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.

A natural model for architecture : the nature of the evolutionary model 1995

John Frazer's architectural work is inspired by living and generative processes. Both evolutionary and revolutionary, it explores informatin ecologies and the dynamics of the spaces between objects. Fuelled by an interest in the cybernetic work of Gordon Pask and Norbert Wiener, and the possibilities of the computer and the "new science" it has facilitated, Frazer and his team of collaborators have conducted a series of experiments that utilize genetic algorithms, cellular automata, emergent behaviour, complexity and feedback loops to create a truly dynamic architecture. Frazer studied at the Architectural Association (AA) in London from 1963 to 1969, and later became unit master of Diploma Unit 11 there. He was subsequently Director of Computer-Aided Design at the University of Ulter - a post he held while writing An Evolutionary Architecture in 1995 - and a lecturer at the University of Cambridge. In 1983 he co-founded Autographics Software Ltd, which pioneered microprocessor graphics. Frazer was awarded a person chair at the University of Ulster in 1984. In Frazer's hands, architecture becomes machine-readable, formally open-ended and responsive. His work as computer consultant to Cedric Price's Generator Project of 1976 (see P84)led to the development of a series of tools and processes; these have resulted in projects such as the Calbuild Kit (1985) and the Universal Constructor (1990). These subsequent computer-orientated architectural machines are makers of architectural form beyond the full control of the architect-programmer. Frazer makes much reference to the multi-celled relationships found in nature, and their ongoing morphosis in response to continually changing contextual criteria. He defines the elements that describe his evolutionary architectural model thus: "A genetic code script, rules for the development of the code, mapping of the code to a virtual model, the nature of the environment for the development of the model and, most importantly, the criteria for selection. In setting out these parameters for designing evolutionary architectures, Frazer goes beyond the usual notions of architectural beauty and aesthetics. Nevertheless his work is not without an aesthetic: some pieces are a frenzy of mad wire, while others have a modularity that is reminiscent of biological form. Algorithms form the basis of Frazer's designs. These algorithms determine a variety of formal results dependent on the nature of the information they are given. His work, therefore, is always dynamic, always evolving and always different. Designing with algorithms is also critical to other architects featured in this book, such as Marcos Novak (see p150). Frazer has made an unparalleled contribution to defining architectural possibilities for the twenty-first century, and remains an inspiration to architects seeking to create responsive environments. Architects were initially slow to pick up on the opportunities that the computer provides. These opportunities are both representational and spatial: computers can help architects draw buildings and, more importantly, they can help architects create varied spaces, both virtual and actual. Frazer's work was groundbreaking in this respect, and well before its time.

Membrane associated transporter protein gene (SLC45A2) and the genetic basis of normal human pigmentation variation

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

The mechanics of disc degeneration from an engineering and computational modelling viewpoint

The anatomy and microstructure of the spine and in particular the intervertebral disc are intimately linked to how they operate in vivo and how they distribute loads to the adjacent musculature and bony anatomy. The degeneration of the intervertebral discs may be characterised by a loss of hydration, loss of disc height, a granular texture and the presence of annular lesions. As such, degeneration of the intervertebral discs compromises the mechanical integrity of their components and results in adaption and modification in the mechanical means by which loads are distributed between adjacent spinal motion segments.

Protocol engineering for protection against denial-of-service attacks

Denial-of-service attacks (DoS) and distributed denial-of-service attacks (DDoS) attempt to temporarily disrupt users or computer resources to cause service un- availability to legitimate users in the internetworking system. The most common type of DoS attack occurs when adversaries °ood a large amount of bogus data to interfere or disrupt the service on the server. The attack can be either a single-source attack, which originates at only one host, or a multi-source attack, in which multiple hosts coordinate to °ood a large number of packets to the server. Cryptographic mechanisms in authentication schemes are an example ap- proach to help the server to validate malicious tra±c. Since authentication in key establishment protocols requires the veri¯er to spend some resources before successfully detecting the bogus messages, adversaries might be able to exploit this °aw to mount an attack to overwhelm the server resources. The attacker is able to perform this kind of attack because many key establishment protocols incorporate strong authentication at the beginning phase before they can iden- tify the attacks. This is an example of DoS threats in most key establishment protocols because they have been implemented to support con¯dentiality and data integrity, but do not carefully consider other security objectives, such as availability. The main objective of this research is to design denial-of-service resistant mechanisms in key establishment protocols. In particular, we focus on the design of cryptographic protocols related to key establishment protocols that implement client puzzles to protect the server against resource exhaustion attacks. Another objective is to extend formal analysis techniques to include DoS- resistance. Basically, the formal analysis approach is used not only to analyse and verify the security of a cryptographic scheme carefully but also to help in the design stage of new protocols with a high level of security guarantee. In this research, we focus on an analysis technique of Meadows' cost-based framework, and we implement DoS-resistant model using Coloured Petri Nets. Meadows' cost-based framework is directly proposed to assess denial-of-service vulnerabil- ities in the cryptographic protocols using mathematical proof, while Coloured Petri Nets is used to model and verify the communication protocols using inter- active simulations. In addition, Coloured Petri Nets are able to help the protocol designer to clarify and reduce some inconsistency of the protocol speci¯cation. Therefore, the second objective of this research is to explore vulnerabilities in existing DoS-resistant protocols, as well as extend a formal analysis approach to our new framework for improving DoS-resistance and evaluating the performance of the new proposed mechanism. In summary, the speci¯c outcomes of this research include following results; 1. A taxonomy of denial-of-service resistant strategies and techniques used in key establishment protocols; 2. A critical analysis of existing DoS-resistant key exchange and key estab- lishment protocols; 3. An implementation of Meadows's cost-based framework using Coloured Petri Nets for modelling and evaluating DoS-resistant protocols; and 4. A development of new e±cient and practical DoS-resistant mechanisms to improve the resistance to denial-of-service attacks in key establishment protocols.

Towards model round-trip engineering : an abductive approach

Providing support for reversible transformations as a basis for round-trip engineering is a significant challenge in model transformation research. While there are a number of current approaches, they require the underlying transformation to exhibit an injective behaviour when reversing changes. This however, does not serve all practical transformations well. In this paper, we present a novel approach to round-trip engineering that does not place restrictions on the nature of the underlying transformation. Based on abductive logic programming, it allows us to compute a set of legitimate source changes that equate to a given change to the target model. Encouraging results are derived from an initial prototype that supports most concepts of the Tefkat transformation language

The effects of habitat fragmentation on the demography and population genetic structure of Uromys Caudimaculatus

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Generative and evolutionary models for design

The paper describes three design models that make use of generative and evolutionary systems. The models describe overall design methods and processes. Each model defines a set of tasks to be performed by the design team, and in each case one of the tasks requires a generative or evolutionary design system. The architectures of these systems are also broadly described.

Understanding preservice teachers’ predispositions for teaching engineering education in Australian schools.

Engineering education is underrepresented in Australia at the primary, middle school and high school levels. Understanding preservice teachers’ preparedness to be involved in engineering will be important for developing an engineering curriculum. This study administered a literature-based survey to 36 preservice teachers, which gathered data about their perceptions of engineering and their predispositions for teaching engineering. Findings indicated that the four constructs associated with the survey had acceptable Cronbach alpha scores (i.e., personal professional attributes .88, student motivation .91, pedagogical knowledge .91, and fused curricula .89). However, there was no “disagree” or “strongly disagree” response greater than 22% for any of the 25 survey items. Generally, these preservice teachers indicated predispositions for teaching engineering in the middle school. Extensive scaffolding and support with education programs will assist preservice teachers to develop confidence in this field. Governments and education departments need to recognise the importance of engineering education, and universities must take a stronger role in developing engineering education curricula.

A genetic algorithm for the multi-source and multi-sink minimum vertex cut problem and its applications

We present a new penalty-based genetic algorithm for the multi-source and multi-sink minimum vertex cut problem, and illustrate the algorithm’s usefulness with two real-world applications. It is proved in this paper that the genetic algorithm always produces a feasible solution by exploiting some domain-specific knowledge. The genetic algorithm has been implemented on the example applications and evaluated to show how well it scales as the problem size increases.