Numerical methods for fractional partial differential equations with Riesz space fractional derivatives

In this paper, we consider the numerical solution of a fractional partial differential equation with Riesz space fractional derivatives (FPDE-RSFD) on a finite domain. Two types of FPDE-RSFD are considered: the Riesz fractional diffusion equation (RFDE) and the Riesz fractional advection–dispersion equation (RFADE). The RFDE is obtained from the standard diffusion equation by replacing the second-order space derivative with the Riesz fractional derivative of order αset membership, variant(1,2]. The RFADE is obtained from the standard advection–dispersion equation by replacing the first-order and second-order space derivatives with the Riesz fractional derivatives of order βset membership, variant(0,1) and of order αset membership, variant(1,2], respectively. Firstly, analytic solutions of both the RFDE and RFADE are derived. Secondly, three numerical methods are provided to deal with the Riesz space fractional derivatives, namely, the L1/L2-approximation method, the standard/shifted Grünwald method, and the matrix transform method (MTM). Thirdly, the RFDE and RFADE are transformed into a system of ordinary differential equations, which is then solved by the method of lines. Finally, numerical results are given, which demonstrate the effectiveness and convergence of the three numerical methods.

Multi-factor password-authenticated key exchange

We consider a new form of authenticated key exchange which we call multi-factor password-authenticated key exchange, where session establishment depends on successful authentication of multiple short secrets that are complementary in nature, such as a long-term password and a one-time response, allowing the client and server to be mutually assured of each other's identity without directly disclosing private information to the other party. Multi-factor authentication can provide an enhanced level of assurance in higher-security scenarios such as online banking, virtual private network access, and physical access because a multi-factor protocol is designed to remain secure even if all but one of the factors has been compromised. We introduce a security model for multi-factor password-authenticated key exchange protocols, propose an efficient and secure protocol called MFPAK, and provide a security argument to show that our protocol is secure in this model. Our security model is an extension of the Bellare-Pointcheval-Rogaway security model for password-authenticated key exchange and accommodates an arbitrary number of symmetric and asymmetric authentication factors.

Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity

Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages over other expression systems such as lower production costs, rapid scale up of production, similar post-translational modification as animals and the low likelihood of contamination with animal pathogens, microbial toxins or oncogenic sequences. However, improving recombinant protein yield remains one of the greatest challenges to molecular farming. In-Plant Activation (InPAct) is a newly developed technology that offers activatable and high-level expression of heterologous proteins in plants. InPAct vectors contain the geminivirus cis elements essential for rolling circle replication (RCR) and are arranged such that the gene of interest is only expressed in the presence of the cognate viral replication-associated protein (Rep). The expression of Rep in planta may be controlled by a tissue-specific, developmentally regulated or chemically inducible promoter such that heterologous protein accumulation can be spatially and temporally controlled. One of the challenges for the successful exploitation of InPAct technology is the control of Rep expression as even very low levels of this protein can reduce transformation efficiency, cause abnormal phenotypes and premature activation of the InPAct vector in regenerated plants. Tight regulation over transgene expression is also essential if expressing cytotoxic products. Unfortunately, many tissue-specific and inducible promoters are unsuitable for controlling expression of Rep due to low basal activity in the absence of inducer or in tissues other than the target tissue. This PhD aimed to control Rep activity through the production of single chain variable fragments (scFvs) specific to the motif III of Tobacco yellow dwarf virus (TbYDV) Rep. Due to the important role played by the conserved motif III in the RCR, it was postulated that such scFvs can be used to neutralise the activity of the low amount of Rep expressed from a “leaky” inducible promoter, thus preventing activation of the TbYDV-based InPAct vector until intentional induction. Such scFvs could also offer the potential to confer partial or complete resistance to TbYDV, and possibly heterologous viruses as motif III is conserved between geminiviruses. Studies were first undertaken to determine the levels of TbYDV Rep and TbYDV replication-associated protein A (RepA) required for optimal transgene expression from a TbYDV-based InPAct vector. Transient assays in a non-regenerable Nicotiana tabacum (NT-1) cell line were undertaken using a TbYDV-based InPAct vector containing the uidA reporter gene (encoding GUS) in combination with TbYDV Rep and RepA under the control of promoters with high (CaMV 35S) or low (Banana bunchy top virus DNA-R, BT1) activity. The replication enhancer protein of Tomato leaf curl begomovirus (ToLCV), REn, was also used in some co-bombardment experiments to examine whether RepA could be substituted by a replication enhancer from another geminivirus genus. GUS expression was observed both quantitatively and qualitatively by fluorometric and histochemical assays, respectively. GUS expression from the TbYDV-based InPAct vector was found to be greater when Rep was expected to be expressed at low levels (BT1 promoter) rather than high levels (35S promoter). GUS expression was further enhanced when Rep and RepA were co-bombarded with a low ratio of Rep to RepA. Substituting TbYDV RepA with ToLCV REn also enhanced GUS expression but more importantly highest GUS expression was observed when cells were co-transformed with expression vectors directing low levels of Rep and high levels of RepA irrespective of the level of REn. In this case, GUS expression was approximately 74-fold higher than that from a non-replicating vector. The use of different terminators, namely CaMV 35S and Nos terminators, in InPAct vectors was found to influence GUS expression. In the presence of Rep, GUS expression was greater using pInPActGUS-Nos rather than pInPActGUS-35S. The only instance of GUS expression being greater from vectors containing the 35S terminator was when comparing expression from cells transformed with Rep, RepA and REnexpressing vectors and either non-replicating vectors, p35SGS-Nos or p35SGS-35S. This difference was most likely caused by an interaction of viral replication proteins with each other and the terminators. These results indicated that (i) the level of replication associated proteins is critical to high transgene expression, (ii) the choice of terminator within the InPAct vector may affect expression levels and (iii) very low levels of Rep can activate InPAct vectors hence controlling its activity is critical. Prior to generating recombinant scFvs, a recombinant TbYDV Rep was produced in E. coli to act as a control to enable the screening for Rep-specific antibodies. A bacterial expression vector was constructed to express recombinant TbYDV Rep with an Nterminal His-tag (N-His-Rep). Despite investigating several purification techniques including Ni-NTA, anion exchange, hydrophobic interaction and size exclusion chromatography, N-His-Rep could only be partially purified using a Ni-NTA column under native conditions. Although it was not certain that this recombinant N-His-Rep had the same conformation as the native TbYDV Rep and was functional, results from an electromobility shift assay (EMSA) showed that N-His-Rep was able to interact with the TbYDV LIR and was, therefore, possibly functional. Two hybridoma cell lines from mice, immunised with a synthetic peptide containing the TbYDV Rep motif III amino acid sequence, were generated by GenScript (USA). Monoclonal antibodies secreted by the two hybridoma cell lines were first screened against denatured N-His-Rep in Western analysis. After demonstrating their ability to bind N-His-Rep, two scFvs (scFv1 and scFv2) were generated using a PCR-based approach. Whereas the variable heavy chain (VH) from both cell lines could be amplified, only the variable light chain (VL) from cell line 2 was amplified. As a result, scFv1 contained VH and VL from cell line 1, whereas scFv2 contained VH from cell line 2 and VL from cell line 1. Both scFvs were first expressed in E. coli in order to evaluate their affinity to the recombinant TbYDV N-His-Rep. The preliminary results demonstrated that both scFvs were able to bind to the denatured N-His-Rep. However, EMSAs revealed that only scFv2 was able to bind to native N-His-Rep and prevent it from interacting with the TbYDV LIR. Each scFv was cloned into plant expression vectors and co-bombarded into NT-1 cells with the TbYDV-based InPAct GUS expression vector and pBT1-Rep to examine whether the scFvs could prevent Rep from mediating RCR. Although it was expected that the addition of the scFvs would result in decreased GUS expression, GUS expression was found to slightly increase. This increase was even more pronounced when the scFvs were targeted to the cell nucleus by the inclusion of the Simian virus 40 large T antigen (SV40) nuclear localisation signal (NLS). It was postulated that the scFvs were binding to a proportion of Rep, leaving a small amount available to mediate RCR. The outcomes of this project provide evidence that very high levels of recombinant protein can theoretically be expressed using InPAct vectors with judicious selection and control of viral replication proteins. However, the question of whether the scFvs generated in this project have sufficient affinity for TbYDV Rep to prevent its activity in a stably transformed plant remains unknown. It may be that other scFvs with different combinations of VH and VL may have greater affinity for TbYDV Rep. Such scFvs, when expressed at high levels in planta, might also confer resistance to TbYDV and possibly heterologous geminiviruses.

Hydrogen bonding in the water stabilized structure of the modified unsymmetrically substituted viologen chromophore, N-ethyl-N'-(2-phosphonomethyl)-4,4'-bipyridylium dichloride

The crystal structure of the modified unsymmetrically N, N'-substituted viologen chromophore, N-ethyl- N'-(2-phosphonoethyl)-4, 4'-bipyridinium dichloride 0.75 hydrate. (1) has been determined. Crystals are triclinic, space group P-1 with Z = 2 in a cell with a = 7.2550(1), b = 13.2038(5), c = 18.5752(7) Å, α = 86.495(3), β = 83.527(2), γ = 88.921(2)o. The two independent but pseudo-symmetrically related cations in the asymmetric unit form one-dimensional hydrogen-bonded chains through short homomeric phosphonic acid O-H...O links [2.455(4), 2.464(4)A] while two of the chloride anions are similarly strongly linked to phosphonic acid groups [O-H…Cl, 2.889(4), 2.896(4)Å]. The other two chloride anions together with the two water molecules of solvation (one with partial occupancy) form unusual cyclic hydrogen-bonded bis(Cl...water) dianion units which lie between the layers of bipyridylium rings of the cation chain structures with which they are weakly associated.

The knowledge exchange intermediary as service provider : a discussion and an Australian case

The critical impact of innovation on national and the global economies has been discussed at length in the literature. Economic development requires the diffusion of innovations into markets. It has long been recognised that economic growth and development depends upon a constant stream of innovations. Governments have been keenly aware of the need to ensure this flow does not dry to a trickle and have introduced many and varied industry policies and interventions to assist in seeding, supporting and diffusing innovations. In Australia, as in many countries, Government support for the transfer of knowledge especially from publicly funded research has resulted in the creation of knowledge exchange intermediaries. These intermediaries are themselves service organisations, seeking innovative service offerings for their markets. The choice for most intermediaries is generally a dichotomous one, between market-pull and technology-push knowledge exchange programmes. In this article, we undertake a case analysis of one such innovative intermediary and its flagship programme. We then compare this case with other successful intermediaries in Europe. We put forward a research proposition that the design of intermediary programmes must match the service type they offer. That is, market-pull programmes require market-pull design, in close collaboration with industry, whereas technology programmes can be problem-solving innovations where demand is latent. The discussion reflects the need for an evolution in knowledge transfer policies and programmes beyond the first generation ushered in with the US Bayh-Dole Act (1980) and Stevenson-Wydler Act (1984). The data analysed is a case study comparison of market-pull and technology-push programmes, focusing on primary and secondary socio-economic benefits (using both Australian and international comparisons).

One-time-password-authenticated key exchange

To reduce the damage of phishing and spyware attacks, banks, governments, and other security-sensitive industries are deploying one-time password systems, where users have many passwords and use each password only once. If a single password is compromised, it can be only be used to impersonate the user once, limiting the damage caused. However, existing practical approaches to one-time passwords have been susceptible to sophisticated phishing attacks. ---------- We give a formal security treatment of this important practical problem. We consider the use of one-time passwords in the context of password-authenticated key exchange (PAKE), which allows for mutual authentication, session key agreement, and resistance to phishing attacks. We describe a security model for the use of one-time passwords, explicitly considering the compromise of past (and future) one-time passwords, and show a general technique for building a secure one-time-PAKE protocol from any secure PAKE protocol. Our techniques also allow for the secure use of pseudorandomly generated and time-dependent passwords.

Predicate-based key exchange

We provide the first description of and security model for authenticated key exchange protocols with predicate-based authentication. In addition to the standard goal of session key security, our security model also provides for credential privacy: a participating party learns nothing more about the other party's credentials than whether they satisfy the given predicate. Our model also encompasses attribute-based key exchange since it is a special case of predicate-based key exchange.---------- We demonstrate how to realize a secure predicate-based key exchange protocol by combining any secure predicate-based signature scheme with the basic Diffie-Hellman key exchange protocol, providing an efficient and simple solution.

Attribute-based authenticated key exchange

We introduce the concept of attribute-based authenticated key exchange (AB-AKE) within the framework of ciphertext policy attribute-based systems. A notion of AKE-security for AB-AKE is presented based on the security models for group key exchange protocols and also taking into account the security requirements generally considered in the ciphertext policy attribute-based setting. We also extend the paradigm of hybrid encryption to the ciphertext policy attribute-based encryption schemes. A new primitive called encapsulation policy attribute-based key encapsulation mechanism (EP-AB-KEM) is introduced and a notion of chosen ciphertext security is de�ned for EP-AB-KEMs. We propose an EP-AB-KEM from an existing attribute-based encryption scheme and show that it achieves chosen ciphertext security in the generic group and random oracle models. We present a generic one-round AB-AKE protocol that satis�es our AKE-security notion. The protocol is generically constructed from any EP-AB-KEM that satis�es chosen ciphertext security. Instantiating the generic AB-AKE protocol with our EP-AB-KEM will result in a concrete one-round AB-AKE protocol also secure in the generic group and random oracle models.

Generic one round group key exchange in the standard model

Minimizing complexity of group key exchange (GKE) protocols is an important milestone towards their practical deployment. An interesting approach to achieve this goal is to simplify the design of GKE protocols by using generic building blocks. In this paper we investigate the possibility of founding GKE protocols based on a primitive called multi key encapsulation mechanism (mKEM) and describe advantages and limitations of this approach. In particular, we show how to design a one-round GKE protocol which satisfies the classical requirement of authenticated key exchange (AKE) security, yet without forward secrecy. As a result, we obtain the first one-round GKE protocol secure in the standard model. We also conduct our analysis using recent formal models that take into account both outsider and insider attacks as well as the notion of key compromise impersonation resilience (KCIR). In contrast to previous models we show how to model both outsider and insider KCIR within the definition of mutual authentication. Our analysis additionally implies that the insider security compiler by Katz and Shin from ACM CCS 2005 can be used to achieve more than what is shown in the original work, namely both outsider and insider KCIR.

Urban rural water exchange : PRW in the Lockyer Valley

A significant amount (ca. 15-25 GL/a) of PRW (Purified Recycled Water) from urban areas is foreseen as augmentation of the depleted groundwater resources of the Lockyer Valley (approx. 80 km west of Brisbane). Theresearch project uses field investigations, lab trials and modelling techniques to address the key challenges: (i) how to determine benefits of individual users from the augmentation of a natural common pool resource; (ii) how to minimise impacts of applying different quality water on the Lockyer soils, to creeks and on aquifier materials; (iii) how to minimuse mobilisation of salts in the unsaturated and saturated zones as a result of increased deep drainage; (iv) determination of potential for direct aquifer recharge using injection wells?

Design and analysis of group key exchange protocols

A group key exchange (GKE) protocol allows a set of parties to agree upon a common secret session key over a public network. In this thesis, we focus on designing efficient GKE protocols using public key techniques and appropriately revising security models for GKE protocols. For the purpose of modelling and analysing the security of GKE protocols we apply the widely accepted computational complexity approach. The contributions of the thesis to the area of GKE protocols are manifold. We propose the first GKE protocol that requires only one round of communication and is proven secure in the standard model. Our protocol is generically constructed from a key encapsulation mechanism (KEM). We also suggest an efficient KEM from the literature, which satisfies the underlying security notion, to instantiate the generic protocol. We then concentrate on enhancing the security of one-round GKE protocols. A new model of security for forward secure GKE protocols is introduced and a generic one-round GKE protocol with forward security is then presented. The security of this protocol is also proven in the standard model. We also propose an efficient forward secure encryption scheme that can be used to instantiate the generic GKE protocol. Our next contributions are to the security models of GKE protocols. We observe that the analysis of GKE protocols has not been as extensive as that of two-party key exchange protocols. Particularly, the security attribute of key compromise impersonation (KCI) resilience has so far been ignored for GKE protocols. We model the security of GKE protocols addressing KCI attacks by both outsider and insider adversaries. We then show that a few existing protocols are not secure against KCI attacks. A new proof of security for an existing GKE protocol is given under the revised model assuming random oracles. Subsequently, we treat the security of GKE protocols in the universal composability (UC) framework. We present a new UC ideal functionality for GKE protocols capturing the security attribute of contributiveness. An existing protocol with minor revisions is then shown to realize our functionality in the random oracle model. Finally, we explore the possibility of constructing GKE protocols in the attribute-based setting. We introduce the concept of attribute-based group key exchange (AB-GKE). A security model for AB-GKE and a one-round AB-GKE protocol satisfying our security notion are presented. The protocol is generically constructed from a new cryptographic primitive called encapsulation policy attribute-based KEM (EP-AB-KEM), which we introduce in this thesis. We also present a new EP-AB-KEM with a proof of security assuming generic groups and random oracles. The EP-AB-KEM can be used to instantiate our generic AB-GKE protocol.