Contextual models and the non-Newtonian paradigm

Biological systems exhibit a wide range of contextual effects, and this often makes it difficult to construct valid mathematical models of their behaviour. In particular, mathematical paradigms built upon the successes of Newtonian physics make assumptions about the nature of biological systems that are unlikely to hold true. After discussing two of the key assumptions underlying the Newtonian paradigm, we discuss two key aspects of the formalism that extended it, Quantum Theory (QT). We draw attention to the similarities between biological and quantum systems, motivating the development of a similar formalism that can be applied to the modelling of biological processes.

Fractional models for the migration of biological cells in complex spatial domains

Travelling wave phenomena are observed in many biological applications. Mathematical theory of standard reaction-diffusion problems shows that simple partial differential equations exhibit travelling wave solutions with constant wavespeed and such models are used to describe, for example, waves of chemical concentrations, electrical signals, cell migration, waves of epidemics and population dynamics. However, as in the study of cell motion in complex spatial geometries, experimental data are often not consistent with constant wavespeed. Non-local spatial models have successfully been used to model anomalous diffusion and spatial heterogeneity in different physical contexts. In this paper, we develop a fractional model based on the Fisher-Kolmogoroff equation and analyse it for its wavespeed properties, attempting to relate the numerical results obtained from our simulations to experimental data describing enteric neural crest-derived cells migrating along the intact gut of mouse embryos. The model proposed essentially combines fractional and standard diffusion in different regions of the spatial domain and qualitatively reproduces the behaviour of neural crest-derived cells observed in the caecum and the hindgut of mouse embryos during in vivo experiments.

Use of contract models to improve environmental outcomes in transport infrastructure construction

The type of contract model may have a significant influence on achieving project objectives, including environmental and climate change goals. This research investigates non-standard contract models impacting greenhouse gas emissions (GHG) in transport infrastructure construction in Australia. The research is based on the analysis of two case studies: an Early Contractor Involvement (ECI) contract and a Design and Construct (D&C) contract with GHG reduction requirements embedded in the contractor selection. Main findings support the use of ECIs for better integrating decisions made during the planning phase with the construction activities, and improve environmental outcomes while achieving financial and time savings. Key words: greenhouse gases reduction; road construction; contracting; ECI; D&C

Living walls - a way to green the built environment

Actions Towards Sustainable Outcomes Environmental Issues/Principal Impacts The increasing urbanisation of cities brings with it several detrimental consequences, such as: • Significant energy use for heating and cooling many more buildings has led to urban heat islands and increased greenhouse gas emissions. • Increased amount of hard surfaces, which not only contributes to higher temperatures in cities, but also to increased stormwater runoff. • Degraded air quality and noise. • Health and general well-being of people is frequently compromised, by inadequate indoor air quality. • Reduced urban biodiversity. Basic Strategies In many design situations, boundaries and constraints limit the application of cutting EDGe actions. In these circumstances, designers should at least consider the following: • Living walls are an emerging technology, and many Australian examples function more as internal feature walls. However,as understanding of the benefits and construction of living walls develops this technology could be part of an exterior facade that enhances a building’s thermal performance. • Living walls should be designed to function with an irrigation system using non-potable water. Cutting EDGe Strategies • Living walls can be part of a design strategy that effectively improves the thermal performance of a building, thereby contributing to lower energy use and greenhouse gas emissions. • Including living walls in the initial stages of design would provide greater flexibility to the design, especially of the facade, structural supports, mechanical ventilation and watering systems, thus lowering costs. • Designing a building with an early understanding of living walls can greatly reduce maintenance costs. • Including plant species and planting media that would be able to remove air impurities could contribute to improved indoor air quality, workplace productivity and well-being. Synergies and References • Living walls are a key research topic at the Centre for Subtropical Design, Queensland University of Technology: http://www.subtropicaldesign.bee.qut.edu.au • BEDP Environment Design Guide: DES 53: Roof and Facade Gardens • BEDP Environment Design Guide: GEN 4: Positive Development – Designing for Net Positive Impacts (see green scaffolding and green space frame walls). • Green Roofs Australia: www.greenroofs.wordpress.com • Green Roofs for Healthy Cities USA: www.greenroofs.org

Longitudinal modelling of the influence of individual differences and the workplace on well-being and work engagement

A set of non-nested longitudinal models tested the relationships between personal and workplace resources, well-being and work engagement. The reciprocal model, trimmed of trivial paths had the best fit and parsimony. The model showed the strong influences of concurrent functioning, stability of variables over time and weaker reciprocal relationships between variables across time. Individuals with greater confidence in themselves and the future experience better work conditions and have greater well-being and work engagement. These day-to-day influences are equalled by the long term strength and stability of Individual Factors, Positive Workplace Factors, and Overall Well-Being. Whilst the reciprocal paths had only weak to mild effects, there was mutual reinforcement of Individual Factors and Overall Well-Being, with Positive Workplace Factors and Work Engagement counterbalancing each other, indicating a more complex relationship. Well-being, particularly, is anchored in the immediate and distant past and provides a robust stability to functioning into the future.

A Raman and infrared spectroscopic study of the mineral delvauxite CaFe3+4(PO4,SO4)2(OH)8•4-6H2O- a ‘colloidal’ mineral

The mineral delvauxite CaFe3+4(PO4,SO4)2(OH)8•4-6H2O has been characterised by Raman spectroscopy and infrared spectroscopy. The mineral is associated with the minerals diadochite and destinezite. Delvauxite appears to vary in crystallinity from amorphous to semi-crystalline. The mineral is often X-ray non-diffracting. The minerals are found in soils and may be described as ‘colloidal’ minerals. Vibrational spectroscopy enables determination of the molecular structure of delvauxite. Bands are assigned to phosphate and sulphate stretching and bending modes. Two symmetric stretching modes for both the phosphate and sulphate symmetric stretching modes support the concept of non-equivalent phosphate and sulphate units in the mineral structure. Multiple water bending and stretching modes imply that non-equivalent water molecules in the structure exist with different hydrogen bond strengths.

A vibrational spectroscopic study of the mixed anion mineral sanjuanite Al2(PO4)(SO4)(OH)•9H2O

The mineral sanjuanite Al2(PO4)(SO4)(OH)•9H2O has been characterised by Raman spectroscopy complimented by infrared spectroscopy. The mineral is characterised by an intense Raman band at 984 cm-1, assigned to the (PO4)3- ν1 symmetric stretching mode. A shoulder band at 1037 cm-1 is attributed to the (SO4)2- ν1 symmetric stretching mode. Two Raman bands observed at 1102 and 1148 cm-1 are assigned to (PO4)3- and (SO4)2- ν3 antisymmetric stretching modes. Multiple bands provide evidence for the reduction in symmetry of both anions. This concept is supported by the multiple sulphate and phosphate bending modes. Raman spectroscopy shows that there are more than one non-equivalent water molecules in the sanjuanite structure. There is evidence that structural disorder exists, shown by the complex set of overlapping bands in the Raman and infrared spectra. At least two types of water are identified with different hydrogen bond strengths. The involvement of water in the sanjuanite structure is essential for the mineral stability.

Raman spectroscopic study of the minerals diadochite and destinezite Fe3+2(PO4,SO4)2(OH)•6H2O – implications for soil science

The two minerals diadochite and destinezite of formula Fe2(PO4,SO4)2(OH)•6H2O have been characterised by Raman spectroscopy and complimented with infrared spectroscopy. These two minerals are both found in soils and are identical except for their morphology. Diadochite is amorphous whereas destinezite is highly crystalline. The spectra of diadochite are broad and ill-defined, whereas the spectra of destinezite are intense and well defined. Bands are assigned to phosphate and sulphate stretching and bending modes. Two symmetric stretching modes for both the phosphate and sulphate symmetric stretching modes support the concept of non-equivalent phosphate and sulphate units in the mineral structure. Multiple water bending and stretching modes imply that non-equivalent water molecules in the structure exist with different hydrogen bond strengths.

Is the mineral borickyite (Ca,Mg)(Fe3+,Al)4(PO4,SO4,CO3)(OH)8•3-7.5H2O the same as delvauxite CaFe3+4(PO4,SO4)2(OH)8•4-6H2O?

The two minerals borickyite and delvauxite CaFe3+4(PO4,SO4)2(OH)8•4-6H2O have the same formula. Are the minerals identical or different? The minerals borickyite and delvauxite have been characterised by Raman spectroscopy. The minerals are related to the minerals diadochite and destinezite. Both minerals are amorphous. Delvauxite appears to vary in crystallinity from amorphous to semi-crystalline. The minerals are often X-ray non-diffracting. The minerals are found in soils and may be described as ‘colloidal’ minerals. Vibrational spectroscopy enables an assessment of the molecular structure of borickyite and delvauxite. Bands are assigned to phosphate and sulphate stretching and bending modes. Multiple water bending and stretching modes imply that non-equivalent water molecules in the structure exist with different hydrogen bond strengths. The two minerals show differing spectra and must be considered as different minerals.

Electromechanical wave in power systems : theory and applications

The continuum model is a key paradigm describing the behavior of electromechanical transients in power systems. In the past two decades, much research work has been done on applying the continuum model to analyze the electromechanical wave in power systems. In this work, the uniform and non-uniform continuum models are first briefly described, and some explanations borrowing concepts and tools from other fields are given. Then, the existing approaches of investigating the resulting wave equations are summarized. An application named the zero reflection controller based on the idea of the wave equations is next presented.

Sneak peek: Dance audience relationships during open rehearsals

Over the past decade there has been a surge of interest in behind-the-scenes events from mainstream dance companies and audiences alike. Online videos, open classes, open rehearsals, and backstage tours all provide insights for audiences about daily life in a dance company and how dance work is made. This article focuses on the use of open rehearsals in studio sites and investigates audience experience and relationship with dancers during these events. Applying Clare Dyson’s (2010) scales of audience engagement, I analyse two open rehearsal models that I observed as an audience participant in 2013: Friends Open Days with English National Ballet (London), and Inner Workings with Chunky Move (Melbourne). Through this analysis, open rehearsals emerge as an experience with elements reminiscent of both the traditional presentation paradigm and non-traditional presentation models. Elements such as close audience-dancer proximity, authenticity, and experiences in liminal sites, such as staircases and green rooms, present the possibility of new audience-dancer relationship within the mainstream dance company context.

Role of 3D visual conceptualisation of groundwater system models as a management support tool

After the recent prolonged drought conditions in many parts of Australia it is increasingly recognised that many groundwater systems are under stress. Although this is obvious for systems that are utilised for intensive irrigation many other groundwater systems are also impacted.Management strategies are highly variable to non-existent. Policy and regulation are also often inadequate, and are reactive or politically driven. In addition, there is a wide range of opinion by water users and other stakeholders as to what is “reasonable”management practice. These differences are often related to the “value”that is put on the groundwater resource. Opinions vary from “our right to free water”to an awareness that without effective management the resource will be degraded. There is also often misunderstanding of surface water-groundwater linkages, recharge processes, and baseflow to drainage systems.

Using Bayesian methods for the estimation of uncertainty in complex statistical models

The research objectives of this thesis were to contribute to Bayesian statistical methodology by contributing to risk assessment statistical methodology, and to spatial and spatio-temporal methodology, by modelling error structures using complex hierarchical models. Specifically, I hoped to consider two applied areas, and use these applications as a springboard for developing new statistical methods as well as undertaking analyses which might give answers to particular applied questions. Thus, this thesis considers a series of models, firstly in the context of risk assessments for recycled water, and secondly in the context of water usage by crops. The research objective was to model error structures using hierarchical models in two problems, namely risk assessment analyses for wastewater, and secondly, in a four dimensional dataset, assessing differences between cropping systems over time and over three spatial dimensions. The aim was to use the simplicity and insight afforded by Bayesian networks to develop appropriate models for risk scenarios, and again to use Bayesian hierarchical models to explore the necessarily complex modelling of four dimensional agricultural data. The specific objectives of the research were to develop a method for the calculation of credible intervals for the point estimates of Bayesian networks; to develop a model structure to incorporate all the experimental uncertainty associated with various constants thereby allowing the calculation of more credible credible intervals for a risk assessment; to model a single day’s data from the agricultural dataset which satisfactorily captured the complexities of the data; to build a model for several days’ data, in order to consider how the full data might be modelled; and finally to build a model for the full four dimensional dataset and to consider the timevarying nature of the contrast of interest, having satisfactorily accounted for possible spatial and temporal autocorrelations. This work forms five papers, two of which have been published, with two submitted, and the final paper still in draft. The first two objectives were met by recasting the risk assessments as directed, acyclic graphs (DAGs). In the first case, we elicited uncertainty for the conditional probabilities needed by the Bayesian net, incorporated these into a corresponding DAG, and used Markov chain Monte Carlo (MCMC) to find credible intervals, for all the scenarios and outcomes of interest. In the second case, we incorporated the experimental data underlying the risk assessment constants into the DAG, and also treated some of that data as needing to be modelled as an ‘errors-invariables’ problem [Fuller, 1987]. This illustrated a simple method for the incorporation of experimental error into risk assessments. In considering one day of the three-dimensional agricultural data, it became clear that geostatistical models or conditional autoregressive (CAR) models over the three dimensions were not the best way to approach the data. Instead CAR models are used with neighbours only in the same depth layer. This gave flexibility to the model, allowing both the spatially structured and non-structured variances to differ at all depths. We call this model the CAR layered model. Given the experimental design, the fixed part of the model could have been modelled as a set of means by treatment and by depth, but doing so allows little insight into how the treatment effects vary with depth. Hence, a number of essentially non-parametric approaches were taken to see the effects of depth on treatment, with the model of choice incorporating an errors-in-variables approach for depth in addition to a non-parametric smooth. The statistical contribution here was the introduction of the CAR layered model, the applied contribution the analysis of moisture over depth and estimation of the contrast of interest together with its credible intervals. These models were fitted using WinBUGS [Lunn et al., 2000]. The work in the fifth paper deals with the fact that with large datasets, the use of WinBUGS becomes more problematic because of its highly correlated term by term updating. In this work, we introduce a Gibbs sampler with block updating for the CAR layered model. The Gibbs sampler was implemented by Chris Strickland using pyMCMC [Strickland, 2010]. This framework is then used to consider five days data, and we show that moisture in the soil for all the various treatments reaches levels particular to each treatment at a depth of 200 cm and thereafter stays constant, albeit with increasing variances with depth. In an analysis across three spatial dimensions and across time, there are many interactions of time and the spatial dimensions to be considered. Hence, we chose to use a daily model and to repeat the analysis at all time points, effectively creating an interaction model of time by the daily model. Such an approach allows great flexibility. However, this approach does not allow insight into the way in which the parameter of interest varies over time. Hence, a two-stage approach was also used, with estimates from the first-stage being analysed as a set of time series. We see this spatio-temporal interaction model as being a useful approach to data measured across three spatial dimensions and time, since it does not assume additivity of the random spatial or temporal effects.

Tests and Models of Non-compositional Concepts

The question of under what conditions conceptual representation is compositional remains debatable within cognitive science. This paper proposes a well developed mathematical apparatus for a probabilistic representation of concepts, drawing upon methods developed in quantum theory to propose a formal test that can determine whether a specific conceptual combination is compositional, or not. This test examines a joint probability distribution modeling the combination, asking whether or not it is factorizable. Empirical studies indicate that some combinations should be considered non-compositionally.