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.

Analysis of rural activity spaces and transport disadvantage using a multi-method approach

Current knowledge about the relationship between transport disadvantage and activity space size is limited to urban areas, and as a result, very little is known about this link in a rural context. In addition, although research has identified transport disadvantaged groups based on their size of activity space, these studies have, however, not empirically explained such differences and the result is often a poor identification of the problems facing disadvantaged groups. Research has shown that transport disadvantage varies over time. The static nature of analysis using the activity space concept in previous research studies has lacked the ability to identify transport disadvantage in time. Activity space is a dynamic concept; and therefore possesses a great potential in capturing temporal variations in behaviour and access opportunities. This research derives measures of the size and fullness of activity spaces for 157 individuals for weekdays, weekends, and for a week using weekly activity-travel diary data from three case study areas located in rural Northern Ireland. Four focus groups were also conducted in order to triangulate quantitative findings and to explain the differences between different socio-spatial groups. The findings of this research show that despite having a smaller sized activity space, individuals were not disadvantaged because they were able to access their required activities locally. Car-ownership was found to be an important life line in rural areas. Temporal disaggregation of the data reveals that this is true only on weekends due to a lack of public transport services. In addition, despite activity spaces being at a similar size, the fullness of activity spaces of low-income individuals was found to be significantly lower compared to their high-income counterparts. Focus group data shows that financial constraint, poor connections both between public transport services and between transport routes and opportunities forced individuals to participate in activities located along the main transport corridors.

Developing sustainable housing through building utilities and transport innovation

Sustainability concerns every citizen. Housing affordability and sustainable solutions are being highlighted in research and practice in many parts of the world. This paper discusses the development of a Commuter Energy and Building Utilities System (CEBUS) in sustainable housing projects as a means of bridging the gap between current median house pricing and target affordable house pricing for low income earners. Similar scales of sustainable housing development cannot be achieved through independent application of current best practice methods in ecologically sustainable development strategies or transit oriented development master plans. This paper presents the initial stage of research on first capital and ongoing utilities and transport cost savings available from these sustainable design methods. It also outlines further research and development of a CEBUS Dynamic Simulation Model and Conceptual Framework for the Australian property development and construction industry.

An analytical solution for diffusion and nonlinear uptake of oxygen in a spherical cell

We develop a new analytical solution for a reactive transport model that describes the steady-state distribution of oxygen subject to diffusive transport and nonlinear uptake in a sphere. This model was originally reported by Lin (Journal of Theoretical Biology, 1976 v60, pp449–457) to represent the distribution of oxygen inside a cell and has since been studied extensively by both the numerical analysis and formal analysis communities. Here we extend these previous studies by deriving an analytical solution to a generalized reaction-diffusion equation that encompasses Lin’s model as a particular case. We evaluate the solution for the parameter combinations presented by Lin and show that the new solutions are identical to a grid-independent numerical approximation.

A conditional retransmission enabled transport protocol for real-time networked control systems

Real-time networked control systems (NCSs) over data networks are being increasingly implemented on a massive scale in industrial applications. Along with this trend, wireless network technologies have been promoted for modern wireless NCSs (WNCSs). However, popular wireless network standards such as IEEE 802.11/15/16 are not designed for real-time communications. Key issues in real-time applications include limited transmission reliability and poor transmission delay performance. Considering the unique features of real-time control systems, this paper develops a conditional retransmission enabled transport protocol (CRETP) to improve the delay performance of the transmission control protocol (TCP) and also the reliability performance of the user datagram protocol (UDP) and its variants. Key features of the CRETP include a connectionless mechanism with acknowledgement (ACK), conditional retransmission and detection of ineffective data packets on the receiver side.

Evaluating the transport impacts of transit oriented developments (TODS)

Sustainable transport has become a necessity instead of an option, to address the problems of congestion and urban sprawl, whose effects include increased trip lengths and travel time. A more sustainable form of development, known as Transit Oriented Development (TOD) is presumed to offer sustainable travel choices with reduced need to travel to access daily destinations, by providing a mixture of land uses together with good quality of public transport service, infrastructure for walking and cycling. However, performance assessment of these developments with respect to travel characteristics of their inhabitants is required. This research proposes a five step methodology for evaluating the transport impacts of TODs. The steps for TOD evaluation include pre–TOD assessment, traffic and travel data collection, determination of traffic impacts, determination of travel impacts, and drawing outcomes. Typically, TODs are comprised of various land uses; hence have various types of users. Assessment of characteristics of all user groups is essential for obtaining an accurate picture of transport impacts. A case study TOD, Kelvin Grove Urban Village (KGUV), located 2km of north west of the Brisbane central business district in Australia was selected for implementing the proposed methodology and to evaluate the transport impacts of a TOD from an Australian perspective. The outcomes of this analysis indicated that KGUV generated 27 to 48 percent less traffic compared to standard published rates specified for homogeneous uses. Further, all user groups of KGUV used more sustainable modes of transport compared to regional and similarly located suburban users, with higher trip length for shopping and education trips. Although the results from this case study development support the transport claims of reduced traffic generation and sustainable travel choices by way of TODs, further investigation is required, considering different styles, scales and locations of TODs. The proposed methodology may be further refined by using results from new TODs and a framework for TOD evaluation may be developed.

An advanced meshless method for time fractional diffusion equation

Recently, because of the new developments in sustainable engineering and renewable energy, which are usually governed by a series of fractional partial differential equations (FPDEs), the numerical modelling and simulation for fractional calculus are attracting more and more attention from researchers. The current dominant numerical method for modeling FPDE is Finite Difference Method (FDM), which is based on a pre-defined grid leading to inherited issues or shortcomings including difficulty in simulation of problems with the complex problem domain and in using irregularly distributed nodes. Because of its distinguished advantages, the meshless method has good potential in simulation of FPDEs. This paper aims to develop an implicit meshless collocation technique for FPDE. The discrete system of FPDEs is obtained by using the meshless shape functions and the meshless collocation formulation. The stability and convergence of this meshless approach are investigated theoretically and numerically. The numerical examples with regular and irregular nodal distributions are used to validate and investigate accuracy and efficiency of the newly developed meshless formulation. It is concluded that the present meshless formulation is very effective for the modeling and simulation of fractional partial differential equations.

Quantification of particle emission characteristics and development of an emission model for use in transport microenvironments affected by traffic emissions

Vehicle emitted particles are of significant concern based on their potential to influence local air quality and human health. Transport microenvironments usually contain higher vehicle emission concentrations compared to other environments, and people spend a substantial amount of time in these microenvironments when commuting. Currently there is limited scientific knowledge on particle concentration, passenger exposure and the distribution of vehicle emissions in transport microenvironments, partially due to the fact that the instrumentation required to conduct such measurements is not available in many research centres. Information on passenger waiting time and location in such microenvironments has also not been investigated, which makes it difficult to evaluate a passenger’s spatial-temporal exposure to vehicle emissions. Furthermore, current emission models are incapable of rapidly predicting emission distribution, given the complexity of variations in emission rates that result from changes in driving conditions, as well as the time spent in driving condition within the transport microenvironment. In order to address these scientific gaps in knowledge, this work conducted, for the first time, a comprehensive statistical analysis of experimental data, along with multi-parameter assessment, exposure evaluation and comparison, and emission model development and application, in relation to traffic interrupted transport microenvironments. The work aimed to quantify and characterise particle emissions and human exposure in the transport microenvironments, with bus stations and a pedestrian crossing identified as suitable research locations representing a typical transport microenvironment. Firstly, two bus stations in Brisbane, Australia, with different designs, were selected to conduct measurements of particle number size distributions, particle number and PM2.5 concentrations during two different seasons. Simultaneous traffic and meteorological parameters were also monitored, aiming to quantify particle characteristics and investigate the impact of bus flow rate, station design and meteorological conditions on particle characteristics at stations. The results showed higher concentrations of PN20-30 at the station situated in an open area (open station), which is likely to be attributed to the lower average daily temperature compared to the station with a canyon structure (canyon station). During precipitation events, it was found that particle number concentration in the size range 25-250 nm decreased greatly, and that the average daily reduction in PM2.5 concentration on rainy days compared to fine days was 44.2 % and 22.6 % at the open and canyon station, respectively. The effect of ambient wind speeds on particle number concentrations was also examined, and no relationship was found between particle number concentration and wind speed for the entire measurement period. In addition, 33 pairs of average half-hourly PN7-3000 concentrations were calculated and identified at the two stations, during the same time of a day, and with the same ambient wind speeds and precipitation conditions. The results of a paired t-test showed that the average half-hourly PN7-3000 concentrations at the two stations were not significantly different at the 5% confidence level (t = 0.06, p = 0.96), which indicates that the different station designs were not a crucial factor for influencing PN7-3000 concentrations. A further assessment of passenger exposure to bus emissions on a platform was evaluated at another bus station in Brisbane, Australia. The sampling was conducted over seven weekdays to investigate spatial-temporal variations in size-fractionated particle number and PM2.5 concentrations, as well as human exposure on the platform. For the whole day, the average PN13-800 concentration was 1.3 x 104 and 1.0 x 104 particle/cm3 at the centre and end of the platform, respectively, of which PN50-100 accounted for the largest proportion to the total count. Furthermore, the contribution of exposure at the bus station to the overall daily exposure was assessed using two assumed scenarios of a school student and an office worker. It was found that, although the daily time fraction (the percentage of time spend at a location in a whole day) at the station was only 0.8 %, the daily exposure fractions (the percentage of exposures at a location accounting for the daily exposure) at the station were 2.7% and 2.8 % for exposure to PN13-800 and 2.7% and 3.5% for exposure to PM2.5 for the school student and the office worker, respectively. A new parameter, “exposure intensity” (the ratio of daily exposure fraction and the daily time fraction) was also defined and calculated at the station, with values of 3.3 and 3.4 for exposure to PN13-880, and 3.3 and 4.2 for exposure to PM2.5, for the school student and the office worker, respectively. In order to quantify the enhanced emissions at critical locations and define the emission distribution in further dispersion models for traffic interrupted transport microenvironments, a composite line source emission (CLSE) model was developed to specifically quantify exposure levels and describe the spatial variability of vehicle emissions in traffic interrupted microenvironments. This model took into account the complexity of vehicle movements in the queue, as well as different emission rates relevant to various driving conditions (cruise, decelerate, idle and accelerate), and it utilised multi-representative segments to capture the accurate emission distribution for real vehicle flow. This model does not only helped to quantify the enhanced emissions at critical locations, but it also helped to define the emission source distribution of the disrupted steady flow for further dispersion modelling. The model then was applied to estimate particle number emissions at a bidirectional bus station used by diesel and compressed natural gas fuelled buses. It was found that the acceleration distance was of critical importance when estimating particle number emission, since the highest emissions occurred in sections where most of the buses were accelerating and no significant increases were observed at locations where they idled. It was also shown that emissions at the front end of the platform were 43 times greater than at the rear of the platform. The CLSE model was also applied at a signalled pedestrian crossing, in order to assess increased particle number emissions from motor vehicles when forced to stop and accelerate from rest. The CLSE model was used to calculate the total emissions produced by a specific number and mix of light petrol cars and diesel passenger buses including 1 car travelling in 1 direction (/1 direction), 14 cars / 1 direction, 1 bus / 1 direction, 28 cars / 2 directions, 24 cars and 2 buses / 2 directions, and 20 cars and 4 buses / 2 directions. It was found that the total emissions produced during stopping on a red signal were significantly higher than when the traffic moved at a steady speed. Overall, total emissions due to the interruption of the traffic increased by a factor of 13, 11, 45, 11, 41, and 43 for the above 6 cases, respectively. In summary, this PhD thesis presents the results of a comprehensive study on particle number and mass concentration, together with particle size distribution, in a bus station transport microenvironment, influenced by bus flow rates, meteorological conditions and station design. Passenger spatial-temporal exposure to bus emitted particles was also assessed according to waiting time and location along the platform, as well as the contribution of exposure at the bus station to overall daily exposure. Due to the complexity of the interrupted traffic flow within the transport microenvironments, a unique CLSE model was also developed, which is capable of quantifying emission levels at critical locations within the transport microenvironment, for the purpose of evaluating passenger exposure and conducting simulations of vehicle emission dispersion. The application of the CLSE model at a pedestrian crossing also proved its applicability and simplicity for use in a real-world transport microenvironment.

Determining indicators of transportation disadvantage for establishing knowledge-based environments

Although, transportation disadvantage or imbalance between travel needs and supply of transportation system is a great harm to knowledge based environments, quantification and objectively measuring the state of transportation disadvantaged remain to be a great challenge for researcher due to its ambiguity. This poses questions of whether the current indicators are accurately linked with transportation disadvantages and the effectiveness of the current policies. Using current indicators of transportation disadvantages, the state of transportation disadvantage is often exaggerated due to limited afford has been put forward to provide clear assessment on the existed relationship between transportation disadvantage indicators with travel performance or capability. This paper proposes a structural equation model of transportation disadvantage using household variables gained from the 2006-2008 South-East Queensland Travel Survey (SEQTS). The underlying relationships between social economics and demographic characteristics of household with travel performance are modelled using a latent variable approach. The final model has been able to fit the data gathered from SEQTS and explained established links between key household factors with travel capability and determined key indicator of travel capability. The model recognises that travel capability is directly influenced by household factors; vehicle ratio, license possession, retirees and pensioners.

Design of sustainable transport : opportunities

The need to find an alternative to our current transport situation is widely accepted. In most cities of the world, traffic congestion is commonplace and air pollution is normal. Road fatalities are a regular and almost accepted event. And (in most developed nations) as an indirect consequence of our transport choices, obesity is increasing at an alarming rate. The car is undeniably a major contributor to this situation. Additionally the very structure of our cities has evolved to the point that it can be creditably claimed that the city belongs to the car and not to humans. There are however alternatives. There is a plethora of experimental vehicles in all shapes and configurations. And yet, the car is still king. The question is, how do we pick a winner? What are the aspects of the car that make it so appealing? Are these aspects able to be translated into a more sustainable version? What do we need to incorporate in our designs of new vehicles to make them more appealing to the consumers? In this paper I explore these questions and propose a list of design criteria for more sustainable transport options.

The role of transport infrastructure in facilitating the survival and growth of micro-enterprises in developing economies

Transport and logistics are essential to effective business. Very little is currently known about the impact of improved transport on micro-enterprises in developing economies and whether improvements in this area would assist the very poor. This paper looks at the obstacles of an inefficient transport facilitation system and the high costs incurred by 22 survival micro-entrepreneurs funded by the same local NGO and operating in diverse industry sectors in a peri-urban context in Mozambique. Six case studies are selected to illustrate the most common constraints they face. The perspectives of the micro-business owners are confronted with those of government officials and community leaders for two reasons: to identify any mismatch and to discuss possible solutions. Significant discrepancies are detected between government agenda and needs of the population, while community-based entrepreneurship (CBE) is discussed as a possible collective strategy in dealing with the problem.