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.

Assessing students in senior science: an analysis of questions in contextualised chemistry exams

This study explores the development of a coding system for analysing test questions in two context-based chemistry exams. We describe our unique analytical procedures before contrasting the data from both tests. Our findings indicate that when a new curriculum is developed such as a context-based curriculum, teachers are required to combine the previously separate domains of context and concept to develop contextualised assessment. We argue that constructing contextualised assessment items requires teachers to view concepts and context as interconnected rather than as separate entities that may polarise scientific endeavour. Implications for practice, curriculum and assessment-development in context-based courses are proposed.

Process mining manifesto

Process mining techniques are able to extract knowledge from event logs commonly available in today’s information systems. These techniques provide new means to discover, monitor, and improve processes in a variety of application domains. There are two main drivers for the growing interest in process mining. On the one hand, more and more events are being recorded, thus, providing detailed information about the history of processes. On the other hand, there is a need to improve and support business processes in competitive and rapidly changing environments. This manifesto is created by the IEEE Task Force on Process Mining and aims to promote the topic of process mining. Moreover, by defining a set of guiding principles and listing important challenges, this manifesto hopes to serve as a guide for software developers, scientists, consultants, business managers, and end-users. The goal is to increase the maturity of process mining as a new tool to improve the (re)design, control, and support of operational business processes.

Strategic project evaluation for open pit mining ventures using real options and allied econometric techniques

Open pit mine operations are complex businesses that demand a constant assessment of risk. This is because the value of a mine project is typically influenced by many underlying economic and physical uncertainties, such as metal prices, metal grades, costs, schedules, quantities, and environmental issues, among others, which are not known with much certainty at the beginning of the project. Hence, mining projects present a considerable challenge to those involved in associated investment decisions, such as the owners of the mine and other stakeholders. In general terms, when an option exists to acquire a new or operating mining project, , the owners and stock holders of the mine project need to know the value of the mining project, which is the fundamental criterion for making final decisions about going ahead with the venture capital. However, obtaining the mine project’s value is not an easy task. The reason for this is that sophisticated valuation and mine optimisation techniques, which combine advanced theories in geostatistics, statistics, engineering, economics and finance, among others, need to be used by the mine analyst or mine planner in order to assess and quantify the existing uncertainty and, consequently, the risk involved in the project investment. Furthermore, current valuation and mine optimisation techniques do not complement each other. That is valuation techniques based on real options (RO) analysis assume an expected (constant) metal grade and ore tonnage during a specified period, while mine optimisation (MO) techniques assume expected (constant) metal prices and mining costs. These assumptions are not totally correct since both sources of uncertainty—that of the orebody (metal grade and reserves of mineral), and that about the future behaviour of metal prices and mining costs—are the ones that have great impact on the value of any mining project. Consequently, the key objective of this thesis is twofold. The first objective consists of analysing and understanding the main sources of uncertainty in an open pit mining project, such as the orebody (in situ metal grade), mining costs and metal price uncertainties, and their effect on the final project value. The second objective consists of breaking down the wall of isolation between economic valuation and mine optimisation techniques in order to generate a novel open pit mine evaluation framework called the ―Integrated Valuation / Optimisation Framework (IVOF)‖. One important characteristic of this new framework is that it incorporates the RO and MO valuation techniques into a single integrated process that quantifies and describes uncertainty and risk in a mine project evaluation process, giving a more realistic estimate of the project’s value. To achieve this, novel and advanced engineering and econometric methods are used to integrate financial and geological uncertainty into dynamic risk forecasting measures. The proposed mine valuation/optimisation technique is then applied to a real gold disseminated open pit mine deposit to estimate its value in the face of orebody, mining costs and metal price uncertainties.

Practical considerations for integrating alternate reality gaming into science education

In this article, I present my experience with integrating an alternate reality gaming (ARG) framework into a pre-service science teacher education course. My goal is to provide an account of my experiences that can inform other science education practitioners at the tertiary and secondary levels that wish to adopt a similar approach in their classes. A game was designed to engage pre-service teachers with issues surrounding the declining enrolments in science, technology, engineering and mathematics disciplines (i.e., the STEM crisis; Tytler, 2007) and ways of re-engaging learners with STEM subjects. The use of ARG in science education is highly innovative. Literature on the use of ARG for educational purposes is scarce so in the article I have drawn on a range of available literature on gaming and ARG to define what it is and to suggest how it can be included in school science classrooms.

Re-imagining STEM : peer scaffolding ICT in initial teacher education

In this paper, we report on how peer scaffolding was used to effect change in tertiary teaching practice and academic disposition in the use of Information and Communication Technology (ICT) in Science teaching and learning. We present a small-scale case study investigating the practice of one of this paper’s authors. It is told through two salient episodes which narratively describe the scaffolding used to support a teaching experiment. This was made possible through the national Teaching Teachers for the Future Project (2011-2012) which aimed to enhance the technological pedagogical capability of pre-service teachers across Australia. The outcome was a demonstrable shift in the academic’s disposition towards the use and benefits of ICT in teaching science and an increase in skills and confidence for both the academic and his students. This study and its outcomes fit within the contemporary push to “re-imagine” the teaching of Science, and more broadly of STEM, in schools.

Re-imagining STEM : peer scaffolding ICT in Initial Teacher Education

In this paper, we report on how peer scaffolding was used to effect change in tertiary teaching practice and academic disposition in the use of Information and Communication Technology (ICT) in Science teaching and learning. We present a small-scale case study investigating the practice of one of this paper’s authors. It is told through two salient episodes which narratively describe the scaffolding used to support a teaching experiment. This was made possible through the national Teaching Teachers for the Future Project (2011-2012) which aimed to enhance the technological pedagogical capability of pre-service teachers across Australia. The outcome was a demonstrable shift in the academic’s disposition towards the use and benefits of ICT in teaching science and an increase in skills and confidence for both the academic and his students. This study and its outcomes fit within the contemporary push to “re-imagine” the teaching of Science, and more broadly of STEM, in schools.

Raman and infrared spectroscopic characterization of beryllonite, a sodium and beryllium phosphate mineral : implications for mineral collectors

The mineral beryllonite has been characterized by the combination of Raman spectroscopy and infrared spectroscopy. SEM–EDX was used for the chemical analysis of the mineral. The intense sharp Raman band at 1011 cm-1, was assigned to the phosphate symmetric stretching mode. Raman bands at 1046, 1053, 1068 and the low intensity bands at 1147, 1160 and 1175 cm-1 are attributed to the phosphate antisymmetric stretching vibrations. The number of bands in the antisymmetric stretching region supports the concept of symmetry reduction of the phosphate anion in the beryllonite structure. This concept is supported by the number of bands found in the out-of-plane bending region. Multiple bands are also found in the in-plane bending region with Raman bands at 399, 418, 431 and 466 cm-1. Strong Raman bands at 304 and 354 cm-1 are attributed to metal oxygen vibrations. Vibrational spectroscopy served to determine the molecular structure of the mineral. The pegmatitic phosphate minerals such as beryllonite are more readily studied by Raman spectroscopy than infrared spectroscopy.

A vibrational spectroscopic study of the phosphate mineral zanazziite - Ca2(MgFe2+)(MgFe2+Al)4Be4(PO4)6⋅6(H2O)

Zanazziite is the magnesium member of a complex beryllium calcium phosphate mineral group named roscherite. The studied samples were collected from the Ponte do Piauí mine, located in Itinga, Minas Gerais. The mineral was studied by electron microprobe, Raman and infrared spectroscopy. The chemical formula can be expressed as Ca2.00(Mg3.15,Fe0.78,Mn0.16,Zn0.01,Al0.26,Ca0.14)Be4.00(PO4)6.09(OH)4.00⋅5.69(H2O) and shows an intermediate member of the zanazziite–greinfeinstenite series, with predominance of zanazziite member. The molecular structure of the mineral zanazziite has been determined using a combination of Raman and infrared spectroscopy. A very intense Raman band at 970 cm−1 is assigned to the phosphate symmetric stretching mode whilst the Raman bands at 1007, 1047, 1064 and 1096 cm−1 are attributed to the phosphate antisymmetric stretching mode. The infrared spectrum is broad and the antisymmetric stretching bands are prominent. Raman bands at 559, 568, 589 cm−1 are assigned to the ν4 out of plane bending modes of the PO4 and HPO4 units. The observation of multiple bands supports the concept that the symmetry of the phosphate unit in the zanazziite structure is reduced in symmetry. Raman bands at 3437 and 3447 cm−1 are attributed to the OH stretching vibrations; Raman bands at 3098 and 3256 are attributed to water stretching vibrations. The width and complexity of the infrared spectral profile in contrast to the well resolved Raman spectra, proves that the pegmatitic phosphates are better studied with Raman spectroscopy.

The moral status of babies

In their controversial paper 'After-birth abortion', Alberto Giubilini and Francesca Minerva argue that there is no rational basis for allowing abortion but prohibiting infanticide ('after-birth abortion'). We ought in all consistency either to allow both or prohibit both. This paper rejects their claim, arguing that much-neglected considerations in philosophical discussions of this issue are capable of explaining why we currently permit abortion in some cases, while prohibiting infanticide.

Exploring emotional climate in preservice science teacher education

Classroom emotional climates are interrelated with students’ engagement with university courses. Despite growing interest in emotions and emotional climate research, little is known about the ways in which social interactions and different subject matter mediate emotional climates in preservice science teacher education classes. In this study we investigated the emotional climate and associated classroom interactions in a preservice science teacher education class. We were interested in the ways in which salient classroom interactions were related to the emotional climate during lessons centered on debates about science-based issues (e.g., nuclear energy alternatives). Participants used audience response technology to indicate their perceptions of the emotional climate. Analysis of conversation for salient video clips and analysis of non-verbal conduct (acoustic parameters, body movements, and facial expressions) supplemented emotional climate data. One key contribution that this study makes to preservice science teacher education is to identify the micro-processes of successful and unsuccessful class interactions that were associated with positive and neutral emotional climate. The structure of these interactions can inform the practice of other science educators who wish to produce positive emotional climates in their classes. The study also extends and explicates the construct of intensity of emotional climate.

Higher order thinking in chemistry curriculum and its assessment

Higher-order thinking has featured persistently in the reform agenda for science education. The intended curriculum in various countries sets out aspirational statements for the levels of higher-order thinking to be attained by students. This study reports the extent to which chemistry examinations from four Australian states align and facilitate the intended higher-order thinking skills stipulated in curriculum documents. Through content analysis, the curriculum goals were identified for each state and compared to the nature of question items in the corresponding examinations. Categories of higher-order thinking were adapted from the OECD’s PISA Science test to analyze question items. There was considerable variation in the extent to which the examinations from the states supported the curriculum intent of developing and assessing higher-order thinking. Generally, examinations that used a marks-based system tended to emphasize lower-order thinking, with a greater distribution of marks allocated for lower-order thinking questions. Examinations associated with a criterion-referenced examination tended to award greater credit for higher-order thinking questions. The level of complexity of chemistry was another factor that limited the extent to which examination questions supported higher-order thinking. Implications from these findings are drawn for the authorities responsible for designing curriculum and assessment procedures and for teachers.