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.

The undirected feedback vertex set problem has a Poly(k) Kernel

Resolving a noted open problem, we show that the Undirected Feedback Vertex Set problem, parameterized by the size of the solution set of vertices, is in the parameterized complexity class Poly(k), that is, polynomial-time pre-processing is sufficient to reduce an initial problem instance (G, k) to a decision-equivalent simplified instance (G', k') where k' � k, and the number of vertices of G' is bounded by a polynomial function of k. Our main result shows an O(k11) kernelization bound.

Responding to rapid change in higher education : enabling university departments responsible for work related programs through boundary spanning

Boundary spanning links organisations to one another in order to create mutually beneficial relationships; it is a concept developed and used in organisational theory but rarely used to understand organisational structures in higher education (Pruitt & Schwartz, 1999). Yet understanding boundary spanning activity has the capacity to help universities respond to demands for continuous quality improvement, and to increase capacity to react to environmental uncertainty. At a time of rapid change characterised by a fluctuating economic environment, globalisation, increased mobility, and ecological issues, boundary spanning could be viewed as a key element in assisting institutions in effectively understanding and responding to such change. The literature suggests that effective boundary spanning could help universities improve organisational performance, use of infrastructure and resources, intergroup relations, leadership styles, performance and levels of job satisfaction, technology transfer, knowledge creation, and feedback processes, amongst other things. Our research aims to put a face on boundary spanning (Miller, 2008) by contextualising it within organisational systems and structures in university departments responsible for work related programs i.e. Work Integrated Learning (WIL) and Co-operative Education (Co-op). In this paper these approaches are referred to collectively as work related programs. The authors formed a research team in Victoria, British Columbia in 2009 at a sponsored international research forum, Two Days in June. The purpose of the invitation-only forum was to investigate commonalities and differences across programs and to formulate an international research agenda for work related programs over the next five to ten years. Researchers from Queensland University of Technology, University of Cincinnati, Baden-Wuerttemberg Cooperative State University, University of Ottawa,and Dublin City University agreed that further research was needed into the impact stakeholders, organisational systems, structures, policies, and practices have on departments delivering work related programs. This paper illustrates how policy and practice across the five institutions can be better understood through the lens of boundary spanning. It is argued that boundary spanning is an area of theory and practice with great applicability to a better understanding of the activity of these departments. The paper concludes by proposing topics for future research to examine how boundary spanning can be used to better understand practice and change in work related programs.

Preventing injuries on a state-wide basis : researchers and parliamentary committees are partners in turning injury prevention and safety research into practice and policy

Context: Parliamentary committees established in Westminster parliaments, such as Queensland, provide a cross-party structure that enables them to recommend policy and legislative changes that may otherwise be difficult for one party to recommend. The overall parliamentary committee process tends to be more cooperative and less adversarial than the main chamber of parliament and, as a result, this process permits parliamentary committees to make recommendations more on the available research evidence and less on political or party considerations. Objectives: This paper considers the contributions that parliamentary committees in Queensland have made in the past in the areas of road safety, drug use as well as organ and tissue donation. The paper also discusses the importance of researchers actively engaging with parliamentary committees to ensure the best evidence based policy outcomes. Key messages: In the past, parliamentary committees have successfully facilitated important safety changes with many committee recommendations based on research results. In order to maximise the benefits of the parliamentary committee process it is essential that researchers inform committees about their work and become key stakeholders in the inquiry process. Researchers can keep committees informed by making submissions to their inquiries, responding to requests for information and appearing as witnesses at public hearings. Researchers should emphasise the key findings and implications of their research as well as considering the jurisdictional implications and political consequences. It is important that researchers understand the differences between lobbying and providing informed recommendations when interacting with committees. Discussion and conclusions: Parliamentary committees in Queensland have successfully assisted in the introduction of evidence based policy and legislation. In order to present best practice recommendations, committees rely on the evidence presented to them including the results of researchers. Actively engaging with parliamentary committees will help researchers to turn their results into practice with a corresponding decrease in injuries and fatalities. Developing an understanding of parliamentary committees, and the typical inquiry process used by these committees, will help researchers to present their research results in a manner that will encourage the adoption of their ideas by parliamentary committees, the presentation of these results as recommendations within the report and the subsequent enactment of the committee’s recommendations by the government.

State of the art and future challenges for information literacy research

This short paper focuses on strategic issues and important research questions.

Feedback information and consumer motivation : the moderation role of positive and negative reference values in self-regulation

Marketers spend considerable resources to motivate people to consume their products and services as a means of goal attainment (Bagozzi and Dholakia, 1999). Why people increase, decrease, or stop consuming some products is based largely on how well they perceive they are doing in pursuit of their goals (Carver and Scheier, 1992). Yet despite the importance for marketers in understanding how current performance influences a consumer’s future efforts, this topic has received little attention in marketing research. Goal researchers generally agree that feedback about how well or how poorly people are doing in achieving their goals affects their motivation (Bandura and Cervone, 1986; Locke and Latham, 1990). Yet there is less agreement about whether positive and negative performance feedback increases or decreases future effort (Locke and Latham, 1990). For instance, while a customer of a gym might cancel his membership after receiving negative feedback about his fitness, the same negative feedback might cause another customer to visit the gym more often to achieve better results. A similar logic can apply to many products and services from the use of cosmetics to investing in mutual funds. The present research offers managers key insights into how to engage customers and keep them motivated. Given that connecting customers with the company is a top research priority for managers (Marketing Science Institute, 2006), this article provides suggestions for performance metrics including four questions that managers can use to apply the findings.

Volatile properties of particles emitted by compressed natural gas and diesel buses during steady state and transient driving modes

Volatile properties of particle emissions from four compressed natural gas (CNG) and four diesel buses were investigated under steady state and transient driving modes on a chassis dynamometer. The exhaust was diluted utilising a full-flow continuous volume sampling system and passed through a thermodenuder at controlled temperature. Particle number concentration and size distribution were measured with a condensation particle counter and a scanning mobility particle sizer, respectively. We show that, while almost all the particles emitted by the CNG buses were in the nanoparticle size range, at least 85% and 98% were removed at 100ºC and 250ºC, respectively. Closer analysis of the volatility of particles emitted during transient cycles showed that volatilisation began at around 40°C with the majority occurring by 80°C. Particles produced during hard acceleration from rest exhibited lower volatility than that produced during other times of the cycle. Based on our results and the observation of ash deposits on the walls of the tailpipes, we suggest that these non-volatile particles were composed mostly of ash from lubricating oil. Heating the diesel bus emissions to 100ºC removed ultrafine particle numbers by 69% to 82% when a nucleation mode was present and just 18% when it was not.

Gatekeeping, gatewatching, real-time feedback : new challenges for Journalism

How bloggers and other independent online commentators criticise, correct, and otherwise challenge conventional journalism has been known for years, but has yet to be fully accepted by journalists; hostilities between the media establishment and the new generation of citizen journalists continue to flare up from time to time. The old gatekeeping monopoly of the mass media has been challenged by the new practice of gatewatching: by individual bloggers and by communities of commentators which may not report the news first-hand, but curate and evaluate the news and other information provided by official sources, and thus provide an important service. And this now takes place ever more rapidly, almost in real time: using the latest social networks, which disseminate, share, comment, question, and debunk news reports within minutes, and using additional platforms that enable fast and effective ad hoc collaboration between users. When hundreds of volunteers can prove within a few days that a German minister has been guilty of serious plagiarism, when the world first learns of earthquakes and tsunamis via Twitter – how does journalism manage to keep up?

State convergence and the effectiveness of time-memory-data tradeoffs

Various time-memory tradeoffs attacks for stream ciphers have been proposed over the years. However, the claimed success of these attacks assumes the initialisation process of the stream cipher is one-to-one. Some stream cipher proposals do not have a one-to-one initialisation process. In this paper, we examine the impact of this on the success of time-memory-data tradeoff attacks. Under the circumstances, some attacks are more successful than previously claimed while others are less. The conditions for both cases are established.