Stochastic models and simulation of ion channel dynamics

The behaviour of ion channels within cardiac and neuronal cells is intrinsically stochastic in nature. When the number of channels is small this stochastic noise is large and can have an impact on the dynamics of the system which is potentially an issue when modelling small neurons and drug block in cardiac cells. While exact methods correctly capture the stochastic dynamics of a system they are computationally expensive, restricting their inclusion into tissue level models and so approximations to exact methods are often used instead. The other issue in modelling ion channel dynamics is that the transition rates are voltage dependent, adding a level of complexity as the channel dynamics are coupled to the membrane potential. By assuming that such transition rates are constant over each time step, it is possible to derive a stochastic differential equation (SDE), in the same manner as for biochemical reaction networks, that describes the stochastic dynamics of ion channels. While such a model is more computationally efficient than exact methods we show that there are analytical problems with the resulting SDE as well as issues in using current numerical schemes to solve such an equation. We therefore make two contributions: develop a different model to describe the stochastic ion channel dynamics that analytically behaves in the correct manner and also discuss numerical methods that preserve the analytical properties of the model.

Teachers’ and parents’ perspectives of digital technology in the lives of young children

The pervasiveness of technology in the 21st Century has meant that adults and children live in a society where digital devices are integral to their everyday lives and participation in society. How we communicate, learn, work, entertain ourselves, and even shop is influenced by technology. Therefore, before children begin school they are potentially exposed to a range of learning opportunities mediated by digital devices. These devices include microwaves, mobile phones, computers, and console games such as Playstations® and iPods®. In Queensland preparatory classrooms and in the homes of these children, teachers and parents support and scaffold young children’s experiences, providing them with access to a range of tools that promote learning and provide entertainment. This paper examines teachers’ and parents’ perspectives and considers whether they are techno-optimists who advocate for and promote the inclusion of digital technology, or whether they are they techno-pessimists, who prefer to exclude digital devices from young children’s everyday experiences. An exploratory, single case study design was utilised to gather data from three teachers and ten parents of children in the preparatory year. Teacher data was collected through interviews and email correspondence. Parent data was collected from questionnaires and focus groups. All parents who responded to the research invitation were mothers. The results of data analysis identified a misalignment among adults’ perspectives. Teachers were identified as techno-optimists and parents were identified as techno-pessimists with further emergent themes particular to each category being established. This is concerning because both teachers and mothers influence young children’s experiences and numeracy knowledge, thus, a shared understanding and a common commitment to supporting young children’s use of technology would be beneficial. Further research must investigate fathers’ perspectives of digital devices and the beneficial and detrimental roles that a range of digital devices, tools, and entertainment gadgets play in 21st Century children’s lives.

Stochastic simulation for spatial modelling of dynamic process in a living cell

One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.

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.

Neo-planning: Location-based social media to engage Australia’s new digital locals

Community engagement with time poor and seemingly apathetic citizens continues to challenge local governments. Capturing the attention of a digitally literate community who are technology and socially savvy adds a new quality to this challenge. Community engagement is resource and time intensive, yet local governments have to manage on continually tightened budgets. The benefits of assisting citizens in taking ownership in making their community and city a better place to live in collaboration with planners and local governments are well established. This study investigates a new collaborative form of civic participation and engagement for urban planning that employs in-place digital augmentation. It enhances people’s experience of physical spaces with digital technologies that are directly accessible within that space, in particular through interaction with mobile phones and public displays. The study developed and deployed a system called Discussions in Space (DIS) in conjunction with a major urban planning project in Brisbane. Planners used the system to ask local residents planning-related questions via a public screen, and passers-by sent responses via SMS or Twitter onto the screen for others to read and reflect, hence encouraging in-situ, real-time, civic discourse. The low barrier of entry proved to be successful in engaging a wide range of residents who are generally not heard due to their lack of time or interest. The system also reflected positively on the local government for reaching out in this way. Challenges and implications of the short-texted and ephemeral nature of this medium were evaluated in two focus groups with urban planners. The paper concludes with an analysis of the planners’ feedback evaluating the merits of the data generated by the system to better engage with Australia’s new digital locals.

Functional fixation : experimental evidence on the presentation of financial information through different digital formats

This study examines whether, in the presentation of financial information, digital formats address the concern over users’ functional fixation. The accounting literature indicates that the presentation of financial information either within the financial statements or in the notes to the financial statements often creates functional fixation where users of financial statements fail to adjust for differences in accounting policy. This leads users to judge what would otherwise be identical financial situations as being different due to the different accounting policies and methods adopted. It has been suggested that the use of digital formats in presenting financial reports may overcome functional fixation. Using an experimental design involving accountants in public practice, the results indicate that the use of digital formats to present financial reports does not fully overcome the issue of functional fixation in the processing of financial information. Although the participants were able to identify and extract relevant information, irrespective of whether or not the information was presented within the financial statements or in the notes to the accounts, the evidence indicates that functional fixation remained when the participants made final decisions based on available information. This suggests that functional fixation may not be caused by access to or extraction of information but by the level of perceived significance based on where the information is reported in the financial statements. In general, the results indicate that current technology may not be able to fully reduce functional fixation in the evaluation of financial information prepared in accordance with different accounting policies and methods.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

“Prosuming” across cultures : youth creating digital media across borders

The Scratch Online Community is a space that enables young people to share their creative digital projects internationally with a level of ease that was impossible only a few years ago. Like all creative communities, Scratch is not just a space for sharing products, work, techniques and tips and tricks, but also a space for social interaction. Media literacy educators have unprecedented challenges and opportunities in digital environments like Scratch to harness the vast amount of knowledge in the community to enhance students’ learning. They also have challenges and opportunities in terms of implementing a form of digital media literacy education that is responsive to social and cultural representation. One role of digital media literacy is to help young people to challenge unfair and derogatory portrayals of people and to break down processes of social and cultural ‘othering’ so that all community members feel included and safe to express themselves. This article considers how online community spaces might draw on social interaction to enhance cross-cultural understandings and learning through dialogue and creative practice. The article uses statistics to indicate the amount of international interaction in the Scratch community. It then uses qualitative analysis of forum discussions and creative digital work to analyse the types of cross cultural interaction that occurs.

A traffic simulation standard based on data marts

Traffic Simulation models tend to have their own data input and output formats. In an effort to standardise the input for traffic simulations, we introduce in this paper a set of data marts that aim to serve as a common interface between the necessaary data, stored in dedicated databases, and the swoftware packages, that require the input in a certain format. The data marts are developed based on real world objects (e.g. roads, traffic lights, controllers) rather than abstract models and hence contain all necessary information that can be transformed by the importing software package to their needs. The paper contains a full description of the data marts for network coding, simulation results, and scenario management, which have been discussed with industry partners to ensure sustainability.

Scaling digital radiographs for templating in total hip arthroplasty using conventional acetate templates independent of calibration markers

We describe a scaling method for templating digital radiographs using conventional acetate templates independent of template magnification without the need for a calibration marker. The mean magnification factor for the radiology department was determined (119.8%, range117%-123.4%). This fixed magnification factor was used to scale the radiographs by the method described. 32 femoral heads on postoperative THR radiographs were then measured and compared to the actual size. The mean absolute accuracy was within 0.5% of actual head size (range 0 to 3%) with a mean absolute difference of 0.16mm (range 0-1mm, SD 0.26mm). Intraclass Correlation Coefficient (ICC) showed excellent reliability for both inter and intraobserver measurements with ICC scores of 0.993 (95% CI 0.988-0.996) for interobserver measurements and intraobserver measurements ranging between 0.990-0.993 (95% CI 0.980-0.997).

Reflection of My Digital Mind

This artwork visualised my digital mind which is built on my technology experience. The contemporary technologies make available many small pieces of factual information that have affected the formation of my identity. This results that multiple identities can exist in a rhizomatic form through a vertical gene transfer. This does not refer to schizophrenia, but an ongoing transformation of digital mind.

Developing a digital image watermarking model

This paper presents a key based generic model for digital image watermarking. The model aims at addressing an identified gap in the literature by providing a basis for assessing different watermarking requirements in various digital image applications. We start with a formulation of a basic watermarking system, and define system inputs and outputs. We then proceed to incorporate the use of keys in the design of various system components. Using the model, we also define a few fundamental design and evaluation parameters. To demonstrate the significance of the proposed model, we provide an example of how it can be applied to formally define common attacks.

A study of abrasive water jet characteristics by CFD simulation

Computational fluid dynamics (CFD) models for ultrahigh velocity waterjets and abrasive waterjets (AWJs) are established using the Fluent 6 flow solver. Jet dynamic characteristics for the flow downstream from a very fine nozzle are then simulated under steady state, turbulent, two-phase and three-phase flow conditions. Water and particle velocities in a jet are obtained under different input and boundary conditions to provide an insight into the jet characteristics and a fundamental understanding of the kerf formation process in AWJ cutting. For the range of downstream distances considered, the results indicate that a jet is characterised by an initial rapid decay of the axial velocity at the jet centre while the cross-sectional flow evolves towards a top-hat profile downstream.

High fidelity simulation; challenges encountered in developing and implementing student learning experiences, staff education and researching approaches to learning

High fidelity simulation as a teaching and learning approach is being embraced by many schools of nursing. Our school embarked on integrating high fidelity (HF) simulation into the undergraduate clinical education program in 2011. Low and medium fidelity simulation has been used for many years, but this did not simplify the integration of HF simulation. Alongside considerations of how and where HF simulation would be integrated, issues arose with: student consent and participation for observed activities; data management of video files; staff development, and conceptualising how methods for student learning could be researched. Simulation for undergraduate student nurses commenced as a formative learning activity, undertaken in groups of eight, where four students undertake the ‘doing’ role and four are structured observers, who then take a formal role in the simulation debrief. Challenges for integrating simulation into student learning included conceptualising and developing scenarios to trigger students’ decision making and application of skills, knowledge and attitudes explicit to solving clinical ‘problems’. Developing and planning scenarios for students to ‘try out’ skills and make decisions for problem solving lay beyond choosing pre-existing scenarios inbuilt with the software. The supplied scenarios were not concept based but rather knowledge, skills and technology (of the manikin) focussed. Challenges lay in using the technology for the purpose of building conceptual mastery rather than using technology simply because it was available. As we integrated use of HF simulation into the final year of the program, focus was on building skills, knowledge and attitudes that went beyond technical skill, and provided an opportunity to bridge the gap with theory-based knowledge that students often found difficult to link to clinical reality. We wished to provide opportunities to develop experiential knowledge based on application and clinical reasoning processes in team environments where problems are encountered, and to solve them, the nurse must show leadership and direction. Other challenges included students consenting for simulations to be videotaped and ethical considerations of this. For example if one student in a group of eight did not consent, did this mean they missed the opportunity to undertake simulation, or that others in the group may be disadvantaged by being unable to review their performance. This has implications for freely given consent but also for equity of access to learning opportunities for students who wished to be taped and those who did not. Alongside this issue were the details behind data management, storage and access. Developing staff with varying levels of computer skills to use software and undertake a different approach to being the ‘teacher’ required innovation where we took an experiential approach. Considering explicit learning approaches to be trialled for learning was not a difficult proposition, but considering how to enact this as research with issues of blinding, timetabling of blinded groups, and reducing bias for testing results of different learning approaches along with gaining ethical approval was problematic. This presentation presents examples of these challenges and how we overcame them.