A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Physical characteristics of small ions and their interaction with ultrafine particles in the urban environment

In recent years, the effect of ions and ultrafine particles on ambient air quality and human health has been well documented, however, knowledge about their sources, concentrations and interactions within different types of urban environments remains limited. This thesis presents the results of numerous field studies aimed at quantifying variations in ion concentration with distance from the source, as well as identifying the dynamics of the particle ionisation processes which lead to the formation of charged particles in the air. In order to select the most appropriate measurement instruments and locations for the studies, a literature review was also conducted on studies that reported ion and ultrafine particle emissions from different sources in a typical urban environment. The initial study involved laboratory experiments on the attachment of ions to aerosols, so as to gain a better understanding of the interaction between ions and particles. This study determined the efficiency of corona ions at charging and removing particles from the air, as a function of different particle number and ion concentrations. The results showed that particle number loss was directly proportional to particle charge concentration, and that higher small ion concentrations led to higher particle deposition rates in all size ranges investigated. Nanoparticles were also observed to decrease with increasing particle charge concentration, due to their higher Brownian mobility and subsequent attachment to charged particles. Given that corona discharge from high voltage powerlines is considered one of the major ion sources in urban areas, a detailed study was then conducted under three parallel overhead powerlines, with a steady wind blowing in a perpendicular direction to the lines. The results showed that large sections of the lines did not produce any corona at all, while strong positive emissions were observed from discrete components such as a particular set of spacers on one of the lines. Measurements were also conducted at eight upwind and downwind points perpendicular to the powerlines, spanning a total distance of about 160m. The maximum positive small and large ion concentrations, and DC electric field were observed at a point 20 m downwind from the lines, with median values of 4.4×103 cm-3, 1.3×103 cm-3 and 530 V m-1, respectively. It was estimated that, at this point, less than 7% of the total number of particles was charged. The electrical parameters decreased steadily with increasing downwind distance from the lines but remained significantly higher than background levels at the limit of the measurements. Moreover, vehicles are one of the most prevalent ion and particle emitting sources in urban environments, and therefore, experiments were also conducted behind a motor vehicle exhaust pipe and near busy motorways, with the aim of quantifying small ion and particle charge concentration, as well as their distribution as a function of distance from the source. The study found that approximately equal numbers of positive and negative ions were observed in the vehicle exhaust plume, as well as near motorways, of which heavy duty vehicles were believed to be the main contributor. In addition, cluster ion concentration was observed to decrease rapidly within the first 10-15 m from the road and ion-ion recombination and ion-aerosol attachment were the most likely cause of ion depletion, rather than dilution and turbulence related processes. In addition to the above-mentioned dominant ion sources, other sources also exist within urban environments where intensive human activities take place. In this part of the study, airborne concentrations of small ions, particles and net particle charge were measured at 32 different outdoor sites in and around Brisbane, Australia, which were classified into seven different groups as follows: park, woodland, city centre, residential, freeway, powerlines and power substation. Whilst the study confirmed that powerlines, power substations and freeways were the main ion sources in an urban environment, it also suggested that not all powerlines emitted ions, only those with discrete corona discharge points. In addition to the main ion sources, higher ion concentrations were also observed environments affected by vehicle traffic and human activities, such as the city centre and residential areas. A considerable number of ions were also observed in a woodland area and it is still unclear if they were emitted directly from the trees, or if they originated from some other local source. Overall, it was found that different types of environments had different types of ion sources, which could be classified as unipolar or bipolar particle sources, as well as ion sources that co-exist with particle sources. In general, fewer small ions were observed at sites with co-existing sources, however particle charge was often higher due to the effect of ion-particle attachment. In summary, this study quantified ion concentrations in typical urban environments, identified major charge sources in urban areas, and determined the spatial dispersion of ions as a function of distance from the source, as well as their controlling factors. The study also presented ion-aerosol attachment efficiencies under high ion concentration conditions, both in the laboratory and in real outdoor environments. The outcomes of these studies addressed the aims of this work and advanced understanding of the charge status of aerosols in the urban environment.

Sequential Monte Carlo for Bayesian sequentially designed experiments for discrete data

In this paper we present a sequential Monte Carlo algorithm for Bayesian sequential experimental design applied to generalised non-linear models for discrete data. The approach is computationally convenient in that the information of newly observed data can be incorporated through a simple re-weighting step. We also consider a flexible parametric model for the stimulus-response relationship together with a newly developed hybrid design utility that can produce more robust estimates of the target stimulus in the presence of substantial model and parameter uncertainty. The algorithm is applied to hypothetical clinical trial or bioassay scenarios. In the discussion, potential generalisations of the algorithm are suggested to possibly extend its applicability to a wide variety of scenarios

A phenomenological model for the structure-composition relationship of the high Tc cuprates based on simple chemical principles

A simple phenomenological model for the relationship between structure and composition of the high Tc cuprates is presented. The model is based on two simple crystal chemistry principles: unit cell doping and charge balance within unit cells. These principles are inspired by key experimental observations of how the materials accommodate large deviations from stoichiometry. Consistent explanations for significant HTSC properties can be explained without any additional assumptions while retaining valuable insight for geometric interpretation. Combining these two chemical principles with a review of Crystal Field Theory (CFT) or Ligand Field Theory (LFT), it becomes clear that the two oxidation states in the conduction planes (typically d8 and d9) belong to the most strongly divergent d-levels as a function of deformation from regular octahedral coordination. This observation offers a link to a range of coupling effects relating vibrations and spin waves through application of Hund’s rules. An indication of this model’s capacity to predict physical properties for HTSC is provided and will be elaborated in subsequent publications. Simple criteria for the relationship between structure and composition in HTSC systems may guide chemical syntheses within new material systems.

Assessment of operability and maintainability success factors in provision of extended constructability principles

The concept of constructability integrates individual construction functions and experiences through suitable and timely inputs into early stages of project planning and design. It aims to ease construction processes for a more effective and efficient achievement of overall project objectives. Similarly, the concepts of operability and maintainability integrate the functions and experiences of Operation and Maintenance (O&M) into project planning and design. Various studies suggested that these concepts have been implemented in isolation of each other and thus preventing optimum result in delivering infrastructure projects. This paper explores the integration of these three concepts in order to maximize the benefits of their implementation. It reviews the literature to identify the main O&M concerns, and assesses their association with constructability principles. This provides a structure to develop an extended constructability model that includes O&M concerns. It is anticipated that an extended constructability model that include O&M considerations can lead to a more efficient and effective delivery of infrastructure projects.

Solder joint defects classification using the Log-Gabor Filter, the Discrete Wavelet Transform and the Discrete Cosine Transform

Inspection of solder joints has been a critical process in the electronic manufacturing industry to reduce manufacturing cost, improve yield, and ensure project quality and reliability. This paper proposes the use of the Log-Gabor filter bank, Discrete Wavelet Transform and Discrete Cosine Transform for feature extraction of solder joint images on Printed Circuit Boards (PCBs). A distance based on the Mahalanobis Cosine metric is also presented for classification of five different types of solder joints. From the experimental results, this methodology achieved high accuracy and a well generalised performance. This can be an effective method to reduce cost and improve quality in the production of PCBs in the manufacturing industry.

Mind games : applying White’s principles of narrative therapy to the creation of a cabaret about depression and bipolar disorder

This PhD represents my attempt to make sense of my personal experiences of depression through the form of cabaret. I first experienced depression in 2006. Previously, I had considered myself to be a happy and optimistic person. I found the experience of depression to be a shock: both in the experience itself, and also in the way it effected my own self image. These personal experiences, together with my professional history as a songwriter and cabaret performer, have been the motivating force behind the research project. This study has explored the question: What are the implications of applying principles of Michael White’s narrative therapy to the creation of a cabaret performance about depression and bipolar disorder? There is a 50 percent weighting on the creative work, the cabaret performance Mind Games, and a 50 percent weighting on the written exegesis. This research has focussed on the illustration of therapeutic principles in order to play games of truth within a cabaret performance. The research project investigates ways of telling my own story in relation to others’ stories through three re-authoring principles articulated in Michael White’s narrative therapy: externalisation, an autonomous ethic of living and rich descriptions. The personal stories presented in the cabaret were drawn from my own experiences and from interviews with individuals with depression or bipolar disorder. The cabaret focussed on the illustration of therapeutic principles, and was not focussed on therapeutic ends for myself or the interviewees. The research question has been approached through a methodology combining autoethnographic, practice-led and action research. Auto ethnographic research is characterised by close investigation of assumptions, attitudes, and beliefs. The combination of autoethnographic, practice-led, action research has allowed me to bring together personal experiences of mental illness, research into therapeutic techniques, social attitudes and public discourses about mental illness and forms of contemporary cabaret to facilitate the creation of a one-woman cabaret performance. The exegesis begins with a discussion of games of truth as informed by Michel Foucault and Michael White and self-stigma as informed by Michael White and Erving Goffman. These concepts form the basis for a discussion of my own personal experiences. White’s narrative therapy is focused on individuals re-authoring their stories, or telling their stories in different ways. White’s principles are influenced by Foucault’s notions of truth and power. Foucault’s term games of truth has been used to describe the effect of a ‘truth in flux’ that occurs through White’s re-authoring process. This study argues that cabaret is an appropriate form to represent this therapeutic process because it favours heightened performativity over realism, and showcases its ‘constructedness’ and artificiality. Thus cabaret is well suited to playing games of truth. A contextual review compares two major cabaret trends, personal cabaret and provocative cabaret, in reference to the performer’s relationship with the audience in terms of distance and intimacy. The study draws a parallel between principles of distance and intimacy in Michael White’s narrative therapy and relates these to performative terms of distance and intimacy. The creative component of this study, the cabaret Mind Games, used principles of narrative therapy to present the character ‘Jo’ playing games of truth through: externalising an aspect of her personality (externalisation); exploring different life values (an autonomous ethic of living); and enacting multiple versions of her identity (rich descriptions). This constant shifting between distance and intimacy within the cabaret created the effect of a truth in ‘constant flux’, to use one of White’s terms. There are three inter-related findings in the study. The first finding is that the application of principles of White’s narrative therapy was able to successfully combine provocative and empathetic elements within the cabaret. The second finding is that the personal agenda of addressing my own self-stigma within the project limited the effective portrayal of a ‘truth in flux’ within the cabaret. The third finding presents the view that the cabaret expressed ‘Jo’ playing games of truth in order to journey towards her own "preferred identity claim" (White 2004b) through an act of "self care" (Foucault 2005). The contribution to knowledge of this research project is the application of therapeutic principles to the creation of a cabaret performance. This process has focussed on creating a self-revelatory cabaret that questions notions of a ‘fixed truth’ through combining elements of existing cabaret forms in new ways. Two major forms in contemporary cabaret, the personal cabaret and the provocative cabaret use the performer-audience relationship in distinctive ways. Through combining elements of these two cabaret forms, I have explored ways to create a provocative cabaret focussed on the act of self-revelation.

Corona ions from high-voltage power lines : nature of emission and dispersion

Positive and negative small ions, aerosol ion and number concentration and dc electric fields were monitored at an overhead high-voltage power line site. We show that the emission of corona ions was not spatially uniform along the lines and occurred from discrete components such as a particular set of spacers. Maximum ion concentrations and atmospheric dc electric fields were observed at a point 20 m downwind of the lines. It was estimated that less than 7% of the total number of aerosol particles was charged. The electrical parameters decreased steadily with further downwind distance but remained significantly higher than background.

Principles of taxation law (4th Edition)

Taxation law can be an incredibly complex subject to absorb, particularly when time is limited. Written specifically for students, Principles of Taxation Law 2011 brings much needed clarity to this area of law. Utilising many methods to make this often daunting subject achievable, particular features of the 2011 edition include: • seven parts: overview and structure, principles of income, deductions and offsets, timing issues, investment and business entities, tax avoidance and administration, and indirect taxes; • clearly structured chapters within those parts grouped under helpful headings; • flowcharts, diagrams and tables, end of chapter practice questions, and case summaries; • an appendix containing all of the up to date and relevant rates; and • the online self-testing component mentor, which provides questions for students of both business and law. Every major aspect of the Australian tax system is covered, with chapters on topics such as goods and services tax, superannuation, offsets, partnerships, capital gains tax, trusts, company tax and tax administration. All chapters have been thoroughly revised. Principles of Taxation Law 2011 is the perfect tool to guide the reader from their initial exposure to the subject to success in taxation law exams. [from publisher's website]

Principles of taxation law 2012

Taxation law can be an incredibly complex subject to absorb, particularly when time is limited. Written specifically for students, Principles of Taxation Law 2012 brings much needed clarity to this area of law. Utilising many methods to make this often daunting subject achievable, particular features of the 2012 edition include: * seven parts: overview and structure, principles of income, deductions and offsets, timing issues, investment and business entities, tax avoidance and administration, and indirect taxes; * clearly structured chapters within those parts grouped under helpful headings; * flowcharts, diagrams and tables, end of chapter practice questions, and case summaries; * an appendix containing all of the up to date and relevant rates; and * the online self-testing component mentor, which provides questions for students of both business and law. Every major aspect of the Australian tax system is covered, with chapters on topics such as goods and services tax, superannuation, offsets, partnerships, capital gains tax, trusts, company tax and tax administration. All chapters have been thoroughly revised. Principles of Taxation Law 2012 is the perfect tool to guide the reader from their initial exposure to the subject to success in taxation law exams.

Copyright enforcement in the networked society : guiding principles for protecting copyright

This paper argues that any future copyright policy should be proportional and flexible and be developed from a clear and evidence-based approach. An approach is required that carefully balances the incentives and rewards provided to economic rights holders against fundamental rights of privacy, self-expression, due process and the user rights embodied in copyright law to protect access, learning, critique, and reuse. This paper also suggests that while adequate enforcement measures are certainly part of a solution to a well functioning lawful, enforcement alone can never solve the root cause of unlawful file-sharing, since it utterly fails to address supply-side market barriers. Focus on enforcement measures alone continues to leave out a legitimate but un-served market demand, susceptible to unlawful alternatives. A competitive and consumer friendly digital content market and an appropriate legal framework to enable easy lawful access to digital content are essential preconditions for the creation of a culture of lawful, rather than unlawful, consumption.

Principles of taxation law 2008

Covers the fundamental principles of the Australian tax system, providing students with guidance on reading and using tax resources such as legislation, case law and Australian Taxation Office rulings -- Back cover.

Principles of taxation law [2nd Ed.]

"With its clear and concise explanations of taxation law concepts, Principles of Taxation Law 2009 is the ideal text for students studying this complex subject. It covers all major topics underpinning the Australian tax system, including income, deductions, capital gains, tax accounting, international issues, fringe benefits, tax administration, goods and services tax and, in this new edition, offsets and superannuation. Importantly, the book commences with a special chapter on how to study tax law and succeed in taxation law exams."--Publisher description.

Principles of taxation law 2011 [4th ed.]

Taxation law can be an incredibly complex subject to absorb, particularly when time is limited. Written specifically for students, Principles of Taxation Law 2011 brings much needed clarity to this area of law -- Back cover.