion is discussed.

Journal Article↗

PubMed2004

Phase diagram of silica from computer simulation.

We evaluate the phase diagram of the "BKS" potential [Phys. Rev. Lett. 64, 1955 (1990)]], a model of silica widely used in molecular dynamics (MD) simulations. We conduct MD simulations of the liquid, and three crystals ( beta -quartz, coesite, and stishovite) over wide ranges of temperature and density, and evaluate the total Gibbs free energy of each phase. The phase boundaries are determined by the intersection of these free energy surfaces. Not unexpectedly for a classical pair potential, our results reveal quantitative discrepancies between the locations of the BKS and real silica phase boundaries. At the same time, we find that the topology of the real phase diagram is reproduced, confirming that the BKS model provides a satisfactory qualitative description of a silicalike material. We also compare the phase boundaries with the locations of liquid-state thermodynamic anomalies identified in previous studies of the BKS model.

Journal Article↗

PubMed2004

Free energy and configurational entropy of liquid silica: fragile-to-strong crossover and polyamorphism.

Recent molecular dynamics (MD) simulations of liquid silica, using the "BKS" model [Phys. Rev. Lett. 64, 1955 (1990)]], have demonstrated that the liquid undergoes a dynamical crossover from super-Arrhenius, or "fragile" behavior, to Arrhenius, or "strong" behavior, as temperature T is decreased. From extensive MD simulations, we show that this fragile-to-strong crossover (FSC) can be connected to changes in the properties of the potential energy landscape, or surface (PES), of the liquid. To achieve this, we use thermodynamic integration to evaluate the absolute free energy of the liquid over a wide range of density and T. We use this free energy data, along with the concept of "inherent structures" of the PES, to evaluate the absolute configurational entropy S(c) of the liquid. We find that the temperature dependence of the diffusion coefficient and of S(c) are consistent with the prediction of Adam and Gibbs, including in the region where we observe the FSC to occur. We find that the FSC is related to a change in the properties of the PES explored by the liquid, specifically an inflection in the T dependence of the average inherent structure energy. In addition, we find that the high T behavior of S(c) suggests that the liquid entropy might approach zero at finite T, behavior associated with the so-called Kauzmann paradox. However, we find that the change in the PES that underlies the FSC is associated with a change in the T dependence of S(c) that elucidates how the Kauzmann paradox is avoided in this system. Finally, we also explore the relation of the observed PES changes to the recently discussed possibility that BKS silica exhibits a liquid-liquid phase transition, a behavior that has been proposed to underlie the observed polyamorphism of amorphous solid silica.

Journal Article↗

PubMed2001

Influence of mass polydispersity on dynamics of simple liquids and colloids.

We conduct molecular-dynamics computer simulations of a system of Lennard-Jones particles, polydisperse in both size and mass, at a fixed density and temperature. We test for and quantify systematic changes in dynamical properties that result from polydispersity, by measuring the pair-distribution function, diffusion coefficient, velocity autocorrelation function, and non-Gaussian parameter, as a function of the degree of polydispersity. Our results elucidate the interpretation of experimental studies of collective particle motion in colloids, and we discuss the implications of polydispersity for observations of dynamical heterogeneity, in both simulations of simple liquids and colloid experiments.

Journal Article↗