Generalised growth models for aquatic species with an application to blacklip abalone (Haliotis rubra)

This paper presents a maximum likelihood method for estimating growth parameters for an aquatic species that incorporates growth covariates, and takes into consideration multiple tag-recapture data. Individual variability in asymptotic length, age-at-tagging, and measurement error are also considered in the model structure. Using distribution theory, the log-likelihood function is derived under a generalised framework for the von Bertalanffy and Gompertz growth models. Due to the generality of the derivation, covariate effects can be included for both models with seasonality and tagging effects investigated. Method robustness is established via comparison with the Fabens, improved Fabens, James and a non-linear mixed-effects growth models, with the maximum likelihood method performing the best. The method is illustrated further with an application to blacklip abalone (Haliotis rubra) for which a strong growth-retarding tagging effect that persisted for several months was detected. (C) 2013 Elsevier B.V. All rights reserved.

The kinetics and reactivity of several polyatomic free radicals in reactions with NO2, O2, Cl2, and HCl

In this thesis, the kinetics of several alkyl, halogenated alkyl, and alkenyl free radical reactions with NO2, O2, Cl2, and HCl reactants were studied over a wide temperature range in time resolved conditions. Laser photolysis photoionisation mass spectrometer coupled to a flow reactor was the experimental method employed and this thesis present the first measurements performed with the experimental system constructed. During this thesis a great amount of work was devoted to the designing, building, testing, and improving the experimental apparatus. Carbon-centred free radicals were generated by the pulsed 193 or 248 nm photolysis of suitable precursors along the tubular reactor. The kinetics was studied under pseudo-first-order conditions using either He or N2 buffer gas. The temperature and pressure ranges employed were between 190 and 500 K, and 0.5 45 torr, respectively. The possible role of heterogeneous wall reactions was investigated employing reactor tubes with different sizes, i.e. to significantly vary the surface to volume ratio. In this thesis, significant new contributions to the kinetics of carbon-centred free radical reactions with nitrogen dioxide were obtained. Altogether eight substituted alkyl (CH2Cl, CHCl2, CCl3, CH2I, CH2Br, CHBr2, CHBrCl, and CHBrCH3) and two alkenyl (C2H3, C3H3) free radical reactions with NO2 were investigated as a function of temperature. The bimolecular rate coefficients of all these reactions were observed to possess negative temperature dependencies, while pressure dependencies were not noticed for any of these reactions. Halogen substitution was observed to moderately reduce the reactivity of substituted alkyl radicals in the reaction with NO2, while the resonance stabilisation of the alkenyl radical lowers its reactivity with respect to NO2 only slightly. Two reactions relevant to atmospheric chemistry, CH2Br + O2 and CH2I + O2, were also investigated. It was noticed that while CH2Br + O2 reaction shows pronounced pressure dependence, characteristic of peroxy radical formation, no such dependence was observed for the CH2I + O2 reaction. Observed primary products of the CH2I + O2 reaction were the I-atom and the IO radical. Kinetics of CH3 + HCl, CD3 + HCl, CH3 + DCl, and CD3 + DCl reactions were also studied. While all these reactions possess positive activation energies, in contrast to the other systems investigated in this thesis, the CH3 + HCl and CD3 + HCl reactions show a non-linear temperature dependency on the Arrhenius plot. The reactivity of substituted methyl radicals toward NO2 was observed to increase with decreasing electron affinity of the radical. The same trend was observed for the reactions of substituted methyl radicals with Cl2. It is proposed that interactions of frontier orbitals are responsible to these observations and Frontier Orbital Theory could be used to explain the observed reactivity trends of these highly exothermic reactions having reactant-like transition states.

Analysis of two degrees of freedom systems through weighted mean square linearization approach

In this paper a study of the free, forced and self-excited vibrations of non-linear, two degrees of freedom systems is reported. The responses are obtained by linearizing the nonlinear equations using the weighted mean square linearization approach. The scope of this approach, in terms of the type of non-linearities the method can tackle, is also discussed.

Parameters Affecting the Extraction of Polycyclic Aromatic Hydrocarbons with Pressurised Hot Water

Pressurised hot water extraction (PHWE) exploits the unique temperature-dependent solvent properties of water minimising the use of harmful organic solvents. Water is environmentally friendly, cheap and easily available extraction medium. The effects of temperature, pressure and extraction time in PHWE have often been studied, but here the emphasis was on other parameters important for the extraction, most notably the dimensions of the extraction vessel and the stability and solubility of the analytes to be extracted. Non-linear data analysis and self-organising maps were employed in the data analysis to obtain correlations between the parameters studied, recoveries and relative errors. First, pressurised hot water extraction (PHWE) was combined on-line with liquid chromatography-gas chromatography (LC-GC), and the system was applied to the extraction and analysis of polycyclic aromatic hydrocarbons (PAHs) in sediment. The method is of superior sensitivity compared with the traditional methods, and only a small 10 mg sample was required for analysis. The commercial extraction vessels were replaced by laboratory-made stainless steel vessels because of some problems that arose. The performance of the laboratory-made vessels was comparable to that of the commercial ones. In an investigation of the effect of thermal desorption in PHWE, it was found that at lower temperatures (200ºC and 250ºC) the effect of thermal desorption is smaller than the effect of the solvating property of hot water. At 300ºC, however, thermal desorption is the main mechanism. The effect of the geometry of the extraction vessel on recoveries was studied with five specially constructed extraction vessels. In addition to the extraction vessel geometry, the sediment packing style and the direction of water flow through the vessel were investigated. The geometry of the vessel was found to have only minor effect on the recoveries, and the same was true of the sediment packing style and the direction of water flow through the vessel. These are good results because these parameters do not have to be carefully optimised before the start of extractions. Liquid-liquid extraction (LLE) and solid-phase extraction (SPE) were compared as trapping techniques for PHWE. LLE was more robust than SPE and it provided better recoveries and repeatabilities than did SPE. Problems related to blocking of the Tenax trap and unrepeatable trapping of the analytes were encountered in SPE. Thus, although LLE is more labour intensive, it can be recommended over SPE. The stabilities of the PAHs in aqueous solutions were measured using a batch-type reaction vessel. Degradation was observed at 300ºC even with the shortest heating time. Ketones and quinones and other oxidation products were observed. Although the conditions of the stability studies differed considerably from the extraction conditions in PHWE, the results indicate that the risk of analyte degradation must be taken into account in PHWE. The aqueous solubilities of acenaphthene, anthracene and pyrene were measured, first below and then above the melting point of the analytes. Measurements below the melting point were made to check that the equipment was working, and the results were compared with those obtained earlier. Good agreement was found between the measured and literature values. A new saturation cell was constructed for the solubility measurements above the melting point of the analytes because the flow-through saturation cell could not be used above the melting point. An exponential relationship was found between the solubilities measured for pyrene and anthracene and temperature.

Single network adaptive critic design for power system stabilisers

The recently developed single network adaptive critic (SNAC) design has been used in this study to design a power system stabiliser (PSS) for enhancing the small-signal stability of power systems over a wide range of operating conditions. PSS design is formulated as a discrete non-linear quadratic regulator problem. SNAC is then used to solve the resulting discrete-time optimal control problem. SNAC uses only a single critic neural network instead of the action-critic dual network architecture of typical adaptive critic designs. SNAC eliminates the iterative training loops between the action and critic networks and greatly simplifies the training procedure. The performance of the proposed PSS has been tested on a single machine infinite bus test system for various system and loading conditions. The proposed stabiliser, which is relatively easier to synthesise, consistently outperformed stabilisers based on conventional lead-lag and linear quadratic regulator designs.

Radiation induced depinning of a charge density wave system

The frequency-dependent response of a pinned charge density wave is considered in terms of forced vibration of an oscillator held in an anharmonic well. It is shown that the effective pinning-frequency can be reduced by applying a d.c. field. If a strong a.c. field, superposed on a d.c. field is applied on such a system “jumps” can be observed in the frequency dependent response of the system. The conditions at which these “jumps” occur are investigated with reference to NbSe3. The possibility of observing such phenomena in other systems like superionic conductors, non-linear dielectrics like ferroelectrics is pointed out. The characteristics are expressed in terms of some “scaled variables” — in terms of which the characteristics show a universal behaviour

On a generalized dynamic model of bi-state social interaction processes

A non-linear model, construed as a generalized version of the models put forth earlier for the study of bi-state social interaction processes, is proposed in this study. The feasibility of deriving the dynamics of such processes is demonstrated by establishing equivalence between the non-linear model and a higher order linear model.

Algorithms for 13C metabolic flux analysis

The metabolism of an organism consists of a network of biochemical reactions that transform small molecules, or metabolites, into others in order to produce energy and building blocks for essential macromolecules. The goal of metabolic flux analysis is to uncover the rates, or the fluxes, of those biochemical reactions. In a steady state, the sum of the fluxes that produce an internal metabolite is equal to the sum of the fluxes that consume the same molecule. Thus the steady state imposes linear balance constraints to the fluxes. In general, the balance constraints imposed by the steady state are not sufficient to uncover all the fluxes of a metabolic network. The fluxes through cycles and alternative pathways between the same source and target metabolites remain unknown. More information about the fluxes can be obtained from isotopic labelling experiments, where a cell population is fed with labelled nutrients, such as glucose that contains 13C atoms. Labels are then transferred by biochemical reactions to other metabolites. The relative abundances of different labelling patterns in internal metabolites depend on the fluxes of pathways producing them. Thus, the relative abundances of different labelling patterns contain information about the fluxes that cannot be uncovered from the balance constraints derived from the steady state. The field of research that estimates the fluxes utilizing the measured constraints to the relative abundances of different labelling patterns induced by 13C labelled nutrients is called 13C metabolic flux analysis. There exist two approaches of 13C metabolic flux analysis. In the optimization approach, a non-linear optimization task, where candidate fluxes are iteratively generated until they fit to the measured abundances of different labelling patterns, is constructed. In the direct approach, linear balance constraints given by the steady state are augmented with linear constraints derived from the abundances of different labelling patterns of metabolites. Thus, mathematically involved non-linear optimization methods that can get stuck to the local optima can be avoided. On the other hand, the direct approach may require more measurement data than the optimization approach to obtain the same flux information. Furthermore, the optimization framework can easily be applied regardless of the labelling measurement technology and with all network topologies. In this thesis we present a formal computational framework for direct 13C metabolic flux analysis. The aim of our study is to construct as many linear constraints to the fluxes from the 13C labelling measurements using only computational methods that avoid non-linear techniques and are independent from the type of measurement data, the labelling of external nutrients and the topology of the metabolic network. The presented framework is the first representative of the direct approach for 13C metabolic flux analysis that is free from restricting assumptions made about these parameters.In our framework, measurement data is first propagated from the measured metabolites to other metabolites. The propagation is facilitated by the flow analysis of metabolite fragments in the network. Then new linear constraints to the fluxes are derived from the propagated data by applying the techniques of linear algebra.Based on the results of the fragment flow analysis, we also present an experiment planning method that selects sets of metabolites whose relative abundances of different labelling patterns are most useful for 13C metabolic flux analysis. Furthermore, we give computational tools to process raw 13C labelling data produced by tandem mass spectrometry to a form suitable for 13C metabolic flux analysis.

Spatiotemporal aspects of Hendra Virus infection in Pteropid Bats (Flying-Foxes) in Eastern Australia

Hendra virus (HeV) causes highly lethal disease in horses and humans in the eastern Australian states of Queensland (QLD) and New South Wales (NSW), with multiple equine cases now reported on an annual basis. Infection and excretion dynamics in pteropid bats (flying-foxes), the recognised natural reservoir, are incompletely understood. We sought to identify key spatial and temporal factors associated with excretion in flying-foxes over a 2300 km latitudinal gradient from northern QLD to southern NSW which encompassed all known equine case locations. The aim was to strengthen knowledge of Hendra virus ecology in flying-foxes to improve spillover risk prediction and exposure risk mitigation strategies, and thus better protect horses and humans. Monthly pooled urine samples were collected from under roosting flying-foxes over a three-year period and screened for HeV RNA by quantitative RT-PCR. A generalised linear model was employed to investigate spatiotemporal associations with HeV detection in 13,968 samples from 27 roosts. There was a non-linear relationship between mean HeV excretion prevalence and five latitudinal regions, with excretion moderate in northern and central QLD, highest in southern QLD/northern NSW, moderate in central NSW, and negligible in southern NSW. Highest HeV positivity occurred where black or spectacled flying-foxes were present; nil or very low positivity rates occurred in exclusive grey-headed flying-fox roosts. Similarly, little red flying-foxes are evidently not a significant source of virus, as their periodic extreme increase in numbers at some roosts was not associated with any concurrent increase in HeV detection. There was a consistent, strong winter seasonality to excretion in the southern QLD/northern NSW and central NSW regions. This new information allows risk management strategies to be refined and targeted, mindful of the potential for spatial risk profiles to shift over time with changes in flying-fox species distribution.

Nonlinear surface acoustic waves on an isotropic solid

A systematic derivation of the approximate coupled amplitude equations governing the propagation of a quasi-monochromatic Rayleigh surface wave on an isotropic solid is presented, starting from the non-linear governing differential equations and the non-linear free-surface boundary conditions, using the method of mulitple scales. An explicit solution of these equations for a signalling problem is obtained in terms of hyperbolic functions. In the case of monochromatic excitation, it is shown that the second harmonic amplitude grows initially at the expense of the fundamental and that the amplitudes of the fundamental and second harmonic remain bounded for all time.

Using relationship mapping to understand sustainable housing stakeholders’ actions

The production of sustainable housing requires the cooperation of a variety of participants with different goals, needs, levels of commitment and cultures. To achieve mainstream net zero energy housing objectives, there is arguably a need for a non-linear network of collaboration between all the stakeholders. In order to create and improve such collaborative networks between stakeholders, we first need to map stakeholders’ relationships, processes, and practices. This paper discusses compares and contrasts maps of the sustainable housing production life-cycle in Australia, developed from different perspectives. The paper highlights the strengths and weaknesses of each visualization, clarifying where gaps in connectivity exist within existing industry networks. Understanding these gaps will help researchers and practitioners identify how to improve the collaboration between participants in the housing industry. This in turn may improve decision making across all stakeholder groups, leading to mainstream implementation of sustainability into the housing industry.

Periodic oscillations in feedback systems with combined pulse modulation

This paper presents a systematic method of investigating the existence of limit cycle oscillations in feedback systems with combined integral pulse frequency-pulse width (IPF-P/V) modulation. The method is based on the non-linear discrete equivalence of the continuous feedback system containing the IPF-PW modulator.

Factors influencing kinetic and equilibrium behaviour of sodium ion exchange with strong acid cation resin

This study reports an investigation of the ion exchange treatment of sodium chloride solutions in relation to use of resin technology for applications such as desalination of brackish water. In particular, a strong acid cation (SAC) resin (DOW Marathon C) was studied to determine its capacity for sodium uptake and to evaluate the fundamentals of the ion exchange process involved. Key questions to answer included: impact of resin identity; best models to simulate the kinetics and equilibrium exchange behaviour of sodium ions; difference between using linear least squares (LLS) and non-linear least squares (NLLS) methods for data interpretation; and, effect of changing the type of anion in solution which accompanied the sodium species. Kinetic studies suggested that the exchange process was best described by a pseudo first order rate expression based upon non-linear least squares analysis of the test data. Application of the Langmuir Vageler isotherm model was recommended as it allowed confirmation that experimental conditions were sufficient for maximum loading of sodium ions to occur. The Freundlich expression best fitted the equilibrium data when analysing the information by a NLLS approach. In contrast, LLS methods suggested that the Langmuir model was optimal for describing the equilibrium process. The Competitive Langmuir model which considered the stoichiometric nature of ion exchange process, estimated the maximum loading of sodium ions to be 64.7 g Na/kg resin. This latter value was comparable to sodium ion capacities for SAC resin published previously. Inherent discrepancies involved when using linearized versions of kinetic and isotherm equations were illustrated, and despite their widespread use, the value of this latter approach was questionable. The equilibrium behaviour of sodium ions form sodium fluoride solution revealed that the sodium ions were now more preferred by the resin compared to the situation with sodium chloride. The solution chemistry of hydrofluoric acid was suggested as promoting the affinity of the sodium ions to the resin.

Dynamics of a class of social interaction systems

A mathematical model of social interaction in the form of two coupler! first-order non-linear differential equations, forms the topic of this study. This non-conservative model io representative of such varied social interaction problems as coexisting sub-populations of two different species, arms race between two rival countries and the like. Differential transformation techniques developed elsewhere in the literature are seen to be effective tools of dynamic analysis of this non-linear non-conservative mode! of social interaction process.

Optimal adaptive sequential spatial sampling of soil using pair-copulas

A spatial sampling design that uses pair-copulas is presented that aims to reduce prediction uncertainty by selecting additional sampling locations based on both the spatial configuration of existing locations and the values of the observations at those locations. The novelty of the approach arises in the use of pair-copulas to estimate uncertainty at unsampled locations. Spatial pair-copulas are able to more accurately capture spatial dependence compared to other types of spatial copula models. Additionally, unlike traditional kriging variance, uncertainty estimates from the pair-copula account for influence from measurement values and not just the configuration of observations. This feature is beneficial, for example, for more accurate identification of soil contamination zones where high contamination measurements are located near measurements of varying contamination. The proposed design methodology is applied to a soil contamination example from the Swiss Jura region. A partial redesign of the original sampling configuration demonstrates the potential of the proposed methodology.