Molecular dynamics characterization of n-octyl-beta-D-glucopyranoside micelle structure in aqueous solution

n-Octyl-beta-D-glueopyranoside (OG) is a non-ionic glycolipid, which is used widely in biotechnical and biochemical applications. All-atom molecular dynamics simulations from two different initial coordinates and velocities in explicit solvent have been performed to characterize the structural behaviour of an OG aggregate at equilibrium conditions. Geometric packing properties determined from the simulations and small angle neutron scattering experiment state that OG micelles are more likely to exist in a non-spherical shape, even at the concentration range near to the critical micelle concentration (0.025 M). Despite few large deviations in the principal moment of inertia ratios, the average micelle shape calculated from both simulations is a prolate ellipsoid. The deviations at these time scales are presumably the temporary shape change of a micelle. However, the size of the micelle and the accessible surface areas were constant during the simulations with the micelle surface being rough and partially elongated. Radial distribution functions computed for the hydroxyl oxygen atoms of an OG show sharper peaks at a minimum van der Waals contact distance than the acetal oxygen, ring oxygen, and anomeric carbon atoms. This result indicates that these atoms are pointed outwards at the hydrophilic/hydrophobic interface, form hydrogen bonds with the water molecules, and thus hydrate the micelle surface effectively. (c) 2005 Elsevier Inc. All rights reserved.

Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulation

Discrete stochastic simulations are a powerful tool for understanding the dynamics of chemical kinetics when there are small-to-moderate numbers of certain molecular species. In this paper we introduce delays into the stochastic simulation algorithm, thus mimicking delays associated with transcription and translation. We then show that this process may well explain more faithfully than continuous deterministic models the observed sustained oscillations in expression levels of hes1 mRNA and Hes1 protein.

Non-linear principal components analysis: an alternative method for finding patterns in environmental data

The main purpose of this article is to gain an insight into the relationships between variables describing the environmental conditions of the Far Northern section of the Great Barrier Reef, Australia, Several of the variables describing these conditions had different measurement levels and often they had non-linear relationships. Using non-linear principal component analysis, it was possible to acquire an insight into these relationships. Furthermore. three geographical areas with unique environmental characteristics could be identified. Copyright (c) 2005 John Wiley & Sons, Ltd.

Planar electromagnetic bandgap structures

This article presents various novel and conventional planar electromagnetic bandgap (EBG)-assisted transmission lines. Both microstrip lines and coplanar waveguides (CPWs) are designed with circular, rectangular, annular, plus-sign and fractal-patterned EBGs and dumbbell-shaped defected ground structure (DGS). The dispersion characteristics and the slow-wave factors of the design are investigated. (c) 2006 Wiley Periodicals, Inc.

Prediction of HLA-DQ3.2 beta ligands: evidence of multiple registers in class II binding peptides

Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and hypersensitivity reactions. Sequence-based computational techniques for predicting HLA-DQ binding peptides have encountered limited success, with few prediction techniques developed using three-dimensional models. Methods: We describe a structure-based prediction model for modeling peptide-DQ3.2 beta complexes. We have developed a rapid and accurate protocol for docking candidate peptides into the DQ3.2 beta receptor and a scoring function to discriminate binders from the background. The scoring function was rigorously trained, tested and validated using experimentally verified DQ3.2 beta binding and non-binding peptides obtained from biochemical and functional studies. Results: Our model predicts DQ3.2 beta binding peptides with high accuracy [area under the receiver operating characteristic (ROC) curve A(ROC) > 0.90], compared with experimental data. We investigated the binding patterns of DQ3.2 beta peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders.

Random vibration of the functionally graded laminates in thermal environments

This work deals with the random free vibration of functionally graded laminates with general boundary conditions and subjected to a temperature change, taking into account the randomness in a number of independent input variables such as Young's modulus, Poisson's ratio and thermal expansion coefficient of each constituent material. Based on third-order shear deformation theory, the mixed-type formulation and a semi-analytical approach are employed to derive the standard eigenvalue problem in terms of deflection, mid-plane rotations and stress function. A mean-centered first-order perturbation technique is adopted to obtain the second-order statistics of vibration frequencies. A detailed parametric study is conducted, and extensive numerical results are presented in both tabular and graphical forms for laminated plates that contain functionally graded material which is made of aluminum and zirconia, showing the effects of scattering in thermo-clastic material constants, temperature change, edge support condition, side-to-thickness ratio, and plate aspect ratio on the stochastic characteristics of natural frequencies. (c) 2005 Elsevier B.V. All rights reserved.

Segmenting eukaryotic genomes with the generalized Gibbs sampler

Eukaryotic genomes display segmental patterns of variation in various properties, including GC content and degree of evolutionary conservation. DNA segmentation algorithms are aimed at identifying statistically significant boundaries between such segments. Such algorithms may provide a means of discovering new classes of functional elements in eukaryotic genomes. This paper presents a model and an algorithm for Bayesian DNA segmentation and considers the feasibility of using it to segment whole eukaryotic genomes. The algorithm is tested on a range of simulated and real DNA sequences, and the following conclusions are drawn. Firstly, the algorithm correctly identifies non-segmented sequence, and can thus be used to reject the null hypothesis of uniformity in the property of interest. Secondly, estimates of the number and locations of change-points produced by the algorithm are robust to variations in algorithm parameters and initial starting conditions and correspond to real features in the data. Thirdly, the algorithm is successfully used to segment human chromosome 1 according to GC content, thus demonstrating the feasibility of Bayesian segmentation of eukaryotic genomes. The software described in this paper is available from the author's website (www.uq.edu.au/similar to uqjkeith/) or upon request to the author.

Stochastic models for mainland-island metapopulations in static and dynamic landscapes

This paper has three primary aims: to establish an effective means for modelling mainland-island metapopulations inhabiting a dynamic landscape: to investigate the effect of immigration and dynamic changes in habitat on metapopulation patch occupancy dynamics; and to illustrate the implications of our results for decision-making and population management. We first extend the mainland-island metapopulation model of Alonso and McKane [Bull. Math. Biol. 64:913-958,2002] to incorporate a dynamic landscape. It is shown, for both the static and the dynamic landscape models, that a suitably scaled version of the process converges to a unique deterministic model as the size of the system becomes large. We also establish that. under quite general conditions, the density of occupied patches, and the densities of suitable and occupied patches, for the respective models, have approximate normal distributions. Our results not only provide us with estimates for the means and variances that are valid at all stages in the evolution of the population, but also provide a tool for fitting the models to real metapopulations. We discuss the effect of immigration and habitat dynamics on metapopulations, showing that mainland-like patches heavily influence metapopulation persistence, and we argue for adopting measures to increase connectivity between this large patch and the other island-like patches. We illustrate our results with specific reference to examples of populations of butterfly and the grasshopper Bryodema tuberculata.

A diffusion approach to approximating preservation probabilities for gene duplicates

Consider a haploid population and, within its genome, a gene whose presence is vital for the survival of any individual. Each copy of this gene is subject to mutations which destroy its function. Suppose one member of the population somehow acquires a duplicate copy of the gene, where the duplicate is fully linked to the original gene's locus. Preservation is said to occur if eventually the entire population consists of individuals descended from this one which initially carried the duplicate. The system is modelled by a finite state-space Markov process which in turn is approximated by a diffusion process, whence an explicit expression for the probability of preservation is derived. The event of preservation can be compared to the fixation of a selectively neutral gene variant initially present in a single individual, the probability of which is the reciprocal of the population size. For very weak mutation, this and the probability of preservation are equal, while as mutation becomes stronger, the preservation probability tends to double this reciprocal. This is in excellent agreement with simulation studies.

Using circular statistics to analyse time patterns in crime incidence

A set of techniques referred to as circular statistics has been developed for the analysis of directional and orientational data. The unit of measure for such data is angular (usually in either degrees or radians), and the statistical distributions underlying the techniques are characterised by their cyclic nature-for example, angles of 359.9 degrees are considered close to angles of 0 degrees. In this paper, we assert that such approaches can be easily adapted to analyse time-of-day and time-of-week data, and in particular daily cycles in the numbers of incidents reported to the police. We begin the paper by describing circular statistics. We then discuss how these may be modified, and demonstrate the approach with some examples for reported incidents in the Cardiff area of Wales. (c) 2005 Elsevier Ltd. All rights reserved.

Modelling sediment delivery ratio over the Murray Darling Basin

This paper presents a scientific and technical description of the modelling framework and the main results of modelling the long-term average sediment delivery at hillslope to medium-scale catchments over the entire Murray Darling Basin (MDB). A theoretical development that relates long-term averaged sediment delivery to the statistics of rainfall and catchment parameters is presented. The derived flood frequency approach was adapted to investigate the problem of regionalization of the sediment delivery ratio (SDR) across the Basin. SDR, a measure of catchment response to the upland erosion rate, was modeled by two lumped linear stores arranged in series: hillslope transport to the nearest streams and flow routing in the channel network. The theory shows that the ratio of catchment sediment residence time (SRT) to average effective rainfall duration is the most important control in the sediment delivery processes. In this study, catchment SRTs were estimated using travel time for overland flow multiplied by an enlargement factor which is a function of particle size. Rainfall intensity and effective duration statistics were regionalized by using long-term measurements from 195 pluviograph sites within and around the Basin. Finally, the model was implemented across the MDB by using spatially distributed soil, vegetation, topographical and land use properties under Geographic Information System (GIs) environment. The results predict strong variations in SDR from close to 0 in floodplains to 70% in the eastern uplands of the Basin. (c) 2005 Elsevier Ltd. All rights reserved.

Supermodularity and risk aversion

In this paper, we consider the relationship between supermodularity and risk aversion. We show that supermodularity of the certainty equivalent implies that the certainty equivalent of any random variable is less than its mean. We also derive conditions under which supermodularity of the certainty equivalent is equivalent to aversion to mean-preserving spreads in the sense of Rothschild and Stiglitz. (c) 2006 Elsevier B.V. All rights reserved.

Modelling trickle irrigation: Comparison of analytical and numerical models for estimation of wetting front position with time

Irrigation practices that are profligate in their use of water have come under closer scrutiny by water managers and the public. Trickle irrigation has the propensity to increase water use efficiency but only if the system is designed to meet the soil and plant conditions. Recently we have provided a software tool, WetUp (http://www.clw.csiro.au/products/wetup/), to calculate the wetting patterns from trickle irrigation emitters. WetUp uses an analytical solution to calculate the wetted perimeter for both buried and surface emitters. This analytical solution has a number of assumptions, two of which are that the wetting front is defined by water content at which the hydraulic conductivity (K) is I mm day(-1) and that the flow occurs from a point source. Here we compare the wetting patterns calculated with a 2-dimensional numerical model, HYDRUS2D, for solving the water flow into typical soils with the analytical solution. The results show that the wetting patterns are similar, except when the soil properties result in the assumption of a point source no longer being a good description of the flow regime. Difficulties were also experienced with getting stable solutions with HYDRUS2D for soils with low hydraulic conductivities. (c) 2005 Elsevier Ltd. All rights reserved.

Warranty cost analysis for second-hand products

For second-hand products sold with warranty, the expected warranty cost for an item to the manufacturer, depends on (i) the age and/or usage as well as the maintenance history for the item and (ii) the terms of the warranty policy. The paper develops probabilistic models to compute the expected warranty cost to the manufacturer when the items are sold with free replacement or pro rata warranties. (C) 2000 Elsevier Science Ltd. All rights reserved.

The lattice solid model to simulate the physics of rocks and earthquakes: Incorporation of friction

The particle-based lattice solid model developed to study the physics of rocks and the nonlinear dynamics of earthquakes is refined by incorporating intrinsic friction between particles. The model provides a means for studying the causes of seismic wave attenuation, as well as frictional heat generation, fault zone evolution, and localisation phenomena. A modified velocity-Verlat scheme that allows friction to be precisely modelled is developed. This is a difficult computational problem given that a discontinuity must be accurately simulated by the numerical approach (i.e., the transition from static to dynamical frictional behaviour). This is achieved using a half time step integration scheme. At each half time step, a nonlinear system is solved to compute the static frictional forces and states of touching particle-pairs. Improved efficiency is achieved by adaptively adjusting the time step increment, depending on the particle velocities in the system. The total energy is calculated and verified to remain constant to a high precision during simulations. Numerical experiments show that the model can be applied to the study of earthquake dynamics, the stick-slip instability, heat generation, and fault zone evolution. Such experiments may lead to a conclusive resolution of the heat flow paradox and improved understanding of earthquake precursory phenomena and dynamics. (C) 1999 Academic Press.