Stochastic chemical kinetics and the quasi-steady-state assumption : application to the stochastic simulation algorithm and chemical master equation

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemical systems that involve both relatively fast and slow chemical reactions [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)] and further work has led to the nested and slow-scale SSA. Improved numerical efficiency is obtained by respecting the vastly different time scales characterizing the system and then by advancing only the slow reactions exactly, based on a suitable approximation to the fast reactions. We considerably extend these works by applying the QSSA to numerical methods for the direct solution of the chemical master equation (CME) and, in particular, to the finite state projection algorithm [Munsky and Khammash, J. Chem. Phys. 124, 044104 (2006)], in conjunction with Krylov methods. In addition, we point out some important connections to the literature on the (deterministic) total QSSA (tQSSA) and place the stochastic analogue of the QSSA within the more general framework of aggregation of Markov processes. We demonstrate the new methods on four examples: Michaelis–Menten enzyme kinetics, double phosphorylation, the Goldbeter–Koshland switch, and the mitogen activated protein kinase cascade. Overall, we report dramatic improvements by applying the tQSSA to the CME solver.

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.

Sources of stress experienced by occupational therapists and social workers in mental health settings

This study examined the sources of stress experienced by occupational therapists and social workers employed in Australian public mental health services and identified the demographic and work-related factors related to stress using a cross-sectional survey design. Participants provided demographic and work-related information and completed the Mental Health Professionals Stress Scale. The overall response rate to the survey was 76.6%, consisting of 196 occupational therapists and 108 social workers. Results indicated that lack of resources, relationships and conflicts with other professionals, workload, and professional self-doubt were correlated with increased stress. Working in case management was associated with stress caused by client-related difficulties, lack of resources, and professional self-doubt. The results of this study suggest that Australian occupational therapists and social workers experience stress, with social workers reporting slightly more overall stress than occupational therapists.

Influence of physical and chemical parameters on the treatment of heavy metals in polluted stormwater using zeolite : A review

Zeolite-based technology can provide a cost effective solution for stormwater treatment for the removal of toxic heavy metals under increasing demand of safe water from alternative sources. This paper reviews the currently available knowledge relating to the effect of properties of zeolites such as pore size, surface area and Si:Al ratio and the physico-chemical conditions of the system such as pH, temperature, initial metal concentration and zeolite concentration on heavy metal removal performance. The primary aims are, to consolidate available knowledge and identify knowledge gaps. It was established that an in-depth understanding of operational issues such as, diffusion of metal ions into the zeolite pore structure, pore clogging, zeolite surface coverage by particulates in stormwater as well as the effect of pH on stormwater quality in the presence of zeolites is essential for developing a zeolite-based technology for the treatment of polluted stormwater. The optimum zeolite concentration to treat typical volumes of stormwater and initial heavy metal concentrations in stormwater should also be considered as operational issues in this regard. Additionally, leaching of aluminium and sodium ions from the zeolite structure to solution were identified as key issues requiring further research in the effort to develop cost effective solutions for the removal of heavy metals from stormwater.

Influence of physical and chemical properties of solids on heavy metal adsorption

Partition of heavy metals between particulate and dissolve fraction of stormwater primarily depends on the adsorption characteristics of solids particles. Moreover, the bioavailability of heavy metals is also influenced by the adsorption behaviour of solids. However, due to the lack of fundamental knowledge in relation to the heavy metals adsorption processes of road deposited solids, the effectiveness of stormwater management strategies can be limited. The research study focused on the investigation of the physical and chemical parameters of solids on urban road surfaces and, more specifically, on heavy metal adsorption to solids. Due to the complex nature of heavy metal interaction with solids, a substantial database was generated through a series of field investigations and laboratory experiments. The study sites for the build-up pollutant sample collection were selected from four urbanised suburbs located in a major river catchment. Sixteen road sites were selected from these suburbs and represented typical industrial, commercial and residential land uses. Build-up pollutants were collected using a wet and dry vacuum collection technique which was specially designed to improve fine particle collection. Roadside soil samples were also collected from each suburb for comparison with the road surface solids. The collected build-up solids samples were separated into four particle size ranges and tested for a range of physical and chemical parameters. The solids build-up on road surfaces contained a high fraction (70%) of particles smaller than 150ìm, which are favourable for heavy metal adsorption. These solids particles predominantly consist of soil derived minerals which included quartz, albite, microcline, muscovite and chlorite. Additionally, a high percentage of amorphous content was also identified in road deposited solids. In comparing the mineralogical data of surrounding soil and road deposited solids, it was found that about 30% of the solids consisted of particles generated from traffic related activities on road surfaces. Significant difference in mineralogical composition was noted in different particle sizes of build-up solids. Fine solids particles (<150ìm) consisted of a clayey matrix and high amorphous content (in the region of 40%) while coarse particles (>150ìm) consisted of a sandy matrix at all study sites, with about 60% quartz content. Due to these differences in mineralogical components, particles larger than and smaller than 150ìm had significant differences in their specific surface area (SSA) and effective cation exchange capacity (ECEC). These parameters, in turn, exert a significant influence on heavy metal adsorption. Consequently, heavy metal content in >150ìm particles was lower than in the case of fine particles. The particle size range <75ìm had the highest heavy metal content, corresponding with its high clay forming minerals, high organic matter and low quartz content which increased the SSA, ECEC and the presence of Fe, Al and Mn oxides. The clay forming minerals, high organic matter and Fe, Al and Mn oxides create distinct groups of charge sites on solids surfaces and exhibit different adsorption mechanisms and bond strength, between heavy metal elements and charge sites. Therefore, the predominance of these factors in different particle sizes leads to different heavy metal adsorption characteristics. Heavy metals show preference for association with clay forming minerals in fine solids particles, whilst in coarse particles heavy metals preferentially associate with organic matter. Although heavy metal adsorption to amorphous material is very low, the heavy metals embedded in traffic related materials have a potential impact on stormwater quality.Adsorption of heavy metals is not confined to an individual type of charge site in solids, whereas specific heavy metal elements show preference for adsorption to several different types of charge sites in solids. This is attributed to the dearth of preferred binding sites and the inability to reach the preferred binding sites due to competition between different heavy metal species. This confirms that heavy metal adsorption is significantly influenced by the physical and chemical parameters of solids that lead to a heterogeneity of surface charge sites. The research study highlighted the importance of removal of solids particles from stormwater runoff before they enter into receiving waters to reduce the potential risk posed by the bioavailability of heavy metals. The bioavailability of heavy metals not only results from the easily mobile fraction bound to the solids particles, but can also occur as a result of the dissolution of other forms of bonds by chemical changes in stormwater or microbial activity. Due to the diversity in the composition of the different particle sizes of solids and the characteristics and amount of charge sites on the particle surfaces, investigations using bulk solids are not adequate to gain an understanding of the heavy metal adsorption processes of solids particles. Therefore, the investigation of different particle size ranges is recommended for enhancing stormwater quality management practices.

Attitudes of employees and employers towards older workers in a climate of anti-discrimination

Attitudes and practices towards older workers were surveyed in Brisbane with 525 employees randomly sampled from the electoral roll and executives of 104 companies obtained by stratified random sampling from the Register of Workplaces (response rates, 60% and 80% respectively). The results indicated that “older workers” are young in terms of contemporary life expectancy, and younger for employers than employees; they have some desirable personal qualities (eg. loyalty), but are not perceived as adaptable; workers aged 25–39 were preferred on qualities held to be important in the workplace and there was minimal interest in recruiting anyone over 45 years.

A physico-chemical characterisation of particulate emissions from a compression ignition engine : the influence of biodiesel feedstock

This study undertook a physico-chemical characterisation of particle emissions from a single compression ignition engine operated at one test mode with 3 biodiesel fuels made from 3 different feedstocks (i.e. soy, tallow and canola) at 4 different blend percentages (20%, 40%, 60% and 80%) to gain insights into their particle-related health effects. Particle physical properties were inferred by measuring particle number size distributions both with and without heating within a thermodenuder (TD) and also by measuring particulate matter (PM) emission factors with an aerodynamic diameter less than 10 μm (PM10). The chemical properties of particulates were investigated by measuring particle and vapour phase Polycyclic Aromatic Hydrocarbons (PAHs) and also Reactive Oxygen Species (ROS) concentrations. The particle number size distributions showed strong dependency on feedstock and blend percentage with some fuel types showing increased particle number emissions, whilst others showed particle number reductions. In addition, the median particle diameter decreased as the blend percentage was increased. Particle and vapour phase PAHs were generally reduced with biodiesel, with the results being relatively independent of the blend percentage. The ROS concentrations increased monotonically with biodiesel blend percentage, but did not exhibit strong feedstock variability. Furthermore, the ROS concentrations correlated quite well with the organic volume percentage of particles – a quantity which increased with increasing blend percentage. At higher blend percentages, the particle surface area was significantly reduced, but the particles were internally mixed with a greater organic volume percentage (containing ROS) which has implications for using surface area as a regulatory metric for diesel particulate matter (DPM) emissions.

Physical capital and its consequences for fitness workers in Queensland

Sexual, social and employment success have been linked to the physical capital drawn from having aesthetic attributes of the socially idealised body. In certain workplace settings, such as health and fitness centres, the body becomes a mainstream commodity with physical capital affording the fitness worker a high degree of distinction and adoration as well as employment opportunities. The employment relationship is shaped by 'lookism', with both the employer and employee taking advantage of the fitness worker's idealised form. The worker's physical capital provides a walking billboard advertising the employer's products and services, while exposure to comparison and adoration provides a heightened sense of self-worth, distinction and celebrity. Fitness workers appear to be prepared to ignore poor employment conditions or trade-off standard entitlements for the alternative rewards that their physical capital brings.

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.

Combined time- and space-resolved Raman spectrometer for the non-invasive depth profiling of chemical hazards

A time-resolved inverse spatially offset Raman spectrometer was constructed for depth profiling of Raman-active substances under both the lab and the field environments. The system operating principles and performance are discussed along with its advantages relative to traditional continuous wave spatially offset Raman spectrometer. The developed spectrometer uses a combination of space- and time-resolved detection in order to obtain high-quality Raman spectra from substances hidden behind coloured opaque surface layers, such as plastic and garments, with a single measurement. The time-gated spatially offset Raman spectrometer was successfully used to detect concealed explosives and drug precursors under incandescent and fluorescent background light as well as under daylight. The average screening time was 50 s per measurement. The excitation energy requirements were relatively low (20 mW) which makes the probe safe for screening hazardous substances. The unit has been designed with nanosecond laser excitation and gated detection, making it of lower cost and complexity than previous picosecond-based systems, to provide a functional platform for in-line or in-field sensing of chemical substances.

A fragment of the LG3 peptide of endorepellin is present in the urine of physically active mining workers : a potential marker of physical activity

Biomarker analysis has been implemented in sports research in an attempt to monitor the effects of exertion and fatigue in athletes. This study proposed that while such biomarkers may be useful for monitoring injury risk in workers, proteomic approaches might also be utilised to identify novel exertion or injury markers. We found that urinary urea and cortisol levels were significantly elevated in mining workers following a 12 hour overnight shift. These levels failed to return to baseline over 24h in the more active maintenance crew compared to truck drivers (operators) suggesting a lack of recovery between shifts. Use of a SELDI-TOF MS approach to detect novel exertion or injury markers revealed a spectral feature which was associated with workers in both work categories who were engaged in higher levels of physical activity. This feature was identified as the LG3 peptide, a C-terminal fragment of the anti-angiogenic / anti-tumourigenic protein endorepellin. This finding suggests that urinary LG3 peptide may be a biomarker of physical activity. It is also possible that the activity mediated release of LG3 / endorepellin into the circulation may represent a biological mechanism for the known inverse association between physical activity and cancer risk / survival.

Strengthening the role of the adult education sector in training workers for the digital content industries in Australia and Singapore

In 2009, QUT’s Office of Research and the Institute for Adult Learning Singapore funded a six-month pilot project that represented the first stage of a larger international comparative study. The study is the first of its kind to investigate to what extent and how digital content workers’ learning needs are being met by adult education and training in Australia and Singapore. The pilot project involved consolidating key theoretical literature, studies, policies, programs and statistical data relevant to the digital content industries in Australia and Singapore. This had not been done before, and represented new knowledge generation. Digital content workers include professionals within and beyond the creative industries as follows: Visual effects and animation (including virtual reality and 3D products); Interactive multimedia (e.g. websites, CD-ROMs) and software development; Computer and online games; and Digital film & TV production and film & TV post-production. In the last decade, the digital content industries have been recognised as an industry sector of strong and increasing significance. The project compared Australia and Singapore on aspects of the digital content industries’ labour market, skill requirements, human capital challenges, the role of adult education in building a workforce for the digital content industries, and innovation policies. The consolidated report generated from the project formed the basis of the proposal for an ARC Linkage Project application submitted in the May 2010 round.