Efficient tight-binding Monte Carlo structural sampling of complex materials

While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte Carlo algorithm that makes use of the possibility of quickly evaluating local energies. For the thermalization of a 1000-atom configuration of {\it a}-Si, this algorithm gains about an order of magnitude in speed over standard molecular dynamics. The algorithm can easily be ported to a wide range of materials and can be dynamically optimized for a maximum efficiency.Comment: 5 pages including 3 postscript figure

Structural, electronic, and dynamical properties of amorphous gallium arsenide: a comparison between two topological models

We present a detailed study of the effect of local chemical ordering on the structural, electronic, and dynamical properties of amorphous gallium arsenide. Using the recently-proposed ``activation-relaxation technique'' and empirical potentials, we have constructed two 216-atom tetrahedral continuous random networks with different topological properties, which were further relaxed using tight-binding molecular dynamics. The first network corresponds to the traditional, amorphous, Polk-type, network, randomly decorated with Ga and As atoms. The second is an amorphous structure with a minimum of wrong (homopolar) bonds, and therefore a minimum of odd-membered atomic rings, and thus corresponds to the Connell-Temkin model. By comparing the structural, electronic, and dynamical properties of these two models, we show that the Connell-Temkin network is energetically favored over Polk, but that most properties are little affected by the differences in topology. We conclude that most indirect experimental evidence for the presence (or absence) of wrong bonds is much weaker than previously believed and that only direct structural measurements, i.e., of such quantities as partial radial distribution functions, can provide quantitative information on these defects in a-GaAs.Comment: 10 pages, 7 ps figures with eps

Liquid-liquid phase transition in Stillinger-Weber silicon

It was recently demonstrated that the Stillinger-Weber silicon undergoes a liquid-liquid first-order phase transition deep into the supercooled region (Sastry and Angell, Nature Materials 2, 739 (2003)). Here we study the effects of perturbations on this phase transition. We show that the order of the liquid-liquid transition changes with negative pressure. We also find that the liquid-liquid transition disappears when the three-body term of the potential is strengthened by as little as 5 %. This implies that the details of the potential could affect strongly the nature and even the existence of the liquid-liquid phase.Comment: 13 page

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

Updating models for restoration and management of fiery ecosystems

© 2015 Elsevier B.V. Scientific models that guide restoration/management protocols should be reviewed periodically as new data become available. We examine ecological concepts used to guide restoration of pine savannas and woodlands, historically prominent but now rare habitats in the southern North American Coastal Plain. For many decades, pine savanna management has been guided predominantly by a biome-centric succession model. Pine savannas have been considered early-successional communities that, in the absence of fire, transition rapidly toward closed-canopy hardwood forests. Recurrent fires have been viewed as exogenous disturbances that maintain savanna ecosystems as a sub-climax, blocking succession to an equilibrium steady state (closed-canopy forests). Over recent decades, a vegetation-fire feedback model has emerged in which pine savannas are conceptualized as persistent, non-equilibrium communities maintained by endogenous, co-evolutionary vegetation-fire feedbacks. Endemic plant species are resistant to fires and specialized for post-fire conditions generated by frequent lightning fires, primarily within a distinct fire season. These species produce pyrogenic fine fuels that are easily ignited. The resulting fire regimes, entrained by these vegetation-fire feedbacks, are predicted to result in persistent pine savannas. Local variation over space and time in evolutionary feedback mechanisms between pyrogenic vegetation and fire regimes produces heterogeneous landscapes. Disturbances of these feedbacks, such as human fire suppression, are postulated to result in rapid transition to communities lacking feedback elements, such as closed-canopy forest and those without pyrogenic species. Succession-based management focuses on reversing the transition to forest, primarily by removing hardwoods and reintroducing fire as a disturbance. However, we advocate restoration and management approaches that target reinstitution of functional vegetation-fire feedbacks. Such approaches should favor native pyrogenic plant species and reinstitute fire regimes that mimic historical, evolutionarily derived fire regimes. Vegetation-fire feedback concepts should be useful in addressing resistance and resilience of fiery ecosystems worldwide to inherent changes in feedback mechanisms, constituting a framework useful in addressing global management challenges

Towards device-size atomistic models of amorphous silicon

The atomic structure of amorphous materials is believed to be well described by the continuous random network model. We present an algorithm for the generation of large, high-quality continuous random networks. The algorithm is a variation of the "sillium" approach introduced by Wooten, Winer, and Weaire. By employing local relaxation techniques, local atomic rearrangements can be tried that scale almost independently of system size. This scaling property of the algorithm paves the way for the generation of realistic device-size atomic networks.Comment: 7 pages, 3 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

Lacunar-canalicular network in femoral cortical bone is reduced in aged women and is predominantly due to a loss of canalicular porosity

The lacunar-canalicular network (LCN) of bone contains osteocytes and their dendritic extensions, which allow for intercellular communication, and are believed to serve as the mechanosensors that coordinate the processes of bone modeling and remodeling. Imbalances in remodeling, for example, are linked to bone disease, including fragility associated with aging. We have reported that there is a reduction in scale for one component of the LCN, osteocyte lacunar volume, across the human lifespan in females. In the present study, we explore the hypothesis that canalicular porosity also declines with age. To visualize the LCN and to determine how its components are altered with aging, we examined samples from young (age: 20-23 y; n = 5) and aged (age: 70-86 y; n = 6) healthy women donors utilizing a fluorescent labelling technique in combination with confocal laser scanning microscopy. A large cross-sectional area of cortical bone spanning the endosteal to periosteal surfaces from the anterior proximal femoral shaft was examined in order to account for potential trans-cortical variation in the LCN. Overall, we found that LCN areal fraction was reduced by 40.6% in the samples from aged women. This reduction was due, in part, to a reduction in lacunar density (21.4% decline in lacunae number per given area of bone), but much more so due to a 44.6% decline in canalicular areal fraction. While the areal fraction of larger vascular canals was higher in endosteal vs. periosteal regions for both age groups, no regional differences were observed in the areal fractions of the LCN and its components for either age group. Our data indicate that the LCN is diminished in aged women, and is largely due to a decline in the canalicular areal fraction, and that, unlike vascular canal porosity, this diminished LCN is uniform across the cortex