Service management for multi-domain Active Networks

The Internet is an example of a multi-agent system. In our context, an agent is synonymous with network operators, Internet service providers (ISPs) and content providers. ISPs mutually interact for connectivity's sake, but the fact remains that two peering agents are inevitably self-interested. Egoistic behaviour manifests itself in two ways. Firstly, the ISPs are able to act in an environment where different ISPs would have different spheres of influence, in the sense that they will have control and management responsibilities over different parts of the environment. On the other hand, contention occurs when an ISP intends to sell resources to another, which gives rise to at least two of its customers sharing (hence contending for) a common transport medium. The multi-agent interaction was analysed by simulating a game theoretic approach and the alignment of dominant strategies adopted by agents with evolving traits were abstracted. In particular, the contention for network resources is arbitrated such that a self-policing environment may emerge from a congested bottleneck. Over the past 5 years, larger ISPs have simply peddled as fast as they could to meet the growing demand for bandwidth by throwing bandwidth at congestion problems. Today, the dire financial positions of Worldcom and Global Crossing illustrate, to a certain degree, the fallacies of over-provisioning network resources. The proposed framework in this thesis enables subscribers of an ISP to monitor and police each other's traffic in order to establish a well-behaved norm in utilising limited resources. This framework can be expanded to other inter-domain bottlenecks within the Internet. One of the main objectives of this thesis is also to investigate the impact on multi-domain service management in the future Internet, where active nodes could potentially be located amongst traditional passive routers. The advent of Active Networking technology necessitates node-level computational resource allocations, in addition to prevailing resource reservation approaches for communication bandwidth. Our motivation is to ensure that a service negotiation protocol takes account of these resources so that the response to a specific service deployment request from the end-user is consistent and predictable. To promote the acceleration of service deployment by means of Active Networking technology, a pricing model is also evaluated for computational resources (e.g., CPU time and memory). Previous work in these areas of research only concentrate on bandwidth (i.e., communication) - related resources. Our pricing approach takes account of both guaranteed and best-effort service by adapting the arbitrage theorem from financial theory. The central tenet for our approach is to synthesise insights from different disciplines to address problems in data networks. The greater parts of research experience have been obtained during direct and indirect participation in the 1ST-10561 project known as FAIN (Future Active IP Networks) and ACTS-AC338 project called MIAMI (Mobile Intelligent Agent for Managing the Information Infrastructure). The Inter-domain Manager (IDM) component was integrated as an integral part of the FAIN policy-based network management systems (PBNM). Its monitoring component (developed during the MIAMI project) learns about routing changes that occur within a domain so that the management system and the managed nodes have the same topological view of the network. This enabled our reservation mechanism to reserve resources along the existing route set up by whichever underlying routing protocol is in place

Transmission Electron Microscopy of Biological Samples

During the last 70 years, transmission electron microscopy (TEM) has developed our knowledge about ultrastructure of the cells and tissues. Another aim is the determination of molecular structure, interactions and processes including structure-function relationships at cellular level using a variety of TEM techniques with resolution in atomic to nanometre range. Even with the best transmission electron microscope, it is impossible to obtain real results without optimal sample preparation, respecting both the structure and the antigenicity preservation. Preparation techniques for high-resolution study of both macromolecular complex and organelles within cellular complex are based on fast cryoimmobilisation process, where the sample is in the most native, hydrated state. Next, thin samples are directly visualised under cryo-transmission electron microscopy (cryo-TEM), while thicker samples require a thinning step via cryo-electron microscopy of vitreous sections (CEMOVIS) or cryo-focused ion beam (cryo-FIB) before visualisation. Alternatively, vitrified samples are freeze substituted and embedded in chosen resin for room temperature ultramicrotomy. This preparation technique is suitable for morphological study, 3D analysis of cellular interior and immunoelectron microscopy. A different route for immunolocalisation study is cryosectioning according to the Tokuyasu technique that is a choice for rare or methacrylate-sensitive antigens. Most recently, new hybrid techniques have been developed for difficult-to-fix organisms and antigens or labile and anoxia-sensitive tissues. Another preparation technique is, the oldest but still important, conventional chemical fixation dedicated in a wide range of research interest, involving morphological and immunolocalisation study. In this chapter, we present different sample preparation approaches for transmission electron microscopy of biological samples, including its methodological basis and applications

Performance analysis of mobile networks under signalling storms

There are numerous security challenges in cellular mobile networks, many of which originate from the Internet world. One of these challenges is to answer the problem with increasing rate of signalling messages produced by smart devices. In particular, many services in the Internet are provided through mobile applications in an unobstructed manner, such that users get an always connected feeling. These services, which usually come from instant messaging, advertising and social networking areas, impose significant signalling loads on mobile networks by frequent exchange of control data in the background. Such services and applications could be built intentionally or unintentionally, and result in denial of service attacks known as signalling attacks or storms. Negative consequences, among others, include degradations of mobile network’s services, partial or complete net- work failures, increased battery consumption for infected mobile terminals. This thesis examines the influence of signalling storms on different mobile technologies, and proposes defensive mechanisms. More specifically, using stochastic modelling techniques, this thesis first presents a model of the vulnerability in a single 3G UMTS mobile terminal, and studies the influence of the system’s internal parameters on stability under a signalling storm. Further on, it presents a queueing network model of the radio access part of 3G UMTS and examines the effect of the radio resource control (RRC) inactivity timers. In presence of an attack, the proposed dynamic setting of the timers manage to lower the signalling load in the network and to increase the threshold above which a network failure could happen. Further on, the network model is upgraded into a more generic and detailed model, represent different generations of mobile technologies. It is than used to compare technologies with dedicated and shared organisation of resource allocation, referred to as traditional and contemporary networks, using performance metrics such as: signalling and communication delay, blocking probability, signalling load on the network’s nodes, bandwidth holding time, etc. Finally, based on the carried analysis, two mechanisms are proposed for detection of storms in real time, based on counting of same-type bandwidth allocations, and usage of allocated bandwidth. The mechanisms are evaluated using discrete event simulation in 3G UMTS, and experiments are done combining the detectors with a simple attack mitigation approach.Open Acces

C1, SAP and ZiCo: structural studies of three metal‑binding proteins from a crystallographic perspective

Atomic resolution models of proteins are crucial for understanding their biological mechanisms and provide insights into the relationship between protein sequence and structure. Many protein structures incorporate metal ions, exploiting their unique chemistry as reaction centres or for structural stability. This thesis describes the progress made towards solving the structures of three such metal-binding proteins by means of X-ray crystallography. Complement component C1 is a large protein complex that initiates the first line of immune defence and requires calcium for structural stability. Fragments of C1 have already been solved at high resolution, but there are no accurate models of the assembled complex. In this work, a new method for purifying intact C1 from human serum was developed and the purified complex was characterised by various methods. Finally, attempts were made to crystallise native human C1 with a view to obtaining high-resolution structures of the entire complex. Serum amyloid P is another serum protein, also thought to be involved in the immune response. It is often found associated with amyloid deposits, although SAP binds a variety of ligands in a calcium-dependent manner. While the structure of SAP has been determined, its physiological function is still not fully understood. SAP was purified using established methods and its ligand-binding properties were investigated under various conditions using dynamic light scattering, in an attempt to gather more information about the possible function of this molecule. Finally, ZiCo is a small peptide that was designed to switch between a multimeric coiled coil and a monomeric zinc finger fold on binding zinc. The system has been characterised extensively in solution, but high-resolution structures are required to validate the design. ZiCo was crystallised and diffraction data were collected. The structure of the peptide was partially solved, indicating that the multimeric form of the ZiCo peptide is indeed a trimeric coiled coil

Relating the structure of insect silk proteins to function

Silks are extracorporeal fibrous protein materials. Classically, silkworm (Bombyx mori) and orb-spiders (Arachnida: Araneidae) have served as model organisms in which to investigate silk protein structure-function relationships. However, silk production has evolved multiple times in insects. The silk proteins of many insects do not fold into the beta-sheet structures found in silkworm and spider silks but into coiled-coils, collagen helices or polyglycine helices. Therefore, the structure-function relationships elucidated for silkworm and spider silk proteins may be too narrow to apply to insect silk proteins generally. To increase the available data, I examined silk production by raspy crickets (Orthoptera: Gryllacrididae), silverfish (order Thysanura), praying mantises (order Mantodea), glow-worms (Diptera: Keroplatidae), and sawflies (Hymenoptera: Tenthredinidae). Silk protein primary structures were investigated using transcriptomics, mass spectrometry, and amino acid analysis; secondary and tertiary structures were investigated by infrared and Raman spectroscopy, nuclear magnetic resonance, circular dichroism spectroscopy, and bioinformatics. Novel features of silk production were related to idiosyncrasies of each insect group, while features found in multiple silk-producing groups were associated with general mechanisms of silk production. A comparative analysis of silk proteins revealed a correlation between predominant secondary structure type and more general architectural features such as length and repeat regularity: silk proteins that fold into coiled-coils and collagen helices had low molecular weights and high repeat regularity, suggesting they fold into short semi-rigid rods; beta-sheet-forming silk proteins were found to be more variable in molecular weight and have lower repeat regularity. Based on these data, I propose three major mechanisms of silk fabrication by insects: a) mesogenic ordering of short rod-like proteins, a process for which the coiled-coil and collagen structures are well-suited; b) molecular extension of long flexible protein chains to promote intermolecular bonding, which is suitable for the formation of beta-sheet-rich silks; and c) entanglement of protein chains, which is suited to silks with a high degree of disorder. Thus, many features of insect silk proteins are adaptations for material fabrication. In a few cases, particular structural motifs constituted adaptations conferring a mechanical property required for the silk's function in the solid state. However more often proteins were observed to have features promoting dense protein packing in a general way. I explain these data by consideration of how silk mechanical behaviour relates to the fitness advantage conferred to individual insects by silk production. Specifically, I suggest protein features ensuring structural homogeneity and molecular orientation result in silk materials with mechanical properties sufficient for most purposes. Further increases in properties such as strength lead to little or no fitness increase. Local maxima in the fitness landscape associated with distinct protein secondary structures or fabrication mechanisms trap silk proteins in one of several states. Overall, silk protein evolution can to a large extent be understood as convergence of a number of independently co-opted proteins of other functions toward one of several distinct functional archetypes

Crystal structures of two nucleic acid-binding proteins

S1 nuclease from Aspergillus oryzae is a glycoprotein of 32 kDa molecular weight. The protein has two enzymatic activities: it is an endo-exonuclease with high specificity for single stranded nucleic acids, and it has an additional 3' -nucleotidase activity. S1 nuclease is widely used in molecular biology as a single-strand specific nuclease due to its high stability and efficiency. It cleaves single-stranded regions of nucleic acids producing 5' -nucleotides without significant side-reactions. The crystal structure of S1 nuclease has been determined to 1.7 Å resolution by molecular replacement based on the known structure of PI nuclease from Penicillinum citrinum, which has 49 % sequence identity compared to S1. The overall fold and the active site of S1 nuclease is basically identical to that of PI nuclease, and also very similar to Phospholipase C from Bacillus cereus and alpha-toxin from Clostridium perfringens. The characteristic feature of this family of enzymes is a trinuclear zinc cluster in their active sites. A BLAST search in the sequence databases revealed several other protein sequences from bacteria, protozoa and plants possessing an approximately 30% sequence identity compared to S1 nuclease, but showing an almost complete conservation of structurally and functionally important residues. Soaking and co-crystallisation experiments with substrate analogues have been carried out in order to obtain an enzyme-substrate complex. These efforts have not resulted in the structure determination of any complexes under crystallisation conditions: no binding of substrate has been observed. Nevertheless, an enzyme mechanism has been proposed based on structural data of S1 nuclease and nucleases with similar active sites. In eukaryotes Sm and Sm-like proteins are the core components of the small nuclear ribonucleoprotein particles (snRNPs), which are involved in a variety of functions including rRNA processing, tRNA maturation and pre-mRNA processing. The Sm proteins are 70 to 120 amino acids long and share a common bi-partite signature sequence. The spliceosome, where the transesterification reaction of splicing occurs, is assembled by several snRNPs named after their constituting snRNA: U1, U2, U4, U5 and U6. An snRNA contains a short single stranded, uridine rich sequence motif, where the Sm proteins bind, but the three-dimensional arrangement of the Sm proteins and the mode of binding is unknown. In humans there are seven different canonical Sm proteins, which according to biochemical and electron microscopic studies seem to form a seven membered ring in vitro. Recently two crystal structures of human Sm protein dimers have been published. Interestingly Sm-related protein sequences have been found in the available genomic database of various Archaebacteria based on sequence homology. In contrast with eukaryotes only one or two Sm-related protein sequences have been identified in one organism. Their function is currently unknown, since analogous pre-mRNA splicing does not occur in Archaebacteria. Two Sm-related proteins of Archaeoglobus fulgidus have been cloned and expressed as fusion proteins. One of them called AF-Sm2 has been o crystallised utilising ammonium sulphate as precipitant and solved to 1.95 Å resolution by SIRAS using a single mercury derivative. AF-Sm2 crystallises in a hexagonal space group (P6) and contains one molecule per asymmetric unit. The 77 residue long protein has a very similar fold compared to the solved human Sm protein structures: a short N-terminal α-helix followed by a five stranded, strongly bent, U-shaped β-sheet resulting in a barrel-like overall fold. Six AF-Sm2 molecules form a ring in the crystal structure mediated by extensive hydrophobic and hydrogen-bonding interactions. Gel filtration experiments have indicated a pH dependence of oligomerisation in accordance with the crystallisation experiences. Currently the target of the Sm-related proteins of Archaeoglobus fulgidus and the stochiometry of oligomerisation in vivo is completely unknown

'E da dravudravua e na dela ni noda vutuni-i-yau' : customary land and economic development : case studies from Fiji : a thesis presented in fulfilment of the requirement of the degree of Doctor in Philosophy in Development Studies at Massey University, Palmerston North, Aotearoa

The purpose of this research is to determine how indigenous Fijian communities have been able to establish models of economic undertaking which allow successful business development while retaining control over their customary land and supporting community practices and values. External critics frequently emphasise that customary practices around land restrict economic development and undermine investments in the Pacific. There is also assertion that within the Pacific islands, culture and customary measures are mostly viewed as impediments of hopeful development. This research seeks to switch-over these claims by examining how customary land and measures facilitate successful business forms in Fiji. Along with the overarching qualitative methodology - a novel combination of the Vanua Research Framework, Tali Magimagi Research Framework, and the Bula Vakavanua Research Framework - a critical appreciative enquiry approach was used. This led to the development of the Uvi (yam - dioscorea alata) Framework which brings together the drauna (leaves) representing the capturing of knowledge, vavakada (stake) indicating the support mechanisms for indigenous entrepreneurship on customary land, uvi (yam tuber) signifying the indicators for sustainable development of indigenous business on customary land, and taking into consideration the external factors and community where the indigenous business is located. Case studies on three successful indigenous Fijian businesses based on customary land were conducted in two geographical locations in Fiji, and methods included talanoa, active participant observation, and semi-structured interviews. This study found that customary tenure and cultural values can support socially embedded economic development activities in the Pacific. It also reinstates the inherent value of customary land as an intergenerational resource aiding self-determined and inclusive development, including economic activities that provide holistic returns to communities as in socio-cultural contributions and community development initiatives. The businesses were able to be sustainable by devising mechanisms that balance daily business and community contributions. The study concludes that locally-driven development on customary land could be a model for alternative forms of economic development, thus, helping to reshape understanding of economies in Fiji and the wider Pacific

On distributed ledger technology for the internet of things: design and applications

Distributed ledger technology (DLT) can used to store information in such a way that no individual or organisation can compromise its veracity, contrary to a traditional centralised ledger. This nascent technology has received a great deal of attention from both researchers and practitioners in recent years due to the vast array of open questions related to its design and the assortment novel applications it unlocks. In this thesis, we are especially interested in the design of DLTs suitable for application in the domain of the internet of things (IoT), where factors such as efficiency, performance and scalability are of paramount importance. This work confronts the challenges of designing IoT-oriented distributed ledgers through analysis of ledger properties, development of design tools and the design of a number of core protocol components. We begin by introducing a class of DLTs whose data structures consist of directed acyclic graphs (DAGs) and which possess properties that make them particularly well suited to IoT applications. With a focus on the DAG structure, we then present analysis through mathematical modelling and simulations which provides new insights to the properties of this class of ledgers and allows us to propose novel security enhancements. Next, we shift our focus away from the DAG structure itself to another open problem for DAG-based distributed ledgers, that of access control. Specifically, we present a networking approach which removes the need for an expensive and inefficient mechanism known as Proof of Work, solving an open problem for IoT-oriented distributed ledgers. We then draw upon our analysis of the DAG structure to integrate and test our new access control with other core components of the DLT. Finally, we present a mechanism for orchestrating the interaction between users of a DLT and its operators, seeking to improves the usability of DLTs for IoT applications. In the appendix, we present two projects also carried out during this PhD which showcase applications of this technology in the IoT domain.Open Acces

Digital ecosystems

We view Digital Ecosystems to be the digital counterparts of biological ecosystems, which are considered to be robust, self-organising and scalable architectures that can automatically solve complex, dynamic problems. So, this work is concerned with the creation, investigation, and optimisation of Digital Ecosystems, exploiting the self-organising properties of biological ecosystems. First, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. We then investigated its self-organising aspects, starting with an extension to the definition of Physical Complexity to include the evolving agent populations of our Digital Ecosystem. Next, we established stability of evolving agent populations over time, by extending the Chli-DeWilde definition of agent stability to include evolutionary dynamics. Further, we evaluated the diversity of the software agents within evolving agent populations, relative to the environment provided by the user base. To conclude, we considered alternative augmentations to optimise and accelerate our Digital Ecosystem, by studying the accelerating effect of a clustering catalyst on the evolutionary dynamics of our Digital Ecosystem, through the direct acceleration of the evolutionary processes. We also studied the optimising effect of targeted migration on the ecological dynamics of our Digital Ecosystem, through the indirect and emergent optimisation of the agent migration patterns. Overall, we have advanced the understanding of creating Digital Ecosystems, the self-organisation that occurs within them, and the optimisation of their Ecosystem-Oriented Architecture