A structural comparison of models of colloid-polymer mixtures

We study the structure of colloidal fluids with reference to colloid-polymer mixtures. We compare the one component description of the Asakura-Oosawa (AO) idealisation of colloid-polymer mixtures with the full two-component model. We also consider the Morse potential, a variable range interaction, for which the ground state clusters are known. Mapping the state points between these systems, we find that the pair structure of the full AO model is equally well described by the Morse potential or the one component AO approach. We employ a recently developed method to identify in the bulk fluid the ground state clusters relevant to the Morse potential. Surprisingly, when we measure the cluster populations, we find that the Morse fluid is significantly closer the full AO fluid than the one component AO description.Comment: 13 pages, accepted by J. Phys. Condens: Matter special issue for CECAM meeting 'New Trends in Simulating Colloids: from Models to Applications

Strong geometric frustration in model glassformers

We consider three popular model glassformers, the Kob-Andersen and Wahnstr\"om binary Lennard-Jones models and weakly polydisperse hard spheres. Although these systems exhibit a range of fragilities, all feature a rather similar behaviour in their local structure approaching dynamic arrest. In particular we use the dynamic topological cluster classification to extract a locally favoured structure which is particular to each system. These structures form percolating networks, however in all cases there is a strong decoupling between structural and dynamic lengthscales. We suggest that the lack of growth of the structural lengthscale may be related to strong geometric frustration.Comment: 14 pages, Accepted by J. Non-Crystalline Solids, 7th International Discussion Meeting on Relaxation in Complex Systems Proceeding

Local structure of Liquid-Vapour Interfaces

The structure of a simple liquid may be characterised in terms of ground state clusters of small numbers of atoms of that same liquid. Here we use this sensitive structural probe to consider the effect of a liquid-vapour interface upon the liquid structure. At higher temperatures (above around half the critical temperature) we find that the predominant effect of the interface is to reduce the local density, which significantly suppresses the local cluster populations. At lower temperatures, however, pronounced interfacial layering is found. This appears to be connected with significant orientational ordering of clusters based on 3- and 5-membered rings, with the rings aligning perpendicular and parallel to the interface respectively. At all temperatures, we find that the population of five-fold symmetric structures is suppressed, rather than enhanced, close to the interface.Comment: 10 pages, 8 figures, accepted for publication by Molecular Physic

Identification of structure in condensed matter with the topological cluster classification

We describe the topological cluster classification (TCC) algorithm. The TCC detects local structures with bond topologies similar to isolated clusters which minimise the potential energy for a number of monatomic and binary simple liquids with $m\leq13$ particles. We detail a modified Voronoi bond detection method that optimizes the cluster detection. The method to identify each cluster is outlined, and a test example of Lennard-Jones liquid and crystal phases is considered and critically examined.Comment: 28 pages, 28 figure

Identification of structure in condensed matter with the topological cluster classification

We describe the topological cluster classification (TCC) algorithm. The TCC detects local structures with bond topologies similar to isolated clusters which minimise the potential energy for a number of monatomic and binary simple liquids with $m\leq13$ particles. We detail a modified Voronoi bond detection method that optimizes the cluster detection. The method to identify each cluster is outlined, and a test example of Lennard-Jones liquid and crystal phases is considered and critically examined

Structural changes in gill DNA reveal the effects of contaminants on Puget Sound fish.

Structural differences were identified in gill DNA from two groups of English sole collected from Puget Sound, Washington, in October 2000. One group was from the industrialized Duwamish River (DR) in Seattle and the other from relatively clean Quartermaster Harbor (QMH). Chemical markers of sediment contamination [e.g., polynuclear aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)] established that the DR was substantially more contaminated than QMH. The levels of these chemicals in the sediments of both sites were consistent with levels of cytochrome P450 1A (CYP1A) expression in the gills of English sole from the same sites. Structural differences in gill DNA between the groups were evinced via statistical models of Fourier transform-infrared (FT-IR) spectra. Marked structural damage was found in the gill DNA of the DR fish as reflected in differences in base functional groups (e.g., C-O and NH2) and conformational properties (e.g., arising from perturbations in vertical base stacking interactions). These DNA differences were used to discriminate between the two fish groups through principal components analysis of mean FT-IR spectra. In addition, logistic regression analysis allowed for the development of a "DNA damage index" to assess the effects of contaminants on the gill. The evidence implies that environmental chemicals contribute to the DNA changes in the gill. The damaged DNA is a promising marker for identifying, through gill biopsies, contaminant effects on fish

The photoionization dynamics of the three structural isomers of dichloroethene

Using tunable vacuum-UV radiation from a synchrotron, the threshold photoelectron spectrum, threshold photoelectron photoion coincidence spectrum and ion breakdown diagram of the 1,1, cis-1,2 and trans-1,2 isomers of C$_2$H$_2$Cl$_2$ have been recorded in the range 9-23 eV. The energies of the peaks in the threshold photoelectron spectrum are in good agreement with outer-valence Greens function caculations. The major difference between the isomers, both predicted and observed experimentally is that the F and G states of C$_2$H$_2$Cl$_2^+$ are approximately degenerate for 1,1 and trans-1,2, but well separated for the cis-1,2 isomer. The ground and low-lying valence states of C$_2$H$_2$Cl$_2^+$ are bound, with higher-lying states dissociating to C$_2$H$_2$Cl$^+$ or C$_2$H$_2^+$. The translational kinetic energy release into C$_2$H$_2$Cl$^+$ + Cl is determined as a function of energy. Isolated-state behaviour for the low-lying electronic states of C$_2$H$_2$Cl$_2^+$ becomes more statistical as the energy increases