The development of a model system and high throughput assay for the study of interactions between zinc finger proteins and DNA

It has been recognised for some time that a full code of amino acid-based recognition of DNA sequences would be useful. Several approaches, which utilise small DNA binding motifs called zinc fingers, are presently employed. None of the current approaches successfully combine a combinatorial approach to the elucidation of a code with a single stage high throughput screening assay. The work outlined here describes the development of a model system for the study of DNA protein interactions and the development of a high throughput assay for detection of such interactions. A zinc finger protein was designed which will bind with high affinity and specificity to a known DNA sequence. For future work it is possible to mutate the region of the zinc finger responsible for the specificity of binding, in order to observe the effect on the DNA / protein interactions. The zinc finger protein was initially synthesised as a His tagged product. It was not possible however to develop a high throughput assay using the His tagged zinc finger protein. The gene encoding the zinc finger protein was altered and the protein synthesised as a Glutathione S-Transferase (GST) fusion product. A successful assay was developed using the GST protein and Scintillation Proximity Assay technology (Amersham Pharmacia Biotech). The scintillation proximity assay is a dynamic assay that allows the DNA protein interactions to be studied in "real time". This assay not only provides a high throughput method of screening zinc finger proteins for potential ligands but also allows the effect of addition of reagents or competitor ligands to be monitored.

A solar-powered reverse osmosis system for high recovery of freshwater from saline groundwater

Desalination of groundwater is essential in arid regions that are remote from both seawater and freshwater resources. Desirable features of a groundwater desalination system include a high recovery ratio, operation from a sustainable energy source such as solar, and high water output per unit of energy and land. Here we propose a new system that uses a solar-Rankine cycle to drive reverse osmosis (RO). The working fluid such as steam is expanded against a power piston that actuates a pump piston which in turn pressurises the saline water thus passing it through RO membranes. A reciprocating crank mechanism is used to equalise the forces between the two pistons. The choice of batch mode in preference to continuous flow permits maximum energy recovery and minimal concentration polarisation in the vicinity of the RO membrane. This study analyses the sizing and efficiency of the crank mechanism, quantifies energy losses in the RO separation and predicts the overall performance. For example, a system using a field of linear Fresnel collectors occupying 1000 m2 of land and raising steam at 200 °C and 15.5 bar could desalinate 350 m3/day from saline water containing 5000 ppm of sodium chloride with a recovery ratio of 0.7.

Gamma-shaped long-cavity normal-dispersion mode-locked Er-fiber laser for sub-nanosecond high-energy pulsed generation

We propose the design of a novel ?-shaped fiber laser resonator and apply it to build a long-cavity normaldispersion mode-locked Er-fiber laser which features enhanced functionalities for management and optimization of pulsed lasing regimes. We report the generation of sub-nanosecond pulses with the energy of ~0.5 µJ at a kilohertz-scale repetition rate in an all-fiber system based on the new laser design. A combination of special design solutions in the laser, such as polarization instability compensation in the ultra-long arm of the resonator, intra-cavity spectral selection of radiation with a broadband fiber Bragg grating, and polarization selection by means of a tilted refractive index grating, ensures low amplified spontaneous emission (ASE) noise and high stability of the laser system output parameters.

Ultra small integrated optical fiber sensing system

This paper introduces a revolutionary way to interrogate optical fiber sensors based on fiber Bragg gratings (FBGs) and to integrate the necessary driving optoelectronic components with the sensor elements. Low-cost optoelectronic chips are used to interrogate the optical fibers, creating a portable dynamic sensing system as an alternative for the traditionally bulky and expensive fiber sensor interrogation units. The possibility to embed these laser and detector chips is demonstrated resulting in an ultra thin flexible optoelectronic package of only 40 µm, provided with an integrated planar fiber pigtail. The result is a fully embedded flexible sensing system with a thickness of only 1 mm, based on a single Vertical-Cavity Surface-Emitting Laser (VCSEL), fiber sensor and photodetector chip. Temperature, strain and electrodynamic shaking tests have been performed on our system, not limited to static read-out measurements but dynamically reconstructing full spectral information datasets.

High performance numerical modeling of ultra-short laser pulse propagation based on multithreaded parallel hardware

The focus of this study is development of parallelised version of severely sequential and iterative numerical algorithms based on multi-threaded parallel platform such as a graphics processing unit. This requires design and development of a platform-specific numerical solution that can benefit from the parallel capabilities of the chosen platform. Graphics processing unit was chosen as a parallel platform for design and development of a numerical solution for a specific physical model in non-linear optics. This problem appears in describing ultra-short pulse propagation in bulk transparent media that has recently been subject to several theoretical and numerical studies. The mathematical model describing this phenomenon is a challenging and complex problem and its numerical modeling limited on current modern workstations. Numerical modeling of this problem requires a parallelisation of an essentially serial algorithms and elimination of numerical bottlenecks. The main challenge to overcome is parallelisation of the globally non-local mathematical model. This thesis presents a numerical solution for elimination of numerical bottleneck associated with the non-local nature of the mathematical model. The accuracy and performance of the parallel code is identified by back-to-back testing with a similar serial version.

Ultra-long mode-locked Er-droped fibre lasers

The development of ultra-long (UL) cavity (hundreds of meters to several kilometres) mode-locked fibre lasers for the generation of high-energy light pulses with relatively low (sub-megahertz) repetition rates has emerged as a new rapidly advancing area of laser physics. The first demonstration of high pulse energy laser of this type was followed by a number of publications from many research groups on long-cavity Ytterbium and Erbium lasers featuring a variety of configurations with rather different mode-locked operations. The substantial interest to this new approach is stimulated both by non-trivial underlying physics and by the potential of high pulse energy laser sources with unique parameters for a range of applications in industry, bio-medicine, metrology and telecommunications. It is well known, that pulse generation regimes in mode-locked fibre lasers are determined by the intra-cavity balance between the effects of dispersion and non-linearity, and the processes of energy attenuation and amplification. The highest per-pulse energy has been achieved in normal-dispersion UL fibre lasers mode-locked through nonlinear polarization evolution (NPE) for self-modelocking operation. In such lasers are generated the so-called dissipative optical solitons. The uncompensated net normal dispersion in long-cavity resonatorsusually leads to very high chirp and, consequently, to a relatively long duration of generated pulses. This thesis presents the results of research Er-doped ultra-long (more than 1 km cavity length) fibre lasers mode-locked based on NPE. The self-mode-locked erbium-based 3.5-km-long all-fiber laser with the 1.7 µJ pulse energy at a wavelength of 1.55 µm was developed as a part of this research. It has resulted in direct generation of short laser pulses with an ultralow repetition rate of 35.1 kHz. The laser cavity has net normal-dispersion and has been fabricated from commercially-available telecom fibers and optical-fiber elements. Its unconventional linear-ring design with compensation for polarization instability ensures high reliability of the self-mode-locking operation, despite the use of a non polarization-maintaining fibers. The single pulse generation regime in all-fibre erbium mode-locking laser based on NPE with a record cavity length of 25 km was demonstrated. Modelocked lasers with such a long cavity have never been studied before. Our result shows a feasibility of stable mode-locked operation even for an ultra-long cavity length. A new design of fibre laser cavity – “y-configuration”, that offers a range of new functionalities for optimization and stabilization of mode-locked lasing regimes was proposed. This novel cavity configuration has been successfully implemented into a long-cavity normal-dispersion self-mode-locked Er-fibre laser. In particular, it features compensation for polarization instability, suppression of ASE, reduction of pulse duration, prevention of in-cavity wave breaking, and stabilization of the lasing wavelength. This laser along with a specially designed double-pass EDFA have allowed us to demonstrate anenvironmentally stable all-fibre laser system able to deliver sub-nanosecond high-energy pulses with low level of ASE noise.

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High frequency sensing interrogation system using fiber Bragg grating based microwave photonic filtering

A high frequency sensing interrogation system by using fiber Bragg grating based microwave photonic filtering is proposed, in which the wavelength measurement sensitivity is proportional to the RF modulation frequency applied to the optical signal.

Optical communications applications of ultra-long Raman fiber lasers

Recent work on ultra-long Raman fiber lasers has shown that it is possible to create quasi-lossless transmission conditions in fiber spans long enough to be considered for high speed optical communications. This paper reviews how quasi-lossless transmission conditions are reached and presents experimental results of 40Gb/s transmission in a quasi lossless system. The performance is compared with a conventional EDFA based system.

High-resolution, wavelength-division-multiplexed in-fibre Bragg grating sensor system

A novel wavelength-division-multiplexed in-fibre Bragg grating sensor system combined with high resolution drift-compensated interferometric wavelength-shift detection is described. This crosstalk-free system is based on the use of an interferometric wavelength scanner and a low resolution spectrometer. A four element system is demonstrated for temperature measurement, and a resolution of ±0.1°C has been achieved.

Gamma-shaped long-cavity normal-dispersion mode-locked Er-fiber laser for sub-nanosecond high-energy pulsed generation

We propose the design of a novel ?-shaped fiber laser resonator and apply it to build a long-cavity normaldispersion mode-locked Er-fiber laser which features enhanced functionalities for management and optimization of pulsed lasing regimes. We report the generation of sub-nanosecond pulses with the energy of ~0.5 µJ at a kilohertz-scale repetition rate in an all-fiber system based on the new laser design. A combination of special design solutions in the laser, such as polarization instability compensation in the ultra-long arm of the resonator, intra-cavity spectral selection of radiation with a broadband fiber Bragg grating, and polarization selection by means of a tilted refractive index grating, ensures low amplified spontaneous emission (ASE) noise and high stability of the laser system output parameters.

Ultra small integrated optical fiber sensing system

This paper introduces a revolutionary way to interrogate optical fiber sensors based on fiber Bragg gratings (FBGs) and to integrate the necessary driving optoelectronic components with the sensor elements. Low-cost optoelectronic chips are used to interrogate the optical fibers, creating a portable dynamic sensing system as an alternative for the traditionally bulky and expensive fiber sensor interrogation units. The possibility to embed these laser and detector chips is demonstrated resulting in an ultra thin flexible optoelectronic package of only 40 µm, provided with an integrated planar fiber pigtail. The result is a fully embedded flexible sensing system with a thickness of only 1 mm, based on a single Vertical-Cavity Surface-Emitting Laser (VCSEL), fiber sensor and photodetector chip. Temperature, strain and electrodynamic shaking tests have been performed on our system, not limited to static read-out measurements but dynamically reconstructing full spectral information datasets.

Quasi-lossless data transmission with ultra-long Raman fibre laser based amplification

The project consists of an experimental and numerical modelling study of the applications of ultra-long Raman fibre laser (URFL) based amplification techniques for high-speed multi-wavelength optical communications systems. The research is focused in telecommunications C-band 40 Gb/s transmission data rates with direct and coherent detection. The optical transmission performance of URFL based systems in terms of optical noise, gain bandwidth and gain flatness for different system configurations is evaluated. Systems with different overall span lengths, transmission fibre types and data modulation formats are investigated. Performance is compared with conventional Erbium doped fibre amplifier based system to evaluate system configurations where URFL based amplification provide performance or commercial advantages.

Investigation of the effect of an increased supervisory signal power in a high-loss loopback monitoring system

We present experimental results for the effect of an increased supervisory signal power in a high-loss loopback supervisory system in an optically amplified wavelength division multiplexing (WDM) transmission line. The study focuses on the investigation of increasing the input power for the supervisory signal and the effect on the co-propagating WDM data signals using different channel spacing. This investigation is useful for determining the power limitation of the supervisory signal if extra power is needed to improve the monitoring. The study also shows the effect of spacing on the quality of the supervisory signal itself because of interaction with adjacent data signals. © The Institution of Engineering and Technology 2014.

Broadly tunable quantum-dot based ultra-short pulse laser system with different diffraction grating orders

A broadly tunable quantum-dot based ultra-short pulse master oscillator power amplifier with different diffraction grating orders as an external-cavity resonance feedback is studied. A broader tuning range, narrower optical spectra as well as higher peak power spectal density (maximun of 1.37 W/nm) from the second-order diffraction beam are achieved compared to those from the first-order diffraction beam in spite of slightly broader pulse duration from the secondorder diffraction. © The Institution of Engineering and Technology 2013.