Calculation of volume from crank angle using reconfigurable hardware

Fast calculation of quantities such as in-cylinder volume and indicated power is important in internal combustion engine research. Multiple channels of data including crank angle and pressure were collected for this purpose using a fully instrumented diesel engine research facility. Currently, existing methods use software to post-process the data, first calculating volume from crank angle, then calculating the indicated work and indicated power from the area enclosed by the pressure-volume indicator diagram. Instead, this work investigates the feasibility of achieving real-time calculation of volume and power via hardware implementation on Field Programmable Gate Arrays (FPGAs). Alternative hardware implementations were investigated using lookup tables, Taylor series methods or the CORDIC (CoOrdinate Rotation DIgital Computer) algorithm to compute the trigonometric operations in the crank angle to volume calculation, and the CORDIC algorithm was found to use the least amount of resources. Simulation of the hardware based implementation showed that the error in the volume and indicated power is less than 0.1%.

The development of a virtual reality environment to model the experience of schizophrenia

Virtual Reality (VR) techniques are increasingly being used for education about and in the treatment of certain types of mental illness. Research indicates that VR is delivering on its promised potential to provide enhanced training and treatment outcomes through incorporation of this high-end technology. Schizophrenia is a mental disorder affecting 1-2% of the population, and it is estimated 12-16% of hospital beds in Australia are occupied by patients with psychosis. Tragically, there is also an increased risk of suicide associated with this diagnosis. A significant research project being undertaken across the University of Queensland faculties of Health Sciences and EPSA (Engineering, Physical Sciences and Architecture) has constructed a number of virtual environments that reproduce the phenomena experienced by patients who have psychosis. Symptoms of psychosis include delusions, hallucinations and thought disorder. The VR environment will allow behavioral, exposure therapies to be conducted with exactly controlled exposure stimuli and an expected reduction in risk of harm. This paper reports on the current work of the project, previous stages of software development and the final goal to introduce VR to medical consulting rooms.

A simulation-based training system for surgical wound debridement

A simulation-based training system for surgical wound debridement was developed and comprises a multimedia introduction, a surgical simulator (tutorial component), and an assessment component. The simulator includes two PCs, a haptic device, and mirrored display. Debridement is performed on a virtual leg model with a shallow laceration wound superimposed. Trainees are instructed to remove debris with forceps, scrub with a brush, and rinse with saline solution to maintain sterility. Research and development issues currently under investigation include tissue deformation models using mass-spring system and finite element methods; tissue cutting using a high-resolution volumetric mesh and dynamic topology; and accurate collision detection, cutting, and soft-body haptic rendering for two devices within the same haptic space.

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays (FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri-diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri-Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

Adaption and use of a compressible flow code for turbomachinery design

The present paper presents and discusses the use of dierent codes regarding the numerical simulation of a radial-in ow turbine. A radial-in ow turbine test case was selected from published literature [1] and commercial codes (Fluent and CFX) were used to perform the steady-state numerical simulations. An in-house compressible- ow simulation code, Eilmer3 [2] was also adapted in order to make it suitable to perform turbomachinery simulations and preliminary results are presented and discussed. The code itself as well as its adaptation, comprising the addition of terms for the rotating frame of reference, programmable boundary conditions for periodic boundaries and a mixing plane interface between the rotating and non-rotating blocks are also discussed. Several cases with dierent orders of complexity in terms of geometry were considered and the results were compared across the dierent codes. The agreement between these results and published data is also discussed.

A hybrid simulation framework to assess the impact of renewable generators on a distribution network

With an increasing number of small-scale renewable generator installations, distribution network planners are faced with new technical challenges (intermittent load flows, network imbalances…). Then again, these decentralized generators (DGs) present opportunities regarding savings on network infrastructure if installed at strategic locations. How can we consider both of these aspects when building decision tools for planning future distribution networks? This paper presents a simulation framework which combines two modeling techniques: agent-based modeling (ABM) and particle swarm optimization (PSO). ABM is used to represent the different system units of the network accurately and dynamically, simulating over short time-periods. PSO is then used to find the most economical configuration of DGs over longer periods of time. The infrastructure of the framework is introduced, presenting the two modeling techniques and their integration. A case study of Townsville, Australia, is then used to illustrate the platform implementation and the outputs of a simulation.

Towards Bayesian experimental design for nonlinear models that require a large number of sampling times

The use of Bayesian methodologies for solving optimal experimental design problems has increased. Many of these methods have been found to be computationally intensive for design problems that require a large number of design points. A simulation-based approach that can be used to solve optimal design problems in which one is interested in finding a large number of (near) optimal design points for a small number of design variables is presented. The approach involves the use of lower dimensional parameterisations that consist of a few design variables, which generate multiple design points. Using this approach, one simply has to search over a few design variables, rather than searching over a large number of optimal design points, thus providing substantial computational savings. The methodologies are demonstrated on four applications, including the selection of sampling times for pharmacokinetic and heat transfer studies, and involve nonlinear models. Several Bayesian design criteria are also compared and contrasted, as well as several different lower dimensional parameterisation schemes for generating the many design points.

Utility of the Mild Brain Injury Atypical Symptoms Scale to detect symptom exaggeration : an analogue simulation study

Brief self-report symptom checklists are often used to screen for postconcussional disorder (PCD) and posttraumatic stress disorder (PTSD) and are highly susceptible to symptom exaggeration. This study examined the utility of the five-item Mild Brain Injury Atypical Symptoms Scale (mBIAS) designed for use with the Neurobehavioral Symptom Inventory (NSI) and the PTSD Checklist–Civilian (PCL–C). Participants were 85 Australian undergraduate students who completed a battery of self-report measures under one of three experimental conditions: control (i.e., honest responding, n = 24), feign PCD (n = 29), and feign PTSD (n = 32). Measures were the mBIAS, NSI, PCL–C, Minnesota Multiphasic Personality Inventory–2, Restructured Form (MMPI–2–RF), and the Structured Inventory of Malingered Symptomatology (SIMS). Participants instructed to feign PTSD and PCD had significantly higher scores on the mBIAS, NSI, PCL–C, and MMPI–2–RF than did controls. Few differences were found between the feign PCD and feign PTSD groups, with the exception of scores on the NSI (feign PCD > feign PTSD) and PCL–C (feign PTSD > feign PCD). Optimal cutoff scores on the mBIAS of ≥8 and ≥6 were found to reflect “probable exaggeration” (sensitivity = .34; specificity = 1.0; positive predictive power, PPP = 1.0; negative predictive power, NPP = .74) and “possible exaggeration” (sensitivity = .72; specificity = .88; PPP = .76; NPP = .85), respectively. Findings provide preliminary support for the use of the mBIAS as a tool to detect symptom exaggeration when administering the NSI and PCL–C.

Analysis of heat transfer and fluid flow in a triangular enclosure in presence of an adiabatic fin

Natural convection thermal boundary layer adjacent to the heated inclined wall of a right angled triangle with an adiabatic fin attached to that surface is investigated by numerical simulations. The finite volume based unsteady numerical model is adopted for the simulation. It is revealed from the numerical results that the development of the boundary layer along the inclined surface is characterized by three distinct stages, i.e. a start-up stage, a transitional stage and a steady stage. These three stages can be clearly identified from the numerical simulations. Moreover, in presence of adiabatic fin, the thermal boundary layer adjacent to the inclined wall breaks initially. However, it is reattached with the downstream boundary layer next to the fin. More attention has been given to the boundary layer development near the fin area.

Computational experiments involving population size for FPGA-based implementation of a GA for the TSP

The feasibility of using an in-hardware implementation of a genetic algorithm (GA) to solve the computationally expensive travelling salesman problem (TSP) is explored, especially in regard to hardware resource requirements for problem and population sizes. We investigate via numerical experiments whether a small population size might prove sufficient to obtain reasonable quality solutions for the TSP, thereby permitting relatively resource efficient hardware implementation on field programmable gate arrays (FPGAs). Software experiments on two TSP benchmarks involving 48 and 532 cities were used to explore the extent to which population size can be reduced without compromising solution quality, and results show that a GA allowed to run for a large number of generations with a smaller population size can yield solutions of comparable quality to those obtained using a larger population. This finding is then used to investigate feasible problem sizes on a targeted Virtex-7 vx485T-2 FPGA platform via exploration of hardware resource requirements for memory and data flow operations.

Bayesian algorithms with applications

Advances in algorithms for approximate sampling from a multivariable target function have led to solutions to challenging statistical inference problems that would otherwise not be considered by the applied scientist. Such sampling algorithms are particularly relevant to Bayesian statistics, since the target function is the posterior distribution of the unobservables given the observables. In this thesis we develop, adapt and apply Bayesian algorithms, whilst addressing substantive applied problems in biology and medicine as well as other applications. For an increasing number of high-impact research problems, the primary models of interest are often sufficiently complex that the likelihood function is computationally intractable. Rather than discard these models in favour of inferior alternatives, a class of Bayesian "likelihoodfree" techniques (often termed approximate Bayesian computation (ABC)) has emerged in the last few years, which avoids direct likelihood computation through repeated sampling of data from the model and comparing observed and simulated summary statistics. In Part I of this thesis we utilise sequential Monte Carlo (SMC) methodology to develop new algorithms for ABC that are more efficient in terms of the number of model simulations required and are almost black-box since very little algorithmic tuning is required. In addition, we address the issue of deriving appropriate summary statistics to use within ABC via a goodness-of-fit statistic and indirect inference. Another important problem in statistics is the design of experiments. That is, how one should select the values of the controllable variables in order to achieve some design goal. The presences of parameter and/or model uncertainty are computational obstacles when designing experiments but can lead to inefficient designs if not accounted for correctly. The Bayesian framework accommodates such uncertainties in a coherent way. If the amount of uncertainty is substantial, it can be of interest to perform adaptive designs in order to accrue information to make better decisions about future design points. This is of particular interest if the data can be collected sequentially. In a sense, the current posterior distribution becomes the new prior distribution for the next design decision. Part II of this thesis creates new algorithms for Bayesian sequential design to accommodate parameter and model uncertainty using SMC. The algorithms are substantially faster than previous approaches allowing the simulation properties of various design utilities to be investigated in a more timely manner. Furthermore the approach offers convenient estimation of Bayesian utilities and other quantities that are particularly relevant in the presence of model uncertainty. Finally, Part III of this thesis tackles a substantive medical problem. A neurological disorder known as motor neuron disease (MND) progressively causes motor neurons to no longer have the ability to innervate the muscle fibres, causing the muscles to eventually waste away. When this occurs the motor unit effectively ‘dies’. There is no cure for MND, and fatality often results from a lack of muscle strength to breathe. The prognosis for many forms of MND (particularly amyotrophic lateral sclerosis (ALS)) is particularly poor, with patients usually only surviving a small number of years after the initial onset of disease. Measuring the progress of diseases of the motor units, such as ALS, is a challenge for clinical neurologists. Motor unit number estimation (MUNE) is an attempt to directly assess underlying motor unit loss rather than indirect techniques such as muscle strength assessment, which generally is unable to detect progressions due to the body’s natural attempts at compensation. Part III of this thesis builds upon a previous Bayesian technique, which develops a sophisticated statistical model that takes into account physiological information about motor unit activation and various sources of uncertainties. More specifically, we develop a more reliable MUNE method by applying marginalisation over latent variables in order to improve the performance of a previously developed reversible jump Markov chain Monte Carlo sampler. We make other subtle changes to the model and algorithm to improve the robustness of the approach.

Application-level simulation for network security

NeSSi (network security simulator) is a novel network simulation tool which incorporates a variety of features relevant to network security distinguishing it from general-purpose network simulators. Its capabilities such as profile-based automated attack generation, traffic analysis and support for detection algorithm plug-ins allow it to be used for security research and evaluation purposes. NeSSi has been successfully used for testing intrusion detection algorithms, conducting network security analysis and developing overlay security frameworks. NeSSi is built upon the agent framework JIAC, resulting in a distributed and extensible architecture. In this paper, we provide an overview of the NeSSi architecture as well as its distinguishing features and briefly demonstrate its application to current security research projects.

Optimal power system stabilizer tuning in multi-machine system via an improved differential evolution

Power system stabilizer (PSS) is one of the most important controllers in modern power systems for damping low frequency oscillations. Many efforts have been dedicated to design the tuning methodologies and allocation techniques to obtain optimal damping behaviors of the system. Traditionally, it is tuned mostly for local damping performance, however, in order to obtain a globally optimal performance, the tuning of PSS needs to be done considering more variables. Furthermore, with the enhancement of system interconnection and the increase of system complexity, new tools are required to achieve global tuning and coordination of PSS to achieve optimal solution in a global meaning. Differential evolution (DE) is a recognized as a simple and powerful global optimum technique, which can gain fast convergence speed as well as high computational efficiency. However, as many other evolutionary algorithms (EA), the premature of population restricts optimization capacity of DE. In this paper, a modified DE is proposed and applied for optimal PSS tuning of 39-Bus New-England system. New operators are introduced to reduce the probability of getting premature. To investigate the impact of system conditions on PSS tuning, multiple operating points will be studied. Simulation result is compared with standard DE and particle swarm optimization (PSO).

Numerical simulation of stochastic ordinary differential equations in biomathematical modelling

In this work we discuss the effects of white and coloured noise perturbations on the parameters of a mathematical model of bacteriophage infection introduced by Beretta and Kuang in [Math. Biosc. 149 (1998) 57]. We numerically simulate the strong solutions of the resulting systems of stochastic ordinary differential equations (SDEs), with respect to the global error, by means of numerical methods of both Euler-Taylor expansion and stochastic Runge-Kutta type.

Numerical methods for strong solutions of stochastic differential equations : an overview

This paper gives a review of recent progress in the design of numerical methods for computing the trajectories (sample paths) of solutions to stochastic differential equations. We give a brief survey of the area focusing on a number of application areas where approximations to strong solutions are important, with a particular focus on computational biology applications, and give the necessary analytical tools for understanding some of the important concepts associated with stochastic processes. We present the stochastic Taylor series expansion as the fundamental mechanism for constructing effective numerical methods, give general results that relate local and global order of convergence and mention the Magnus expansion as a mechanism for designing methods that preserve the underlying structure of the problem. We also present various classes of explicit and implicit methods for strong solutions, based on the underlying structure of the problem. Finally, we discuss implementation issues relating to maintaining the Brownian path, efficient simulation of stochastic integrals and variable-step-size implementations based on various types of control.