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.

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

Development of the sustainable building and construction products industry in Australia

This paper draws on a major study the authors conducted for the Australian Government in 2009. It focuses on the diffusion issues surrounding the uptake of sustainable building and construction products in Australia. Innovative sustainable products can minimise the environmental impact during construction, while maximising asset performance, durability and re-use. However, there are significant challenges faced by designers and clients in the selection of appropriate sustainable products in consideration of the integrated design solution, including overall energy efficiency, water conservation, maintenance and durability, low-impact use and consumption. The paper is a review of the current state of sustainable energy and material product innovations in Australia. It examines the system dynamics surrounding these innovations as well as the drivers and obstacles to their diffusion throughout the Australian construction industry. The case product types reviewed comprise: solar energy technology, small wind turbines, advanced concrete technology, and warm-mixed asphalt. The conclusions highlight the important role played by Australian governments in facilitating improved adoption rates. This applies to governments in their various roles, but particularly as clients/owners, regulators, and investors in education, training, research and development. In their role as clients/owners, the paper suggests that government can better facilitate innovation within the construction industry by adjusting specification policies to encourage the uptake of sustainable products. In the role as regulators, findings suggest governments should be encouraging the application of innovative finance options and positive end-user incentives to promote sustainable product uptake. Also, further education for project-based firms and the client/end users about the long-term financial and environmental benefits of innovative sustainable products is required. As more of the economy’s resources are diverted away from business-as-usual and into the use of sustainable products, some project-based firms may face short-term financial pain in re-shaping their businesses. Government policy initiatives can encourage firms make the necessary adjustments to improve innovative sustainable product diffusion throughout the industry.

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.

Periodically forced natural convection through the roof of an attic-shaped building

In this study, numerical simulations of natural convection in an attic space subject to diurnal temperature condition on the sloping wall have been carried out. An explanation of choosing the period of periodic thermal effect has been given with help of the scaling analysis which is available in the literature. Moreover, the effects of the aspect ratio and Rayleigh number on the fluid flow and heat transfer have been discussed in details as well as the formation of a pitchfork bifurcation of the flow at the symmetric line of the enclosure.

Modelling contractor's and subcontractor's trust : a system dynamics approach

A general mistrust within the contactor and subcontractor companies has identified one of the significant barriers to derive benefits from true downstream supply chain integration. Using the general theory of trust in inter-organizational relations and conducting interviews, this research discusses factors that influence development of trust and cooperation in contractor– subcontractor relationships in construction projects. System dynamics is the simulation method is selected in this theory-building effort, based on qualitative data collected from two projects of a construction company in Thailand. Performance, permeability and system based trust are found to make significant contributions toward parties’ trust level. Three strategic policies such as best value contracting, management of subcontractors as internal team and semi project partnering approach are recommended to stimulate the trust factors as well as cooperative long term relationship.

Nobody says no : student self-censorship in a collaborative knowledge building activity

This paper explores student self-censorship within an online learning environment. Self-censorship in group activity can be seen as a two-edged sword. While it can be advantageous that a student censor personal frustration and angst when working with others, if the self-censorship impacts on the cognitive contribution a student makes then this may significantly impact upon the overall quality of the group’s collective knowledge artefact. This paper reports on a study where it was found that students had self censored both their feelings and ideas as they collaboratively worked together.

Planning for SMEs’ Proactive Waste Management in Office Building Retrofit Projects

Office building retrofit projects face many challenges for on-site waste management. While the projects themselves have the potential for a significant level of reuse and recycling from decon-struction and demolition, their unique characteristics often prohibit direct application of existing waste management systems, which are typically based on managing waste generated through new material application in new build projects. Moreover, current waste management plans include no stimuli to involve Small and Medium Enterprises (SMEs) for on-site waste management. As SMEs carry out the majority of on-site work as subcontractors, their active involvements will result in more proactive approaches to waste management and enhance project delivery. This paper discusses the interim results of a continuing research aimed at engaging SMEs in the planning processes of waste management through the collaboration between subcontractors and main contractors of retrofitting projects. It introduces a conceptual model for SMEs to proactively plan and manage on-site waste generation for both deconstruction and construction stages, before traditional waste management plans by the main contractor come into place. The model also suggests a collaboration process between SMEs as subcontractors and large companies as the main contractor to improve the involvement and performance of SMEs in waste management of office building retrofit projects.

Building a USDL repository as a service using MDE

The decision to represent the USDL abstract syntax as a metamodel, shown as a set of UML diagrams, has two main benefits: the ability to show a well- understood standard graphical representation of the concepts and their relation- ships to one another, and the ability to use object-oriented frameworks such as Eclipse Modeling Framework (EMF) to assist in the automated generation of tool support for USDL service descriptions.

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.

Using ‘think aloud’ as a strategy for learning clinical reasoning in high fidelity case-based simulation for undergraduate nursing students

AIMS This paper reports on the implementation of a research project that trials an educational strategy implemented over six months of an undergraduate third year nursing curriculum. This project aims to explore the effectiveness of ‘think aloud’ as a strategy for learning clinical reasoning for students in simulated clinical settings. BACKGROUND Nurses are required to apply and utilise critical thinking skills to enable clinical reasoning and problem solving in the clinical setting [1]. Nursing students are expected to develop and display clinical reasoning skills in practice, but may struggle articulating reasons behind decisions about patient care. For students learning to manage complex clinical situations, teaching approaches are required that make these instinctive cognitive processes explicit and clear [2-5]. In line with professional expectations, nursing students in third year at Queensland University of Technology (QUT) are expected to display clinical reasoning skills in practice. This can be a complex proposition for students in practice situations, particularly as the degree of uncertainty or decision complexity increases [6-7]. The ‘think aloud’ approach is an innovative learning/teaching method which can create an environment suitable for developing clinical reasoning skills in students [4, 8]. This project aims to use the ‘think aloud’ strategy within a simulation context to provide a safe learning environment in which third year students are assisted to uncover cognitive approaches that best assist them to make effective patient care decisions, and improve their confidence, clinical reasoning and active critical reflection on their practice. MEHODS In semester 2 2011 at QUT, third year nursing students will undertake high fidelity simulation, some for the first time commencing in September of 2011. There will be two cohorts for strategy implementation (group 1= use think aloud as a strategy within the simulation, group 2= not given a specific strategy outside of nursing assessment frameworks) in relation to problem solving patient needs. Students will be briefed about the scenario, given a nursing handover, placed into a simulation group and an observer group, and the facilitator/teacher will run the simulation from a control room, and not have contact (as a ‘teacher’) with students during the simulation. Then debriefing will occur as a whole group outside of the simulation room where the session can be reviewed on screen. The think aloud strategy will be described to students in their pre-simulation briefing and allow for clarification of this strategy at this time. All other aspects of the simulations remain the same, (resources, suggested nursing assessment frameworks, simulation session duration, size of simulation teams, preparatory materials). RESULTS Methodology of the project and the challenges of implementation will be the focus of this presentation. This will include ethical considerations in designing the project, recruitment of students and implementation of a voluntary research project within a busy educational curriculum which in third year targets 669 students over two campuses. CONCLUSIONS In an environment of increasingly constrained clinical placement opportunities, exploration of alternate strategies to improve critical thinking skills and develop clinical reasoning and problem solving for nursing students is imperative in preparing nurses to respond to changing patient needs. References 1. Lasater, K., High-fidelity simulation and the development of clinical judgement: students' experiences. Journal of Nursing Education, 2007. 46(6): p. 269-276. 2. Lapkin, S., et al., Effectiveness of patient simulation manikins in teaching clinical reasoning skills to undergraduate nursing students: a systematic review. Clinical Simulation in Nursing, 2010. 6(6): p. e207-22. 3. Kaddoura, M.P.C.M.S.N.R.N., New Graduate Nurses' Perceptions of the Effects of Clinical Simulation on Their Critical Thinking, Learning, and Confidence. The Journal of Continuing Education in Nursing, 2010. 41(11): p. 506. 4. Banning, M., The think aloud approach as an educational tool to develop and assess clinical reasoning in undergraduate students. Nurse Education Today, 2008. 28: p. 8-14. 5. Porter-O'Grady, T., Profound change:21st century nursing. Nursing Outlook, 2001. 49(4): p. 182-186. 6. Andersson, A.K., M. Omberg, and M. Svedlund, Triage in the emergency department-a qualitative study of the factors which nurses consider when making decisions. Nursing in Critical Care, 2006. 11(3): p. 136-145. 7. O'Neill, E.S., N.M. Dluhy, and C. Chin, Modelling novice clinical reasoning for a computerized decision support system. Journal of Advanced Nursing, 2005. 49(1): p. 68-77. 8. Lee, J.E. and N. Ryan-Wenger, The "Think Aloud" seminar for teaching clinical reasoning: a case study of a child with pharyngitis. J Pediatr Health Care, 1997. 11(3): p. 101-10.

Assessment of requirements for establishment of a framework to enhance implementation of quality practices in building projects

Quality, in construction projects should be regarded as the fulfillment of expectation of those contributors involved in such projects. Although a significant amount of quality practices have been introduced within the industry, attainment of reasonable levels of quality in construction projects continues to be an ongoing problem. To date, some research into the introduction and improvement of quality practices and stakeholder management has been undertaken, but so far no major studies have been completed that comprehensively examine how greater consideration of stakeholders’ perspectives of quality can be used to contribute to final project quality outcomes. This paper aims to examine the requirements for development of a framework leading to more effective involvement of stakeholders in quality planning and practices thus ultimately contributing to higher quality outcomes for construction projects. Through an extensive literature review it highlights various perceptions of quality, categorizes quality issues with particular focus on benefits and shortcomings and also examines the viewpoints of major stakeholders on project quality. It proposes a set of criteria to be used as a basis for a quality practice improvement framework, which will provide project managers and owners with the required information and strategic direction to achieve their own and their stakeholders’ targets for implementation of quality practices leading to the achievement of improved quality outcomes on future projects.

Building engaged, sustainable online communities : a case study of an adventure travel website

This paper will provide an overview of a join research initiative being developed by the Queensland University of Technology in conjunction with the Australian Smart Services Cooperative Research Centre in relation to the development and analysis of online communities. The intention of this project is to initially create an exciting and innovative web space around the concept of adventure travel and then to analyse the level of user engagement to uncover possible patterns and processes that could be used in the future development of other virtual online communities. Travel websites are not a new concept and there are many successful examples currently operating and generating profit. The intention of the QUT/Smart Services CRC project is to analyse the site metrics to determine the following: what specific conditions/parameters are required to foster a growing and engaged virtual community; when does the shift occur from external moderation to a more sustainable system of self-moderation within the online community; when do users begin to take ownership of a site and take an invested interested in the content and growth of an online community; and how to retain active contributors and high-impact power users on a long-term basis. With the travel website rapidly approaching release, this paper begins the process of reflection, outlining the process undertaken and the findings so far aggregated whilst also positioning the project within the greater context of current online user participation and user generated content research.