Deterministic generation of tailored-optical-coherent-state superpositions

Pulsed coherent excitation of a two-level atom strongly coupled to a resonant cavity mode will create a superposition of two coherent states of opposite amplitudes in the field. By choosing proper parameters of interaction time and pulse shape the field after the pulse will be almost disentangled from the atom and can be efficiently outcoupled through cavity decay. The fidelity of the generation approaches unity if the atom-field coupling strength is much larger than the atomic and cavity decay rates. This implies a strong difference between even and odd output photon number counts. Alternatively, the coherence of the two generated field components can be proven by phase-dependent annihilation of the generated nonclassical superposition state by a second pulse.

The phasevarion: A genetic system controlling coordinated, random switching of expression of multiple genes

Several host-adapted bacterial pathogens contain methyltransferases associated with type III restriction-modification (R-M) systems that are subject to reversible, high-frequency on/off switching of expression (phase variation). To investigate the role of phase-variable expression of R-M systems, we made a mutant strain lacking the methyltransferase (mod) associated with a type III R-M system of Haemophilus influenzae and analyzed its phenotype. By microarray analysis, we identified a number of genes that were either up- or down-regulated in the mod mutant strain. This system reports the coordinated random switching of a set of genes in a bacterial pathogen and may represent a widely used mechanism.

Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization

Chromogenic (CISH) and fluorescent ( FISH) in situ hybridization have emerged as reliable techniques to identify amplifications and chromosomal translocations. CISH provides a spatial distribution of gene copy number changes in tumour tissue and allows a direct correlation between copy number changes and the morphological features of neoplastic cells. However, the limited number of commercially available gene probes has hindered the use of this technique. We have devised a protocol to generate probes for CISH that can be applied to formalin-fixed, paraffin-embedded tissue sections (FFPETS). Bacterial artificial chromosomes ( BACs) containing fragments of human DNA which map to specific genomic regions of interest are amplified with phi 29 polymerase and random primer labelled with biotin. The genomic location of these can be readily confirmed by BAC end pair sequencing and FISH mapping on normal lymphocyte metaphase spreads. To demonstrate the reliability of the probes generated with this protocol, four strategies were employed: (i) probes mapping to cyclin D1 (CCND1) were generated and their performance was compared with that of a commercially available probe for the same gene in a series of 10 FFPETS of breast cancer samples of which five harboured CCND1 amplification; (ii) probes targeting cyclin-dependent kinase 4 were used to validate an amplification identified by microarray-based comparative genomic hybridization (aCGH) in a pleomorphic adenoma; (iii) probes targeting fibroblast growth factor receptor 1 and CCND1 were used to validate amplifications mapping to these regions, as defined by aCGH, in an invasive lobular breast carcinoma with FISH and CISH; and (iv) gene-specific probes for ETV6 and NTRK3 were used to demonstrate the presence of t(12; 15)(p12; q25) translocation in a case of breast secretory carcinoma with dual colour FISH. In summary, this protocol enables the generation of probes mapping to any gene of interest that can be applied to FFPETS, allowing correlation of morphological features with gene copy number.

Random vibration of the functionally graded laminates in thermal environments

This work deals with the random free vibration of functionally graded laminates with general boundary conditions and subjected to a temperature change, taking into account the randomness in a number of independent input variables such as Young's modulus, Poisson's ratio and thermal expansion coefficient of each constituent material. Based on third-order shear deformation theory, the mixed-type formulation and a semi-analytical approach are employed to derive the standard eigenvalue problem in terms of deflection, mid-plane rotations and stress function. A mean-centered first-order perturbation technique is adopted to obtain the second-order statistics of vibration frequencies. A detailed parametric study is conducted, and extensive numerical results are presented in both tabular and graphical forms for laminated plates that contain functionally graded material which is made of aluminum and zirconia, showing the effects of scattering in thermo-clastic material constants, temperature change, edge support condition, side-to-thickness ratio, and plate aspect ratio on the stochastic characteristics of natural frequencies. (c) 2005 Elsevier B.V. All rights reserved.

Sustainability metrics for coal power generation in Australia

The basis of this work was to investigate the relative environmental impacts of various power generators knowing that all plants are located in totally different environments and that different receptors will experience different impacts. Based on IChemE sustainability metrics paradigm, we calculated potential environmental indicators (P-EI) that represent the environmental burden of masses of potential pollutants discharged into different receiving media. However, a P-EI may not be of significance, as it may not be expressed at all in different conditions, so to try and include some receiver significance we developed a methodology to take into account some specific environmental indicators (S-EI) that refer to the environmental attributes of a specific site. In this context, we acquired site specific environmental data related to the airsheds and water catchment areas in different locations for a limited number of environmental indicators such as human health (carcinogenic) effects, atmospheric acidification, photochemical (ozone) smog and eutrophication. The S-EI results from this particular analysis show that atmospheric acidification has highest impact value while health risks due to fly ash emissions are considered not to be as significant. This is due to the fact that many coal power plants in Australia are located in low population density air sheds. The contribution of coal power plants to photochemical (ozone) smog and eutrophication were not significant. In this study, we have considered emission related data trends to reflect technology performance (e.g., P-EI indicators) while a real sustainability metric can be associated only with the specific environmental conditions of the relevant sites (e.g., S-EI indicators).

Entropy generation for microscale forced convection: effects of different thermal boundary conditions, velocity slip, temperature jump, viscous dissipation, and duct geometry

This work presents closed form solutions for fully developed temperature distribution and entropy generation due to forced convection in microelectromechanical systems (MEMS) in the Slip-flow regime, for which the Knudsen number lies within the range 0.001

UML approach to the generation of test sequences for Java-based concurrent systems

Starting with a UML specification that captures the underlying functionality of some given Java-based concurrent system, we describe a systematic way to construct, from this specification, test sequences for validating an implementation of the system. The approach is to first extend the specification to create UML state machines that directly address those aspects of the system we wish to test. To be specific, the extended UML state machines can capture state information about the number of waiting threads or the number of threads blocked on a given object. Using the SAL model checker we can generate from the extended UML state machines sequences that cover all the various possibilities of events and states. These sequences can then be directly transformed into test sequences suitable for input into a testing tool such as ConAn. As an illustration, the methodology is applied to generate sequences for testing a Java implementation of the producer-consumer system. © 2005 IEEE

The emergence of order in random walk resource discovery protocols

While others have attempted to determine, by way of mathematical formulae, optimal resource duplication strategies for random walk protocols, this paper is concerned with studying the emergent effects of dynamic resource propagation and replication. In particular, we show, via modelling and experimentation, that under any given decay (purge) rate the number of nodes that have knowledge of particular resource converges to a fixed point or a limit cycle. We also show that even for high rates of decay - that is, when few nodes have knowledge of a particular resource - the number of hops required to find that resource is small.

Retrotransposon expression profiling: Unveiling the hidden SINE transcriptome through Next-Generation Sequencing data analysis

Of the ~1.7 million SINE elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which SINE transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq datasets and unique SINE DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual SINE elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci and ~1100 MIR loci corresponding to detectable transcripts, with ~120 and ~60 respectively Alu and MIR loci expressed in at least three cell lines. In vitro transcription of selected SINEs did not reflect their in vivo expression properties, and required the native 5’-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for SINEs nested within Pol II-transcribed genes raising the possibility of an underlying mechanism for Pol II gene regulation by SINE transcriptional units. Moreover the application of our bioinformatic pipeline to both RNA-seq data of cells subjected to an in vitro pro-oncogenic stimulus and of in vivo matched tumor and non-tumor samples allowed us to detect increased Alu RNA expression as well as the source loci of such deregulation. The ability to investigate SINE transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant SINE RNAs and the assessment of SINE expression alteration under pathological conditions.

Advanced receivers for next generation wireless communication systems

Despite extensive progress on the theoretical aspects of spectral efficient communication systems, hardware impairments, such as phase noise, are the key bottlenecks in next generation wireless communication systems. The presence of non-ideal oscillators at the transceiver introduces time varying phase noise and degrades the performance of the communication system. Significant research literature focuses on joint synchronization and decoding based on joint posterior distribution, which incorporate both the channel and code graph. These joint synchronization and decoding approaches operate on well designed sum-product algorithms, which involves calculating probabilistic messages iteratively passed between the channel statistical information and decoding information. Channel statistical information, generally entails a high computational complexity because its probabilistic model may involve continuous random variables. The detailed knowledge about the channel statistics for these algorithms make them an inadequate choice for real world applications due to power and computational limitations. In this thesis, novel phase estimation strategies are proposed, in which soft decision-directed iterative receivers for a separate A Posteriori Probability (APP)-based synchronization and decoding are proposed. These algorithms do not require any a priori statistical characterization of the phase noise process. The proposed approach relies on a Maximum A Posteriori (MAP)-based algorithm to perform phase noise estimation and does not depend on the considered modulation/coding scheme as it only exploits the APPs of the transmitted symbols. Different variants of APP-based phase estimation are considered. The proposed algorithm has significantly lower computational complexity with respect to joint synchronization/decoding approaches at the cost of slight performance degradation. With the aim to improve the robustness of the iterative receiver, we derive a new system model for an oversampled (more than one sample per symbol interval) phase noise channel. We extend the separate APP-based synchronization and decoding algorithm to a multi-sample receiver, which exploits the received information from the channel by exchanging the information in an iterative fashion to achieve robust convergence. Two algorithms based on sliding block-wise processing with soft ISI cancellation and detection are proposed, based on the use of reliable information from the channel decoder. Dually polarized systems provide a cost-and spatial-effective solution to increase spectral efficiency and are competitive candidates for next generation wireless communication systems. A novel soft decision-directed iterative receiver, for separate APP-based synchronization and decoding, is proposed. This algorithm relies on an Minimum Mean Square Error (MMSE)-based cancellation of the cross polarization interference (XPI) followed by phase estimation on the polarization of interest. This iterative receiver structure is motivated from Master/Slave Phase Estimation (M/S-PE), where M-PE corresponds to the polarization of interest. The operational principle of a M/S-PE block is to improve the phase tracking performance of both polarization branches: more precisely, the M-PE block tracks the co-polar phase and the S-PE block reduces the residual phase error on the cross-polar branch. Two variants of MMSE-based phase estimation are considered; BW and PLP.

Coloring random graphs and maximizing local diversity

We study a variation of the graph coloring problem on random graphs of finite average connectivity. Given the number of colors, we aim to maximize the number of different colors at neighboring vertices (i.e. one edge distance) of any vertex. Two efficient algorithms, belief propagation and Walksat are adapted to carry out this task. We present experimental results based on two types of random graphs for different system sizes and identify the critical value of the connectivity for the algorithms to find a perfect solution. The problem and the suggested algorithms have practical relevance since various applications, such as distributed storage, can be mapped onto this problem.

A methodology for the generation and evaluation of biorefinery process chains, in order to identify the most promising biorefineries for the EU

The topic of bioenergy, biofuels and bioproducts remains at the top of the current political and research agenda. Identification of the optimum processing routes for biomass, in terms of efficiency, cost, environment and socio-economics is vital as concern grows over the remaining fossil fuel resources, climate change and energy security. It is known that the only renewable way of producing conventional hydrocarbon fuels and organic chemicals is from biomass, but the problem remains of identifying the best product mix and the most efficient way of processing biomass to products. The aim is to move Europe towards a biobased economy and it is widely accepted that biorefineries are key to this development. A methodology was required for the generation and evaluation of biorefinery process chains for converting biomass into one or more valuable products that properly considers performance, cost, environment, socio-economics and other factors that influence the commercial viability of a process. In this thesis a methodology to achieve this objective is described. The completed methodology includes process chain generation, process modelling and subsequent analysis and comparison of results in order to evaluate alternative process routes. A modular structure was chosen to allow greater flexibility and allowing the user to generate a large number of different biorefinery configurations The significance of the approach is that the methodology is defined and is thus rigorous and consistent and may be readily re-examined if circumstances change. There was the requirement for consistency in structure and use, particularly for multiple analyses. It was important that analyses could be quickly and easily carried out to consider, for example, different scales, configurations and product portfolios and so that previous outcomes could be readily reconsidered. The result of the completed methodology is the identification of the most promising biorefinery chains from those considered as part of the European Biosynergy Project.

Properties of sparse random matrices over finite fields

Typical properties of sparse random matrices over finite (Galois) fields are studied, in the limit of large matrices, using techniques from the physics of disordered systems. For the case of a finite field GF(q) with prime order q, we present results for the average kernel dimension, average dimension of the eigenvector spaces and the distribution of the eigenvalues. The number of matrices for a given distribution of entries is also calculated for the general case. The significance of these results to error-correcting codes and random graphs is also discussed.

Fibre-based devices for next generation photonics communication systems

The future broadband information network will undoubtedly integrate the mobility and flexibility of wireless access systems with the huge bandwidth capacity of photonics solutions to enable a communication system capable of handling the anticipated demand for interactive services. Towards wide coverage and low cost implementations of such broadband wireless photonics communication networks, various aspects of the enabling technologies are continuingly generating intense research interest. Among the core technologies, the optical generation and distribution of radio frequency signals over fibres, and the fibre optic signal processing of optical and radio frequency signals, have been the subjects for study in this thesis. Based on the intrinsic properties of single-mode optical fibres, and in conjunction with the concepts of optical fibre delay line filters and fibre Bragg gratings, a number of novel fibre-based devices, potentially suitable for applications in the future wireless photonics communication systems, have been realised. Special single-mode fibres, namely, the high birefringence (Hi-Bi) fibre and the Er/Yb doped fibre have been employed so as to exploit their merits to achieve practical and cost-effective all-fibre architectures. A number of fibre-based complex signal processors for optical and radio frequencies using novel Hi-Bi fibre delay line filter architectures have been illustrated. In particular, operations such as multichannel flattop bandpass filtering, simultaneous complementary outputs and bidirectional nonreciprocal wavelength interleaving, have been demonstrated. The proposed configurations featured greatly reduced environmental sensitivity typical of coherent fibre delay line filter schemes, reconfigurable transfer functions, negligible chromatic dispersions, and ease of implementation, not easily achievable based on other techniques. A number of unique fibre grating devices for signal filtering and fibre laser applications have been realised. The concept of the superimposed fibre Bragg gratings has been extended to non-uniform grating structures and into Hi-Bi fibres to achieve highly useful grating devices such as overwritten phase-shifted fibre grating structure and widely/narrowly spaced polarization-discriminating filters that are not limited by the intrinsic fibre properties. In terms of the-fibre-based optical millimetre wave transmitters, unique approaches based on fibre laser configurations have been proposed and demonstrated. The ability of the dual-mode distributed feedback (DFB) fibre lasers to generate high spectral purity, narrow linewidth heterodyne signals without complex feedback mechanisms has been illustrated. A novel co-located dual DFB fibre laser configuration, based on the proposed superimposed phase-shifted fibre grating structure, has been further realised with highly desired operation characteristics without the need for costly high frequency synthesizers and complex feedback controls. Lastly, a novel cavity mode condition monitoring and optimisation scheme for short length, linear-cavity fibre lasers has been proposed and achieved. Based on the concept and simplicity of the superimposed fibre laser cavities structure, in conjunction with feedback controls, enhanced output performances from the fibre lasers have been achieved. The importance of such cavity mode assessment and feedback control for optimised fibre laser output performance has been illustrated.

Efficiency improvements to the Groupe Special Mobile (GSM) digital mobile radio system

Groupe Spécial Mobile (GSM) has been developed as the pan-European second generation of digital mobile systems. GSM operates in the 900 MHz frequency band and employs digital technology instead of the analogue technology of its predecessors. Digital technology enables the GSM system to operate in much smaller zones in comparison with the analogue systems. The GSM system will offer greater roaming facilities to its subscribers, extended throughout the countries that have installed the system. The GSM system could be seen as a further enhancement to European integration. GSM has adopted a contention-based protocol for multipoint-to-point transmission. In particular, the slotted-ALOHA medium access protocol is used to coordinate the transmission of the channel request messages between the scattered mobile stations. Collision still happens when more than one mobile station having the same random reference number attempts to transmit on the same time-slot. In this research, a modified version of this protocol has been developed in order to reduce the number of collisions and hence increase the random access channel throughput compared to the existing protocol. The performance evaluation of the protocol has been carried out using simulation methods. Due to the growing demand for mobile radio telephony as well as for data services, optimal usage of the scarce availability radio spectrum is becoming increasingly important. In this research, a protocol has been developed whereby the number of transmitted information packets over the GSM system is increased without any additional increase of the allocated radio spectrum. Simulation results are presented to show the improvements achieved by the proposed protocol. Cellular mobile radio networks commonly respond to an increase in the service demand by using smaller coverage areas. As a result, the volume of the signalling exchanges increases. In this research, a proposal for interconnecting the various entitles of the mobile radio network over the future broadband networks based on the IEEE 802.6 Metropolitan Area Network (MAN) is outlined. Simulation results are presented to show the benefits achieved by interconnecting these entities over the broadband Networks.