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.

The pore system and engineering properties of hardened cement paste

The work described in this thesis is an attempt to elucidate the relationships between the pore system and a number of engineering properties of hardened cement paste, particularly tensile strength and resistances to carbonation and ionic penetration. By examining aspects such as the rate of carbonisation, the pore size distribution, the concentration of ions in the pore solution and the phase composition of cement pastes, relationships between the pore system (pores and pore solution) and the resistance to carbonation were investigated. The study was carried out in two parts. First, cement pastes with different pore systems were compared, whilst secondly comparisons were made between the pore systems of cement pastes with different degrees of carbonation. Relationships between the pore structure and ionic penetration were studied by comparing kinetic data relating to the diffusion of various ions in cement pastes with different pore systems. Diffusion coefficients and activation energies for the diffusion process of Cl- and Na+ ions in carbonated and non-carbonated cement pastes were determined by a quasi-steady state technique. The effect of the geometry of pores on ionic diffusion was studied by comparing the mechanisms of ionic diffusion for ions with different radii. In order to investigate the possible relationship between tensile strength and macroporosity, cement paste specimens with cross sectional areas less than 1mm2 were produced so that the chance of a macropore existing within them was low. The tensile strengths of such specimens were then compared with those of larger specimens.

Range of validity of weakly non-linear theory in Rayleigh-Bénard convection

In this paper we examine the equilibrium states of periodic finite amplitude flow in a horizontal channel with differential heating between the two rigid boundaries. The solutions to the Navier-Stokes equations are obtained by means of a perturbation method for evaluating the Landau coefficients and through a Newton-Raphson iterative method that results from the Fourier expansion of the solutions that bifurcate above the linear stability threshold of infini- tesimal disturbances. The results obtained from these two different methods of evaluating the convective flow are compared in the neighbourhood of the critical Rayleigh number. We find that for small Prandtl numbers the discrepancy of the two methods is noticeable.

Addressing missing data in geochemistry: a non-linear approach

Exploratory analysis of petroleum geochemical data seeks to find common patterns to help distinguish between different source rocks, oils and gases, and to explain their source, maturity and any intra-reservoir alteration. However, at the outset, one is typically faced with (a) a large matrix of samples, each with a range of molecular and isotopic properties, (b) a spatially and temporally unrepresentative sampling pattern, (c) noisy data and (d) often, a large number of missing values. This inhibits analysis using conventional statistical methods. Typically, visualisation methods like principal components analysis are used, but these methods are not easily able to deal with missing data nor can they capture non-linear structure in the data. One approach to discovering complex, non-linear structure in the data is through the use of linked plots, or brushing, while ignoring the missing data. In this paper we introduce a complementary approach based on a non-linear probabilistic model. Generative topographic mapping enables the visualisation of the effects of very many variables on a single plot, while also dealing with missing data. We show how using generative topographic mapping also provides an optimal method with which to replace missing values in two geochemical datasets, particularly where a large proportion of the data is missing.

Approaching the non-linear Shannon limit

We review the recent progress of information theory in optical communications, and describe the current experimental results and associated advances in various individual technologies which increase the information capacity. We confirm the widely held belief that the reported capacities are approaching the fundamental limits imposed by signal-to-noise ratio and the distributed non-linearity of conventional optical fibres, resulting in the reduction in the growth rate of communication capacity. We also discuss the techniques which are promising to increase and/or approach the information capacity limit.

Experimental measurement of switched reluctance motor non-linear characteristics

For a Switched Reluctance Motor (SRM), the flux linkage characteristic is the most basic magnetic characteristic, and many other quantities, including the incremental inductance, back emf, and electromagnetic torque can be determined indirectly from it. In this paper, two methods of measuring the flux linkage profile of an SRM from the phase winding voltage and current measurements, with and without rotor locking devices, are presented. Torque, incremental inductance and back emf characteristics of the SRM are then obtained from the flux linkage measurements. The torque of the SRM is also measured directly as a comparison, and the closeness of the calculated and directly measured torque curves suggests the validity of the method to obtain the SRM torque, incremental inductance and back emf profiles from the flux linkage measurements. © 2013 IEEE.

Some aspects of the solution of non-linear differential equations

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A comparisation of methods for the optimisation of a non-linear function subject to non-linear constraints

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A non-linear encoder using a binary counterfor pulse-code modulation

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Challenges of developing non-linear devices to achieve the linear Shannon limit

To achieve the Shannon Capacity Limit, we need to develop practical, effective and deployable non-linear devices to invert the non-linear effects of the transmission line. In this work, we will summarise the progress we are making to realise these, specifically looking at optical phase conjugation and phase regenerators as methods to improve non-linear tolerances. © 2014 IEEE.

High spectral efficiency transmission emulation for non-linear transmission performance estimation for high order modulation formats

We demonstrate a simple method to experimentally evaluate nonlinear transmission performance of high order modulation formats using a low number of channels and channel-like ASE. We verify it's behaviour is consistent with the AWGN model of transmission.

Travelling-wave model of semiconductor optical amplifier based non-linear loop mirror

A travelling-wave model of a semiconductor optical amplifier based non-linear loop mirror is developed to investigate the importance of travelling-wave effects and gain/phase dynamics in predicting device behaviour. A constant effective carrier recovery lifetime approximation is found to be reasonably accurate (±10%) within a wide range of control pulse energies. Based on this approximation, a heuristic model is developed for maximum computational efficiency. The models are applied to a particular configuration involving feedback.

Non-Linear Network-Flow Model of Lukasiewicz’s Multivalue Logic

The paper presents a new network-flow interpretation of Łukasiewicz’s logic based on models with an increased effectiveness. The obtained results show that the presented network-flow models principally may work for multivalue logics with more than three states of the variables i.e. with a finite set of states in the interval from 0 to 1. The described models give the opportunity to formulate various logical functions. If the results from a given model that are contained in the obtained values of the arc flow functions are used as input data for other models then it is possible in Łukasiewicz’s logic to interpret successfully other sophisticated logical structures. The obtained models allow a research of Łukasiewicz’s logic with specific effective methods of the network-flow programming. It is possible successfully to use the specific peculiarities and the results pertaining to the function ‘traffic capacity of the network arcs’. Based on the introduced network-flow approach it is possible to interpret other multivalue logics – of E.Post, of L.Brauer, of Kolmogorov, etc.

Approaching the non-linear Shannon limit

We review the recent progress of information theory in optical communications, and describe the current experimental results and associated advances in various individual technologies which increase the information capacity. We confirm the widely held belief that the reported capacities are approaching the fundamental limits imposed by signal-to-noise ratio and the distributed non-linearity of conventional optical fibres, resulting in the reduction in the growth rate of communication capacity. We also discuss the techniques which are promising to increase and/or approach the information capacity limit.

Self-Learning Fuzzy Spiking Neural Network as a Nonlinear Pulse-Position Threshold Detection Dynamic System Based on Second-Order Critically Damped Response Units

Architecture and learning algorithm of self-learning spiking neural network in fuzzy clustering task are outlined. Fuzzy receptive neurons for pulse-position transformation of input data are considered. It is proposed to treat a spiking neural network in terms of classical automatic control theory apparatus based on the Laplace transform. It is shown that synapse functioning can be easily modeled by a second order damped response unit. Spiking neuron soma is presented as a threshold detection unit. Thus, the proposed fuzzy spiking neural network is an analog-digital nonlinear pulse-position dynamic system. It is demonstrated how fuzzy probabilistic and possibilistic clustering approaches can be implemented on the base of the presented spiking neural network.