SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Graphene-like nano-sheets for surface acoustic wave gas sensor applications

The gas sensing properties of graphene-like nano-sheets deposited on 36° YX lithium tantalate (LiTaO3) surface acoustic wave (SAW) transducers are reported. The thin graphene-like nano-sheets were produced via the reduction of graphite oxide which was deposited on SAW interdigitated transducers (IDTs). Their sensing performance was assessed towards hydrogen (H2) and carbon monoxide (CO) in a synthetic air carrier gas at room temperature (25 °C) and 40 °C. Raman and X-ray photoelectron spectroscopy (XPS) revealed that the deposited graphite oxide (GO) was not completely reduced creating small, graphitic nanocrystals ∼2.7 nm in size. © 2008 Elsevier B.V.

Train service timetabling in railway open markets by particle swarm optimisation

Railway timetabling is an important process in train service provision as it matches the transportation demand with the infrastructure capacity while customer satisfaction is also considered. It is a multi-objective optimisation problem, in which a feasible solution, rather than the optimal one, is usually taken in practice because of the time constraint. The quality of services may suffer as a result. In a railway open market, timetabling usually involves rounds of negotiations among a number of self-interested and independent stakeholders and hence additional objectives and constraints are imposed on the timetabling problem. While the requirements of all stakeholders are taken into consideration simultaneously, the computation demand is inevitably immense. Intelligent solution-searching techniques provide a possible solution. This paper attempts to employ a particle swarm optimisation (PSO) approach to devise a railway timetable in an open market. The suitability and performance of PSO are studied on a multi-agent-based railway open-market negotiation simulation platform.

But does it work? Effectiveness of scientific visualisations in high school chemistry and physics instruction.

Scientific visualisations such as computer-based animations and simulations are increasingly a feature of high school science instruction. Visualisations are adopted enthusiastically by teachers and embraced by students, and there is good evidence that they are popular and well received. There is limited evidence, however, of how effective they are in enabling students to learn key scientific concepts. This paper reports the results of a quantitative study conducted in Australian physics and chemistry classrooms. In general there was no statistically significant difference between teaching with and without visualisations, however there were intriguing differences around student sex and academic ability.

One approach to finding evidence for the effectiveness of scientific visualisations in high school physics and chemistry education

Enormous amounts of money and energy are being devoted to the development, use and organisation of computer-based scientific visualisations (e.g. animations and simulations) in science education. It seems plausible that visualisations that enable students to gain visual access to scientific phenomena that are too large, too small or occur too quickly or too slowly to be seen by the naked eye, or to scientific concepts and models, would yield enhanced conceptual learning. When the literature is searched, however, it quickly becomes apparent that there is a dearth of quantitative evidence for the effectiveness of scientific visualisations in enhancing students’ learning of science concepts. This paper outlines an Australian project that is using innovative research methodology to gather evidence on this question in physics and chemistry classrooms.

Planning of distribution networks for medium voltage and low voltage

Determination of the placement and rating of transformers and feeders are the main objective of the basic distribution network planning. The bus voltage and the feeder current are two constraints which should be maintained within their standard range. The distribution network planning is hardened when the planning area is located far from the sources of power generation and the infrastructure. This is mainly as a consequence of the voltage drop, line loss and system reliability. Long distance to supply loads causes a significant amount of voltage drop across the distribution lines. Capacitors and Voltage Regulators (VRs) can be installed to decrease the voltage drop. This long distance also increases the probability of occurrence of a failure. This high probability leads the network reliability to be low. Cross-Connections (CC) and Distributed Generators (DGs) are devices which can be employed for improving system reliability. Another main factor which should be considered in planning of distribution networks (in both rural and urban areas) is load growth. For supporting this factor, transformers and feeders are conventionally upgraded which applies a large cost. Installation of DGs and capacitors in a distribution network can alleviate this issue while the other benefits are gained. In this research, a comprehensive planning is presented for the distribution networks. Since the distribution network is composed of low and medium voltage networks, both are included in this procedure. However, the main focus of this research is on the medium voltage network planning. The main objective is to minimize the investment cost, the line loss, and the reliability indices for a study timeframe and to support load growth. The investment cost is related to the distribution network elements such as the transformers, feeders, capacitors, VRs, CCs, and DGs. The voltage drop and the feeder current as the constraints are maintained within their standard range. In addition to minimizing the reliability and line loss costs, the planned network should support a continual growth of loads, which is an essential concern in planning distribution networks. In this thesis, a novel segmentation-based strategy is proposed for including this factor. Using this strategy, the computation time is significantly reduced compared with the exhaustive search method as the accuracy is still acceptable. In addition to being applicable for considering the load growth, this strategy is appropriate for inclusion of practical load characteristic (dynamic), as demonstrated in this thesis. The allocation and sizing problem has a discrete nature with several local minima. This highlights the importance of selecting a proper optimization method. Modified discrete particle swarm optimization as a heuristic method is introduced in this research to solve this complex planning problem. Discrete nonlinear programming and genetic algorithm as an analytical and a heuristic method respectively are also applied to this problem to evaluate the proposed optimization method.

Investigation of the effect of organics on the water uptake of marine aerosols

Water uptake refers to the ability of atmospheric particles to take up water vapour from the surrounding atmosphere. This is an important property that affects particle size and phase and therefore influences many characteristics of aerosols relevant to air quality and climate. However, the water uptake properties of many important atmospheric aerosol systems, including those related to the oceans, are still not fully understood. Therefore, the primary aim of this PhD research program was to investigate the water uptake properties of marine aerosols. In particular, the effect of organics on marine aerosol water uptake was investigated. Field campaigns were conducted at remote coastal sites on the east coast of Australia (Agnes Water; March-April 2007) and west coast of Ireland (Mace Head; June 2007), and laboratory measurements were performed on bubble-generated sea spray aerosols. A combined Volatility-Hygroscopicity-Tandem Differential Mobility Analyser (VH-TDMA) was employed in all experiments. This system probes the changes in the hygroscopic properties of nanoparticles as volatile organic components are progressively evaporated. It also allows particle composition to be inferred from combined volatility-hygroscopicity measurements. Frequent new particle formation and growth events were observed during the Agnes Water campaign. The VH-TDMA was used to investigate freshly nucleated particles (17-22.5 nm) and it was found that the condensation of sulphate and/or organic vapours was responsible for driving particle growth during the events. Aitken mode particles (~40 nm) were also measured with the VH-TDMA. In 3 out of 18 VH-TDMA scans evaporation of a volatile, organic component caused a very large increase in hygroscopicity that could only be explained by an increase in the absolute water uptake of the particle residuals, and not merely an increase in their relative hygroscopicity. This indicated the presence of organic components that were suppressing the hygroscopic growth of mixed particles on the timescale of humidification in the VH-TDMA (6.5 secs). It was suggested that the suppression of water uptake was caused by either a reduced rate of hygroscopic growth due to the presence of organic films, or organic-inorganic interactions in solution droplets that had a negative effect on hygroscopicity. Mixed organic-inorganic particles were rarely observed by the VH-TDMA during the summer campaign conducted at Mace Head. The majority of particles below 100 nm in clean, marine air appeared to be sulphates neutralised to varying degrees by ammonia. On one unique day, 26 June 2007, particularly large concentrations of sulphate aerosol were observed and identified as volcanic emissions from Iceland. The degree of neutralisation of the sulphate aerosol by ammonia was calculated by the VH-TDMA and found to compare well with the same quantity measured by an aerosol mass spectrometer. This was an important verification of the VH-TMDA‘s ability to identify ammoniated sulphate aerosols based on the simultaneous measurement of aerosol volatility and hygroscopicity. A series of measurements were also conducted on sea spray aerosols generated from Moreton Bay seawater samples in a laboratory-based bubble chamber. Accumulation mode sea spray particles (38-173 nm) were found to contain only a minor organic fraction (< 10%) that had little effect on particle hygroscopicity. These results are important because previous studies have observed that accumulation mode sea spray particles are predominantly organic (~80% organic mass fraction). The work presented here suggests that this is not always the case, and that there may be currently unknown factors that are controlling the transfer of organics to the aerosol phase during the bubble bursting process. Taken together, the results of this research program have significantly improved our understanding of organic-containing marine aerosols and the way they interact with water vapour in the atmosphere.

Creating new narratives through shared time and space : the performer/audience connection in multi-site dance events

Site-specific performance provides choices in audience experience via degrees of scale, proximity, levels of immersion and viewing perspectives. Beyond these choices, multi-site promenade events also form a connected audience/performer relationship in which moving together in time and space can produce a shared narrative and aesthetic sensibility of collective, yet individuated and shifting meanings. This paper interrogates this notion through audience/performer experiences in two separate multi-site, dance-led events. here/there/then/now occurred in four intimate sites within the Brisbane Powerhouse, providing a theatricalised platform for audiences to create linked narratives through open-ended and fragmented intertextuality. Accented Body, based on the concept of “the body as site and in site” and notions of connectivity, provided a more expansive platform for a similar, but heightened, shared engagement. Audiences traversed 6 outdoor and 2 indoor Brisbane sites moving to varying levels of a large complex. Eleven, predominantly interactive, screens provided links to other sites as well as to distributed presences in Seoul and London. The differentiation in scale and travel time between sites deepened the immersive experiences of audiences who reported transformative engagements with both site and architecture, accompanied by a sense of extended and yet quickened time.

Velocity-jump models with crowding effects

Velocity jump processes are discrete random walk models that have many applications including the study of biological and ecological collective motion. In particular, velocity jump models are often used to represent a type of persistent motion, known as a “run and tumble”, which is exhibited by some isolated bacteria cells. All previous velocity jump processes are non-interacting, which means that crowding effects and agent-to-agent interactions are neglected. By neglecting these agent-to-agent interactions, traditional velocity jump models are only applicable to very dilute systems. Our work is motivated by the fact that many applications in cell biology, such as wound healing, cancer invasion and development, often involve tissues that are densely packed with cells where cell-to-cell contact and crowding effects can be important. To describe these kinds of high cell density problems using a velocity jump process we introduce three different classes of crowding interactions into a one-dimensional model. Simulation data and averaging arguments lead to a suite of continuum descriptions of the interacting velocity jump processes. We show that the resulting systems of hyperbolic partial differential equations predict the mean behavior of the stochastic simulations very well.

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.

An investigation of commuter exposure to ultrafine particles in Sydney

Commuting in various transport modes represents an activity likely to incur significant exposure to traffic emissions. This study investigated the determinants and characteristics of exposure to ultrafine (< 100 nm) particles (UFPs) in four transport modes in Sydney, with a specific focus on exposure in automobiles, which remain the transport mode of choice for approximately 70% of Sydney commuters. UFP concentrations were measured using a portable condensation particle counter (CPC) inside five automobiles commuting on above ground and tunnel roadways, and in buses, ferries and trains. Determinant factors investigated included wind speed, cabin ventilation (automobiles only) and traffic volume. The results showed that concentrations varied significantly as a consequence of transport mode, vehicle type and ventilation characteristics. The effects of wind speed were minimal relative to those of traffic volume (especially heavy diesel vehicles) and cabin ventilation, with the latter proving to be a strong determinant of UFP ingress into automobiles. The effect of ~70 minutes of commuting on total daily exposure was estimated using a range of UFP concentrations reported for several microenvironments. A hypothetical Sydney resident commuting by automobile and spending 8.5 minutes of their day in the M5 East tunnel could incur anywhere from a lower limit of 3-11% to an upper limit of 37-69% of daily UFP exposure during a return commute, depending on the concentrations they encountered in other microenvironments, the type of vehicle they used and the ventilation setting selected. However, commute-time exposures at either extreme of the values presented are unlikely to occur in practice. The range of exposures estimated for other transport modes were comparable to those of automobiles, and in the case of buses, higher than automobiles.