Generalized binomial Tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol.2, 117–E (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ- DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

Surveying the state of higher education in energy efficiency, in Australian engineering curriculum

This paper presents the method and results of a survey of 27 of the 33 Australian universities teaching engineering education in late 2007, undertaken by The Natural Edge Project (hosted by Griffith University and the Australian National University) and supported by the National Framework for Energy Efficiency. This survey aimed to ascertain the extent of energy efficiency (EE) education, and to identify preferred methods to assist in increasing the extent to which EE education is embedded in engineering curriculum. In this paper the context for the survey is supported by a summary of the key results from a variety of surveys undertaken over the last decade internationally. The paper concludes that EE education across universities and engineering disciplines in Australia is currently highly variable and ad hoc. Based on the results of the survey, this paper highlights a number of preferred options to support educators to embed sustainability within engineering programs, and future opportunities for monitoring EE, within the context of engineering education for sustainable development (EESD).