Binary continuous random networks

Many properties of disordered materials can be understood by looking at idealized structural models, in which the strain is as small as is possible in the absence of long-range order. For covalent amorphous semiconductors and glasses, such an idealized structural model, the continuous-random network, was introduced 70 years ago by Zachariasen. In this model, each atom is placed in a crystal-like local environment, with perfect coordination and chemical ordering, yet longer-range order is nonexistent. Defects, such as missing or added bonds, or chemical mismatches, however, are not accounted for. In this paper we explore under which conditions the idealized CRN model without defects captures the properties of the material, and under which conditions defects are an inherent part of the idealized model. We find that the density of defects in tetrahedral networks does not vary smoothly with variations in the interaction strengths, but jumps from close-to-zero to a finite density. Consequently, in certain materials, defects do not play a role except for being thermodynamical excitations, whereas in others they are a fundamental ingredient of the ideal structure.Comment: Article in honor of Mike Thorpe's 60th birthday (to appear in J. Phys: Cond Matt.

Total coliform and Escherichia coli contamination in rural well water: Analysis for passive surveillance

With increasing stress on our water resources and recent waterborne disease outbreaks, understanding the epidemiology of waterborne pathogens is crucial to build surveillance systems. The purpose of this study was to explore techniques for describing microbial water quality in rural drinking water wells, based on spatiotemporal analysis, time series analysis and relative risk mapping. Tests results for Escherichia coli and coliforms from private and small public well water samples, collected between 2004 and 2012 in Alberta, Canada, were used for the analysis. Overall, 14.6 and 1.5% of the wells were total coliform and E. coli-positive, respectively. Private well samples were more often total coliform or E. coli-positive compared with untreated public well samples. Using relative risk mapping we were able to identify areas of higher risk for bacterial contamination of groundwater in the province not previously identified. Incorporation of time series analysis demonstrated peak contamination occurring for E. coli in July and a later peak for total coliforms in September, suggesting a temporal dissociation between these indicators in terms of groundwater quality, and highlighting the potential need to increase monitoring during certain periods of the year

Event-based relaxation of continuous disordered systems

A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on significant changes in the microscopic structure (events). The application of ART is illustrated with two examples: the structure of amorphous silicon, and the structure of Ni80P20, a metallic glass.Comment: 4 pages, revtex, epsf.sty, 3 figure

Traveling through potential energy landscapes of disordered materials: the activation-relaxation technique

A detailed description of the activation-relaxation technique (ART) is presented. This method defines events in the configurational energy landscape of disordered materials, such as a-Si, glasses and polymers, in a two-step process: first, a configuration is activated from a local minimum to a nearby saddle-point; next, the configuration is relaxed to a new minimum; this allows for jumps over energy barriers much higher than what can be reached with standard techniques. Such events can serve as basic steps in equilibrium and kinetic Monte Carlo schemes.Comment: 7 pages, 2 postscript figure

Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule

Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed study of these thermal fluctuations, including the frequency spectrum, and show that these rule out single-nucleotide resolution under the experimental conditions which we simulated. Two possible ways to improve this resolution are strong stretching of the RNA with a back-pulling voltage across the membrane, and stiffening of the translocated part of the RNA by biochemical means.Comment: Significantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matte

Monte Carlo Simulations of Conformal Theory Predictions for the 3-state Potts and Ising Models

The critical properties of the 2D Ising and 3-state Potts models are investigated using Monte Carlo simulations. Special interest is given to measurement of 3-point correlation functions and associated universal objects, i.e. structure constants. The results agree well with predictions coming from conformal field theory confirming, for these examples, the correctness of the Coulomb gas formalism and the bootstrap method.Comment: 11 pages, 6 Postscript figures, uses Revte

Properties of a continuous-random-network model for amorphous systems

We use a Monte Carlo bond-switching method to study systematically the thermodynamic properties of a "continuous random network" model, the canonical model for such amorphous systems as a-Si and a-SiO$_2$. Simulations show first-order "melting" into an amorphous state, and clear evidence for a glass transition in the supercooled liquid. The random-network model is also extended to study heterogeneous structures, such as the interface between amorphous and crystalline Si.Comment: Revtex file with 4 figure

Determination of the exponent gamma for SAWs on the two-dimensional Manhattan lattice

We present a high-statistics Monte Carlo determination of the exponent gamma for self-avoiding walks on a Manhattan lattice in two dimensions. A conservative estimate is \gamma \gtapprox 1.3425(3), in agreement with the universal value 43/32 on regular lattices, but in conflict with predictions from conformal field theory and with a recent estimate from exact enumerations. We find strong corrections to scaling that seem to indicate the presence of a non-analytic exponent Delta < 1. If we assume Delta = 11/16 we find gamma = 1.3436(3), where the error is purely statistical.Comment: 24 pages, LaTeX2e, 4 figure

Topology of amorphous tetrahedral semiconductors on intermediate lengthscales

Using the recently-proposed ``activation-relaxation technique'' for optimizing complex structures, we develop a structural model appropriate to a-GaAs which is almost free of odd-membered rings, i.e., wrong bonds, and possesses an almost perfect coordination of four. The model is found to be superior to structures obtained from much more computer-intensive tight-binding or quantum molecular-dynamics simulations. For the elemental system a-Si, where wrong bonds do not exist, the cost in elastic energy for removing odd-membered rings is such that the traditional continuous-random network is appropriate. Our study thus provides, for the first time, direct information on the nature of intermediate-range topology in amorphous tetrahedral semiconductors.Comment: 4 pages, Latex and 2 postscript figure