A generative design system based on evolutionary and mathematical functions

Previous work by Professor John Frazer on Evolutionary Architecture provides a basis for the development of a system evolving architectural envelopes in a generic and abstract manner. Recent research by the authors has focused on the implementation of a virtual environment for the automatic generation and exploration of complex forms and architectural envelopes based on solid modelling techniques and the integration of evolutionary algorithms, enhanced computational and mathematical models. Abstract data types are introduced for genotypes in a genetic algorithm order to develop complex models using generative and evolutionary computing techniques. Multi-objective optimisation techniques are employed for defining the fitness function in the evaluation process.

Development of a Rep-inducible, BBTV-based expression system in banana

Banana bunchy top is regarded as the most important viral disease of banana, causing significant yield losses worldwide. The disease is caused by Banana bunchy top virus (BBTV), which is a circular ssDNA virus belonging to the genus Babuvirus in the family Nanoviridae. There are currently few effective control strategies for this and other ssDNA viruses. “In Plant Activation” (InPAct) is a novel technology being developed at QUT for ssDNA virus-activated suicide gene expression. The technology exploits the rolling circle replication mechanism of ssDNA viruses and is based on a unique “split” gene design such that suicide gene expression is only activated in the presence of the viral Rep. This PhD project aimed to develop a BBTV-based InPAct system as a suicide gene strategy to control BBTV. The BBTV-based InPAct vector design requires a BBTV intergenic region (IR) to be embedded within an intron in the gene expression cassette. To ensure that the BBTV IR would not interfere with intron splicing, a TEST vector was initially generated that contained the entire BBTV IR embedded within an intron in a β-glucuronidase (GUS) expression vector. Transient GUS assays in banana embryogenic cell suspensions indicated that cryptic intron splice sites were present within the IR. Transcript analysis revealed two cryptic intron splice sites in the Domain III sequence of the CR-M within the IR. Removal of the CR-M from the TEST vector resulted in an enhancement of GUS expression suggesting that the cryptic intron splice sites had been removed. An InPAct GUS vector was subsequently generated that contained the modified BBTV IR, with the CR-M (minus Domain III) repositioned within the InPAct cassette. Using transient histochemical and fluorometric GUS assays in banana embryogenic cells, the InPAct GUS vector was shown to be activated in the presence of the BBTV Rep. However, the presence of both BBTV Rep and Clink was shown to have a deleterious effect on GUS expression suggesting that these proteins were cytotoxic at the levels expressed. Analysis of replication of the InPAct vectors by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector through the nicking/ligation activity of BBTV Rep. However, Rep-mediated episomal replicons, indicative of rolling circle replication of the released circularised cassettes, were not observed. The inability of the InPAct cassette to be replicated was further investigated. To examine whether the absence of Domain III of the CR-M was responsible, a suite of modified BBTV-based InPAct GUS vectors was constructed that contained the CR-M with the inclusion of Domain III, the CR-M with the inclusion of Domain III and additional upstream IR sequence, or no CR-M. Analysis of replication by Southern hybridisation revealed that neither the presence of Domain III, nor the entire CR-M, had an effect on replication levels. Since the InPAct cassette was significantly larger than the native BBTV genomic components (approximately 1 kb), the effect of InPAct cassette size on replication was also investigated. A suite of size variant BBTV-based vectors was constructed that increased the size of a replication competent cassette to 1.1 kbp through to 2.1 kbp.. Analysis of replication by Southern hybridisation revealed that an increase in vector size above approximately 1.5 - 1.7 kbp resulted in a decrease in replication. Following the demonstration of Rep-mediated release, circularisation and expression from the InPAct GUS vector, an InPAct vector was generated in which the uidA reporter gene was replaced with the ribonuclease-encoding suicide gene, barnase. Initially, a TEST vector was generated to assess the cytotoxicity of Barnase on banana cells. Although transient assays revealed a Barnase-induced cytotoxic effect in banana cells, the expression levels were sub-optimal. An InPAct BARNASE vector was generated and tested for BBTV Rep-activated Barnase expression using transient assays in banana embryogenic cells. High levels of background expression from the InPAct BARNASE vector made it difficult to accurately assess Rep-activated Barnase expression. Analysis of replication by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector but no Rep-mediated episomal replicons indicative of rolling circle replication of the released circularised cassettes were again observed. Despite the inability of the InPAct vectors to replicate to enable high level gene expression, the InPAct BARNASE vector was assessed in planta for BBTV Rep-mediated activation of Barnase expression. Eleven lines of transgenic InPAct BARNASE banana plants were generated by Agrobacterium-mediated transformation and were challenged with viruliferous Pentalonia nigronervosa. At least one clonal plant in each line developed bunchy top symptoms and infection was confirmed by PCR. No localised lesions were observed on any plants, nor was there any localised GUS expression in the one InPAct GUS line challenged with viruliferous aphids. The results presented in this thesis are the first study towards the development of a BBTV-based InPAct system as a Rep-activatable suicide gene expression system to control BBTV. Although further optimisation of the vectors is necessary, the preliminary results suggest that this approach has the potential to be an effective control strategy for BBTV. The use of iterons within the InPAct vectors that are recognised by Reps from different ssDNA plant viruses may provide a broad-spectrum resistance strategy against multiple ssDNA plant viruses. Further, this technology holds great promise as a platform technology for the molecular farming of high-value proteins in vitro or in vivo through expression of the ssDNA virus Rep protein.

Optimal mission path planning (MPP) for an air sampling unmanned aerial system

This paper presents advanced optimization techniques for Mission Path Planning (MPP) of a UAS fitted with a spore trap to detect and monitor spores and plant pathogens. The UAV MPP aims to optimise the mission path planning search and monitoring of spores and plant pathogens that may allow the agricultural sector to be more competitive and more reliable. The UAV will be fitted with an air sampling or spore trap to detect and monitor spores and plant pathogens in remote areas not accessible to current stationary monitor methods. The optimal paths are computed using a Multi-Objective Evolutionary Algorithms (MOEAs). Two types of multi-objective optimisers are compared; the MOEA Non-dominated Sorting Genetic Algorithms II (NSGA-II) and Hybrid Game are implemented to produce a set of optimal collision-free trajectories in three-dimensional environment. The trajectories on a three-dimension terrain, which are generated off-line, are collision-free and are represented by using Bézier spline curves from start position to target and then target to start position or different position with altitude constraints. The efficiency of the two optimization methods is compared in terms of computational cost and design quality. Numerical results show the benefits of coupling a Hybrid-Game strategy to a MOEA for MPP tasks. The reduction of numerical cost is an important point as the faster the algorithm converges the better the algorithms is for an off-line design and for future on-line decisions of the UAV.

UAS Mission Path Planning System, (MPPS) using hybrid-game coupled to multi-objective optimizer

This paper presents the application of advanced optimization techniques to unmanned aerial system mission path planning system (MPPS) using multi-objective evolutionary algorithms (MOEAs). Two types of multi-objective optimizers are compared; the MOEA nondominated sorting genetic algorithm II and a hybrid-game strategy are implemented to produce a set of optimal collision-free trajectories in a three-dimensional environment. The resulting trajectories on a three-dimensional terrain are collision-free and are represented by using Bézier spline curves from start position to target and then target to start position or different positions with altitude constraints. The efficiency of the two optimization methods is compared in terms of computational cost and design quality. Numerical results show the benefits of adding a hybrid-game strategy to a MOEA and for a MPPS.

Reduction of environmental effects of civil aircraft through multi-objective flight plan optimisation

With rising environmental alarm, the reduction of critical aircraft emissions including carbon dioxides (CO2) and nitrogen oxides (NOx) is one of most important aeronautical problems. There can be many possible attempts to solve such problem by designing new wing/aircraft shape, new efficient engine, etc. The paper rather provides a set of acceptable flight plans as a first step besides replacing current aircrafts. The paper investigates a green aircraft design optimisation in terms of aircraft range, mission fuel weight (CO2) and NOx using advanced Evolutionary Algorithms coupled to flight optimisation system software. Two multi-objective design optimisations are conducted to find the best set of flight plans for current aircrafts considering discretised altitude and Mach numbers without designing aircraft shape and engine types. The objectives of first optimisation are to maximise range of aircraft while minimising NOx with constant mission fuel weight. The second optimisation considers minimisation of mission fuel weight and NOx with fixed aircraft range. Numerical results show that the method is able to capture a set of useful trade-offs that reduce NOx and CO2 (minimum mission fuel weight).

Coupling hybrid-game strategies with particle swarm optimisation for multi-objective high lift systems design optimisation

This paper investigates the High Lift System (HLS) application of complex aerodynamic design problem using Particle Swarm Optimisation (PSO) coupled to Game strategies. Two types of optimization methods are used; the first method is a standard PSO based on Pareto dominance and the second method hybridises PSO with a well-known Nash Game strategies named Hybrid-PSO. These optimization techniques are coupled to a pre/post processor GiD providing unstructured meshes during the optimisation procedure and a transonic analysis software PUMI. The computational efficiency and quality design obtained by PSO and Hybrid-PSO are compared. The numerical results for the multi-objective HLS design optimisation clearly shows the benefits of hybridising a PSO with the Nash game and makes promising the above methodology for solving other more complex multi-physics optimisation problems in Aeronautics.

Robust multidisciplinary UAS design optimisation

There are many applications in aeronautical/aerospace engineering where some values of the design parameters states cannot be provided or determined accurately. These values can be related to the geometry(wingspan, length, angles) and or to operational flight conditions that vary due to the presence of uncertainty parameters (Mach, angle of attack, air density and temperature, etc.). These uncertainty design parameters cannot be ignored in engineering design and must be taken into the optimisation task to produce more realistic and reliable solutions. In this paper, a robust/uncertainty design method with statistical constraints is introduced to produce a set of reliable solutions which have high performance and low sensitivity. Robust design concept coupled with Multi Objective Evolutionary Algorithms (MOEAs) is defined by applying two statistical sampling formulas; mean and variance/standard deviation associated with the optimisation fitness/objective functions. The methodology is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing and asynchronous evaluation. It is implemented for two practical Unmanned Aerial System (UAS) design problems; the flrst case considers robust multi-objective (single disciplinary: aerodynamics) design optimisation and the second considers a robust multidisciplinary (aero structures) design optimisation. Numerical results show that the solutions obtained by the robust design method with statistical constraints have a more reliable performance and sensitivity in both aerodynamics and structures when compared to the baseline design.

Optimisation of process parameters for the removal of hydroxycinnamic acids in sugar solutions

Colour is one of the most important parameters in sugar quality and its presence in raw sugar plays a key role in the marketing strategy of sugar industries worldwide. This study investigated the degradation of a mixture of colour precursors using the Fenton oxidation process. These colour precursors are caffeic acid, p–coumaric acid and ferulic acid, which are present in cane juice. Results showed that with a Fe(II) to H2O2 molar ratio of 1:15 in an aqueous system at 25 °C, 77% of the total phenolic acid content was removed at pH 4.72. However, in a synthetic juice solution which contained 13 mass % sucrose (35 °C, pH 5.4), only 60% of the total phenolic acid content was removed.

A hierarchical evolutionary algorithmic design (HEAD) system for generating and evolving building design models

This thesis develops a detailed conceptual design method and a system software architecture defined with a parametric and generative evolutionary design system to support an integrated interdisciplinary building design approach. The research recognises the need to shift design efforts toward the earliest phases of the design process to support crucial design decisions that have a substantial cost implication on the overall project budget. The overall motivation of the research is to improve the quality of designs produced at the author's employer, the General Directorate of Major Works (GDMW) of the Saudi Arabian Armed Forces. GDMW produces many buildings that have standard requirements, across a wide range of environmental and social circumstances. A rapid means of customising designs for local circumstances would have significant benefits. The research considers the use of evolutionary genetic algorithms in the design process and the ability to generate and assess a wider range of potential design solutions than a human could manage. This wider ranging assessment, during the early stages of the design process, means that the generated solutions will be more appropriate for the defined design problem. The research work proposes a design method and system that promotes a collaborative relationship between human creativity and the computer capability. The tectonic design approach is adopted as a process oriented design that values the process of design as much as the product. The aim is to connect the evolutionary systems to performance assessment applications, which are used as prioritised fitness functions. This will produce design solutions that respond to their environmental and function requirements. This integrated, interdisciplinary approach to design will produce solutions through a design process that considers and balances the requirements of all aspects of the design. Since this thesis covers a wide area of research material, 'methodological pluralism' approach was used, incorporating both prescriptive and descriptive research methods. Multiple models of research were combined and the overall research was undertaken following three main stages, conceptualisation, developmental and evaluation. The first two stages lay the foundations for the specification of the proposed system where key aspects of the system that have not previously been proven in the literature, were implemented to test the feasibility of the system. As a result of combining the existing knowledge in the area with the newlyverified key aspects of the proposed system, this research can form the base for a future software development project. The evaluation stage, which includes building the prototype system to test and evaluate the system performance based on the criteria defined in the earlier stage, is not within the scope this thesis. The research results in a conceptual design method and a proposed system software architecture. The proposed system is called the 'Hierarchical Evolutionary Algorithmic Design (HEAD) System'. The HEAD system has shown to be feasible through the initial illustrative paper-based simulation. The HEAD system consists of the two main components - 'Design Schema' and the 'Synthesis Algorithms'. The HEAD system reflects the major research contribution in the way it is conceptualised, while secondary contributions are achieved within the system components. The design schema provides constraints on the generation of designs, thus enabling the designer to create a wide range of potential designs that can then be analysed for desirable characteristics. The design schema supports the digital representation of the human creativity of designers into a dynamic design framework that can be encoded and then executed through the use of evolutionary genetic algorithms. The design schema incorporates 2D and 3D geometry and graph theory for space layout planning and building formation using the Lowest Common Design Denominator (LCDD) of a parameterised 2D module and a 3D structural module. This provides a bridge between the standard adjacency requirements and the evolutionary system. The use of graphs as an input to the evolutionary algorithm supports the introduction of constraints in a way that is not supported by standard evolutionary techniques. The process of design synthesis is guided as a higher level description of the building that supports geometrical constraints. The Synthesis Algorithms component analyses designs at four levels, 'Room', 'Layout', 'Building' and 'Optimisation'. At each level multiple fitness functions are embedded into the genetic algorithm to target the specific requirements of the relevant decomposed part of the design problem. Decomposing the design problem to allow for the design requirements of each level to be dealt with separately and then reassembling them in a bottom up approach reduces the generation of non-viable solutions through constraining the options available at the next higher level. The iterative approach, in exploring the range of design solutions through modification of the design schema as the understanding of the design problem improves, assists in identifying conflicts in the design requirements. Additionally, the hierarchical set-up allows the embedding of multiple fitness functions into the genetic algorithm, each relevant to a specific level. This supports an integrated multi-level, multi-disciplinary approach. The HEAD system promotes a collaborative relationship between human creativity and the computer capability. The design schema component, as the input to the procedural algorithms, enables the encoding of certain aspects of the designer's subjective creativity. By focusing on finding solutions for the relevant sub-problems at the appropriate levels of detail, the hierarchical nature of the system assist in the design decision-making process.

Optimisation of bio-oil extraction process from Beauty Leaf (Calophyllum inophyllum) oil seed as a second generation biodiesel source

The Beauty Leaf tree (Calophyllum inophyllum) is a potential source of non-edible vegetable oil for producing future generation biodiesel because of its ability to grow in a wide range of climate conditions, easy cultivation, high fruit production rate, and the high oil content in the seed. This plant naturally occurs in the coastal areas of Queensland and the Northern Territory in Australia, and is also widespread in south-east Asia, India and Sri Lanka. Although Beauty Leaf is traditionally used as a source of timber and orientation plant, its potential as a source of second generation biodiesel is yet to be exploited. In this study, the extraction process from the Beauty Leaf oil seed has been optimised in terms of seed preparation, moisture content and oil extraction methods. The two methods that have been considered to extract oil from the seed kernel are mechanical oil extraction using an electric powered screw press, and chemical oil extraction using n-hexane as an oil solvent. The study found that seed preparation has a significant impact on oil yields, especially in the screw press extraction method. Kernels prepared to 15% moisture content provided the highest oil yields for both extraction methods. Mechanical extraction using the screw press can produce oil from correctly prepared product at a low cost, however overall this method is ineffective with relatively low oil yields. Chemical extraction was found to be a very effective method for oil extraction for its consistence performance and high oil yield, but cost of production was relatively higher due to the high cost of solvent. However, a solvent recycle system can be implemented to reduce the production cost of Beauty Leaf biodiesel. The findings of this study are expected to serve as the basis from which industrial scale biodiesel production from Beauty Leaf can be made.

User-driven quality of experience modelling for mobile video optimisation

The increasing demand for mobile video has attracted much attention from both industry and researchers. To satisfy users and to facilitate the usage of mobile video, providing optimal quality to the users is necessary. As a result, quality of experience (QoE) becomes an important focus in measuring the overall quality perceived by the end-users, from the aspects of both objective system performance and subjective experience. However, due to the complexity of user experience and diversity of resources (such as videos, networks and mobile devices), it is still challenging to develop QoE models for mobile video that can represent how user-perceived value varies with changing conditions. Previous QoE modelling research has two main limitations: aspects influencing QoE are insufficiently considered; and acceptability as the user value is seldom studied. Focusing on the QoE modelling issues, two aims are defined in this thesis: (i) investigating the key influencing factors of mobile video QoE; and (ii) establishing QoE prediction models based on the relationships between user acceptability and the influencing factors, in order to help provide optimal mobile video quality. To achieve the first goal, a comprehensive user study was conducted. It investigated the main impacts on user acceptance: video encoding parameters such as quantization parameter, spatial resolution, frame rate, and encoding bitrate; video content type; mobile device display resolution; and user profiles including gender, preference for video content, and prior viewing experience. Results from both quantitative and qualitative analysis revealed the significance of these factors, as well as how and why they influenced user acceptance of mobile video quality. Based on the results of the user study, statistical techniques were used to generate a set of QoE models that predict the subjective acceptability of mobile video quality by using a group of the measurable influencing factors, including encoding parameters and bitrate, content type, and mobile device display resolution. Applying the proposed QoE models into a mobile video delivery system, optimal decisions can be made for determining proper video coding parameters and for delivering most suitable quality to users. This would lead to consistent user experience on different mobile video content and efficient resource allocation. The findings in this research enhance the understanding of user experience in the field of mobile video, which will benefit mobile video design and research. This thesis presents a way of modelling QoE by emphasising user acceptability of mobile video quality, which provides a strong connection between technical parameters and user-desired quality. Managing QoE based on acceptability promises the potential for adapting to the resource limitations and achieving an optimal QoE in the provision of mobile video content.