Differential Dynamic Microscopy: a High-Throughput Method for Characterizing the Motility of Microorganism

We present a fast, high-throughput method for characterizing the motility of microorganisms in 3D based on standard imaging microscopy. Instead of tracking individual cells, we analyse the spatio-temporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function (ISF) of the system. We demonstrate our method on two different types of microorganisms: bacteria, both smooth swimming (run only) and wild type (run and tumble) Escherichia coli, and the bi-flagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the ISF, we are able to extract (i) for E. coli: the swimming speed distribution, the fraction of motile cells and the diffusivity, and (ii) for C. reinhardtii: the swimming speed distribution, the amplitude and frequency of the oscillatory dynamics. In both cases, the motility parameters are averaged over \approx 10^4 cells and obtained in a few minutes.

A high-resolution atlas and statistical model of the human heart from multislice CT

Atlases and statistical models play important roles in the personalization and simulation of cardiac physiology. For the study of the heart, however, the construction of comprehensive atlases and spatio-temporal models is faced with a number of challenges, in particular the need to handle large and highly variable image datasets, the multi-region nature of the heart, and the presence of complex as well as small cardiovascular structures. In this paper, we present a detailed atlas and spatio-temporal statistical model of the human heart based on a large population of 3D+time multi-slice computed tomography sequences, and the framework for its construction. It uses spatial normalization based on nonrigid image registration to synthesize a population mean image and establish the spatial relationships between the mean and the subjects in the population. Temporal image registration is then applied to resolve each subject-specific cardiac motion and the resulting transformations are used to warp a surface mesh representation of the atlas to fit the images of the remaining cardiac phases in each subject. Subsequently, we demonstrate the construction of a spatio-temporal statistical model of shape such that the inter-subject and dynamic sources of variation are suitably separated. The framework is applied to a 3D+time data set of 138 subjects. The data is drawn from a variety of pathologies, which benefits its generalization to new subjects and physiological studies. The obtained level of detail and the extendability of the atlas present an advantage over most cardiac models published previously. © 1982-2012 IEEE.

Simultaneous colour search renders other object properties less salient

A common approach to visualise multidimensional data sets is to map every data dimension to a separate visual feature. It is generally assumed that such visual features can be judged independently from each other. However, we have recently shown that interactions between features do exist [Hannus et al. 2004; van den Berg et al. 2005]. In those studies, we first determined individual colour and size contrast or colour and orientation contrast necessary to achieve a fixed level of discrimination performance in single feature search tasks. These contrasts were then used in a conjunction search task in which the target was defined by a combination of a colour and a size or a colour and an orientation. We found that in conjunction search, despite the matched feature discriminability, subjects significantly more often chose an item with the correct colour than one with correct size or orientation. This finding may have consequences for visualisation: the saliency of information coded by objects' size or orientation may change when there is a need to simultaneously search for colour that codes another aspect of the information. In the present experiment, we studied whether a colour bias can also be found in a more complex and continuous task, Subjects had to search for a target in a node-link diagram consisting of SO nodes, while their eye movements were being tracked, Each node was assigned a random colour and size (from a range of 10 possible values with fixed perceptual distances). We found that when we base the distances on the mean threshold contrasts that were determined in our previous experiments, the fixated nodes tend to resemble the target colour more than the target size (Figure 1a). This indicates that despite the perceptual matching, colour is judged with greater precision than size during conjunction search. We also found that when we double the size contrast (i.e. the distances between the 10 possible node sizes), this effect disappears (Figure 1b). Our findings confirm that the previously found decrease in salience of other features during colour conjunction search is also present in more complex (more 'visualisation- realistic') visual search tasks. The asymmetry in visual search behaviour can be compensated for by manipulating step sizes (perceptual distances) within feature dimensions. Our results therefore also imply that feature hierarchies are not completely fixed and may be adapted to the requirements of a particular visualisation. Copyright © 2005 by the Association for Computing Machinery, Inc.

Visualising a stochastic model of California Water Resources Using Sankey Diagrams

This paper describes a novel approach to the analysis of supply and demand of water in California. A stochastic model is developed to assess the future supply of and demand for water resources in California. The results are presented in the form of a Sankey diagram where present and stochastically-varying future fluxes of water in California and its sub-regions are traced from source to services by mapping the various transformations of water from when it is first made available for use, through its treatment, recycling and reuse, to its eventual loss in a variety of sinks. This helps to highlight the connections of water with energy and land resources, including the amount of energy used to pump and treat water, the amount of water used for energy production, and the land resources that create a water demand to produce crops for food. By mapping water in this way, policy-makers can more easily understand the competing uses of water, through the identification of the services it delivers (e.g. sanitation, food production, landscaping), the potential opportunities for improving themanagement of the resource and the connections with other resources which are often overlooked in a traditional sector-based management strategy. This paper focuses on a Sankey diagram for water, but the ultimate aim is the visualisation of linked resource futures through inter-connected Sankey diagrams for energy, land and water, tracking changes from the basic resources for all three, their transformations, and the final services they provide.

Exploring industry dynamics and interactions

Within strategic technology management and innovation, often stakeholders extrapolate past industry dynamics, trends and patterns into the future. One frequently used concept is that of 'lifecycles' - an analogy of a sequence of stages encountered by living organisms. Lifecycle terms - such as technology, product, industry - are frequently used interchangeably and without clear definition. Within the interdisciplinary context of technology management and forecasting, this juxtaposition of dynamics can create confusion rather than simplification. This paper explores some of the dynamics typically associated with technology-based industries, illustrated with data from the early US automotive industry. A wide range of dimensions are seen to have potential to influence the path of industry development, and technology roadmapping architecture is used to present a simplified visualisation of some of these. Stakeholders need to consider the units of analysis, causality and synchronicity of relevant different dynamics, rather than isolated lifecycles. Some graphical curves represent simple aggregation of components; other dynamics have significant impact, but incur time lags, rather than being superimposed. To optimise alignment of the important dimensions within any technology development, and for future strategy decisions, understanding these interactions is critical. © 2012 Elsevier Inc.

Absolute and convective instability in gas turbine fuel injectors

Hydrodynamic instabilities in gas turbine fuel injectors help to mix the fuel and air but can sometimes lock into acoustic oscillations and contribute to thermoacoustic instability. This paper describes a linear stability analysis that predicts the frequencies and strengths of hydrodynamic instabilities and identifies the regions of the flow that cause them. It distinguishes between convective instabilities, which grow in time but are convected away by the flow, and absolute instabilities, which grow in time without being convected away. Convectively unstable flows amplify external perturbations, while absolutely unstable flows also oscillate at intrinsic frequencies. As an input, this analysis requires velocity and density fields, either from a steady but unstable solution to the Navier-Stokes equations, or from time-averaged numerical simulations. In the former case, the analysis is a predictive tool. In the latter case, it is a diagnostic tool. This technique is applied to three flows: a swirling wake at Re = 400, a single stream swirling fuel injector at Re - 106, and a lean premixed gas turbine injector with five swirling streams at Re - 106. Its application to the swirling wake demonstrates that this technique can correctly predict the frequency, growth rate and dominant wavemaker region of the flow. It also shows that the zone of absolute instability found from the spatio-temporal analysis is a good approximation to the wavemaker region, which is found by overlapping the direct and adjoint global modes. This approximation is used in the other two flows because it is difficult to calculate their adjoint global modes. Its application to the single stream fuel injector demonstrates that it can identify the regions of the flow that are responsible for generating the hydrodynamic oscillations seen in LES and experimental data. The frequencies predicted by this technique are within a few percent of the measured frequencies. The technique also explains why these oscillations become weaker when a central jet is injected along the centreline. This is because the absolutely unstable region that causes the oscillations becomes convectively unstable. Its application to the lean premixed gas turbine injector reveals that several regions of the flow are hydrodynamically unstable, each with a different frequency and a different strength. For example, it reveals that the central region of confined swirling flow is strongly absolutely unstable and sets up a precessing vortex core, which is likely to aid mixing throughout the injector. It also reveals that the region between the second and third streams is slightly absolutely unstable at a frequency that is likely to coincide with acoustic modes within the combustion chamber. This technique, coupled with knowledge of the acoustic modes in a combustion chamber, is likely to be a useful design tool for the passive control of mixing and combustion instability. Copyright © 2012 by ASME.

Parallel coordinates in computational engineering design

Modern Engineering Design involves the deployment of many computational tools. Re- search on challenging real-world design problems is focused on developing improvements for the engineering design process through the integration and application of advanced com- putational search/optimization and analysis tools. Successful application of these methods generates vast quantities of data on potential optimum designs. To gain maximum value from the optimization process, designers need to visualise and interpret this information leading to better understanding of the complex and multimodal relations between param- eters, objectives and decision-making of multiple and strongly conflicting criteria. Initial work by the authors has identified that the Parallel Coordinates interactive visualisation method has considerable potential in this regard. This methodology involves significant levels of user-interaction, making the engineering designer central to the process, rather than the passive recipient of a deluge of pre-formatted information. In the present work we have applied and demonstrated this methodology in two differ- ent aerodynamic turbomachinery design cases; a detailed 3D shape design for compressor blades, and a preliminary mean-line design for the whole compressor core. The first case comprises 26 design parameters for the parameterisation of the blade geometry, and we analysed the data produced from a three-objective optimization study, thus describing a design space with 29 dimensions. The latter case comprises 45 design parameters and two objective functions, hence developing a design space with 47 dimensions. In both cases the dimensionality can be managed quite easily in Parallel Coordinates space, and most importantly, we are able to identify interesting and crucial aspects of the relationships between the design parameters and optimum level of the objective functions under con- sideration. These findings guide the human designer to find answers to questions that could not even be addressed before. In this way, understanding the design leads to more intelligent decision-making and design space exploration. © 2012 AIAA.

Experimental studies of an accelerating, pitching, flat plate at low Reynolds number

The understanding of low Reynolds number aerodynamics is becoming increasingly prevalent with the recent surge in interest in advanced Micro-Air Vehicle (MAV) technology. Research in this area has been primarily stimulated by a military need for smaller, more versatile, autonomous, surveillance aircraft. The mechanism for providing the high lift coefficient required forMAV applications is thought to be largely influenced by the formation of a Leading Edge Vortex (LEV). This paper analyses experimentally, the influence of the LEV effect for a flat plate wing (AR = 4) under fast and slow pitch-up motions at Re =10,000 using a combination of dye flow visualisation and PIV measurements. It is found that a fast pitch over 1c shows a flow topology dominant LEV, while for a slow pitch case over 6c, the flow is largely separated. The development of the suction surface flow and the LEV was strongly correlated with the kinematics of the leading edge, suggesting that the effective local angle of incidence at the Leading Edge (LE) is of considerable significance in unsteady pitching motions. © 2013 by P.R.R.J Stevens.

An integrated representation of the services provided by global water resources

Water is essential not only to maintain the livelihoods of human beings but also to sustain ecosystems. Over the last few decades several global assessments have reviewed current and future uses of water, and have offered potential solutions to a possible water crisis. However, these have tended to focus on water supply rather than on the range of demands for all water services (including those of ecosystems). In this paper, a holistic global view of water resources and the services they provide is presented, using Sankey diagrams as a visualisation tool. These diagrams provide a valuable addition to the spatial maps of other global assessments, as they track the sources, uses, services and sinks of water resources. They facilitate comparison of different water services, and highlight trade-offs amongst them. For example, they reveal how increasing the supply of water resources to one service (crop production) can generate a reduction in provision of other water services (e.g., to ecosystem maintenance). The potential impacts of efficiency improvements in the use of water are also highlighted; for example, reduction in soil evaporation from crop production through better farming practices, or the results of improved treatment and re-use of return flows leading to reduction of delivery to final sinks. This paper also outlines the measures needed to ensure sustainable water resource use and supply for multiple competing services in the future, and emphasises that integrated management of land and water resources is essential to achieve this goal. © 2013 Elsevier Ltd.

Dicke superradiance in GaN quantum wells

We numerically modeled the spatio-temporal dynamics of Dicke superradiance in GaN/InGaN heterostructure quantum wells in a ridge waveguide cavity. Model predictions envisage ultrashort pulses of intensities superior to what can be obtained in mode-locked lasers. ©2010 IEEE.

Control of aircraft in the terminal manoeuvring area using parallelised sequential Monte Carlo

This paper reports on the use of a parallelised Model Predictive Control, Sequential Monte Carlo algorithm for solving the problem of conflict resolution and aircraft trajectory control in air traffic management specifically around the terminal manoeuvring area of an airport. The target problem is nonlinear, highly constrained, non-convex and uses a single decision-maker with multiple aircraft. The implementation includes a spatio-temporal wind model and rolling window simulations for realistic ongoing scenarios. The method is capable of handling arriving and departing aircraft simultaneously including some with very low fuel remaining. A novel flow field is proposed to smooth the approach trajectories for arriving aircraft and all trajectories are planned in three dimensions. Massive parallelisation of the algorithm allows solution speeds to approach those required for real-time use.

Detecting bipedal motion from correlated probabilistic trajectories

This paper is about detecting bipedal motion in video sequences by using point trajectories in a framework of classification. Given a number of point trajectories, we find a subset of points which are arising from feet in bipedal motion by analysing their spatio-temporal correlation in a pairwise fashion. To this end, we introduce probabilistic trajectories as our new features which associate each point over a sufficiently long time period in the presence of noise. They are extracted from directed acyclic graphs whose edges represent temporal point correspondences and are weighted with their matching probability in terms of appearance and location. The benefit of the new representation is that it practically tolerates inherent ambiguity for example due to occlusions. We then learn the correlation between the motion of two feet using the probabilistic trajectories in a decision forest classifier. The effectiveness of the algorithm is demonstrated in experiments on image sequences captured with a static camera, and extensions to deal with a moving camera are discussed. © 2013 Elsevier B.V. All rights reserved.

Depicting the future strategic plans of the Royal Australian Navy using a roadmapping framework as a visual composite canvas

Strategic planning can be an arduous and complex task; and, once a plan has been devised, it is often quite a challenge to effectively communicate the principal missions and key priorities to the array of different stakeholders. The communication challenge can be addressed through the application of a clearly and concisely designed visualisation of the strategic plan - to that end, this paper proposes the use of a roadmapping framework to structure a visual canvas. The canvas provides a template in the form of a single composite visual output that essentially allows a 'plan-on-a-page' to be generated. Such a visual representation provides a high-level depiction of the future context, end-state capabilities and the system-wide transitions needed to realise the strategic vision. To demonstrate this approach, an illustrative case study based on the Australian Government's Defence White Paper and the Royal Australian Navy's fleet plan will be presented. The visual plan plots the in-service upgrades for addressing the capability shortfalls and gaps in the Navy's fleet as it transitions from its current configuration to its future end-state vision. It also provides a visualisation of project timings in terms of the decision gates (approval, service release) and specific phases (proposal, contract, delivery) together with how these projects are rated against the key performance indicators relating to the technology acquisition process and associated management activities. © 2013 Taylor & Francis.

Modal stability theory

This article contains a review of modal stability theory. It covers local stability analysis of parallel flows including temporal stability, spatial stability, phase velocity, group velocity, spatio-temporal stability, the linearized Navier-Stokes equations, the Orr-Sommerfeld equation, the Rayleigh equation, the Briggs-Bers criterion, Poiseuille flow, free shear flows, and secondary modal instability. It also covers the parabolized stability equation (PSE), temporal and spatial biglobal theory, 2D eigenvalue problems, 3D eigenvalue problems, spectral collocation methods, and other numerical solution methods. Computer codes are provided for tutorials described in the article. These tutorials cover the main topics of the article and can be adapted to form the basis of research codes. Copyright © 2014 by ASME.

Control of normal shock wave / turbulent boundary-layer interaction using streamwise slots

The effect of streamwise slots on the interaction of a normal shock wave / turbulent boundary layer has been investigated experimentally at a Mach number of 1.3. The surface pressure distribution for the controlled interaction was found to be significantly smeared, featuring a distinct plateau. This was due to a change in shock structure from a typical unseparated normal shock wave boundary layer interaction to a large bifurcated Lambda type shock pattern. Boundary layer velocity measurements downstream of the slots revealed a strong spanwise variation of boundary layer properties whereas the modified shock structure was relatively twodimensional. Oil flow visualisation indicated that in the presence of slots the boundary layer surface flow was highly three dimensional and confirmed that the effect of slots was mainly due to suction and blowing similar to that for passive control with uniform surface ventilation. Three hole probe measurements confirmed that the boundary layer was three dimensional and that the slots introduced vortical motion into the flowfield. Results indicate that when applied to an aerofoil, the control device has the potential to reduce wave drag while incurring only small viscous penalties. The introduction of streamwise vorticity may also be beneficial to delay trailing edge separation and the device is thought to be capable of postponing buffet onset. © 2001 by A N Smith.