A numerical approach to modeling the catalytic voltammetry of surface-confined redox enzymes

A finite difference method for simulating voltammograms of electrochemically driven enzyme catalysis is presented. The method enables any enzyme mechanism to be simulated. The finite difference equations can be represented as a matrix equation containing a nonlinear sparse matrix. This equation has been solved using the software package Mathematica. Our focus is on the use of cyclic voltammetry since this is the most commonly employed electrochemical method used to elucidate mechanisms. The use of cyclic voltammetry to obtain data from systems obeying Michaelis-Menten kinetics is discussed, and we then verify our observations on the Michaelis-Menten system using the finite difference simulation. Finally, we demonstrate how the method can be used to obtain mechanistic information on a real redox enzyme system, the complex bacterial molybdoenzyme xanthine dehydrogenase.

Modelling of two-stage anaerobic digestion using the IWA Anaerobic Digestion Model No. 1 (ADM1)

The aim of the study presented was to implement a process model to simulate the dynamic behaviour of a pilot-scale process for anaerobic two-stage digestion of sewage sludge. The model implemented was initiated to support experimental investigations of the anaerobic two-stage digestion process. The model concept implemented in the simulation software package MATLAB(TM)/Simulink(R) is a derivative of the IWA Anaerobic Digestion Model No.1 (ADM1) that has been developed by the IWA task group for mathematical modelling of anaerobic processes. In the present study the original model concept has been adapted and applied to replicate a two-stage digestion process. Testing procedures, including balance checks and 'benchmarking' tests were carried out to verify the accuracy of the implementation. These combined measures ensured a faultless model implementation without numerical inconsistencies. Parameters for both, the thermophilic and the mesophilic process stage, have been estimated successfully using data from lab-scale experiments described in literature. Due to the high number of parameters in the structured model, it was necessary to develop a customised procedure that limited the range of parameters to be estimated. The accuracy of the optimised parameter sets has been assessed against experimental data from pilot-scale experiments. Under these conditions, the model predicted reasonably well the dynamic behaviour of a two-stage digestion process in pilot scale. (C) 2004 Elsevier Ltd. All rights reserved.

Spontaneous combustion and simulation of mine fires and their effects on mine ventilation systems

The structure of a comprehensive research project into mine fires study applying the Ventgraph mine fire simulation software, preplanning of escape scenarios and general interaction with rescue responses is outlined. The project has Australian Coal Association Research Program (ACARP) funding and also relies on substantial mining company site support. This practical input from mine operators is essential and allows the approach to be introduced in the most creditable way. The effort is built around the introduction of fire simulation computer software to the Australian mining industry and the consequent modelling of fire scenarios in selected different mine layouts. Application of the simulation software package to the changing mine layouts requires experience to achieve realistic outcomes. Most Australian mines of size currently use a ventilation network simulation program. Under the project a small subroutine has been written to transfer the input data from the existing mine ventilation network simulation program to ‘Ventgraph’. This has been tested successfully. To understand fire simulation behaviour on the mine ventilation system, it is necessary to understood the possible effects of mine fires on various mine ventilation systems correctly first. Case studies demonstrating the possible effects of fires on some typical Australian coal mine ventilation circuits have been examined. The situation in which there is some gas make at the face and effects with fire have also been developed to emphasise how unstable and dangerous situations may arise. The primary objective of the part of the study described in this paper is to use mine fire simulation software to gain better understanding of how spontaneous combustion initiated fires can interact with the complex ventilation behaviour underground during a substantial fire. It focuses on the simulation of spontaneous combustion sourced heatings that develop into open fires. Further, it examines ventilation behaviour effects of spontaneous combustion initiated pillar fires and examines the difficulties these can be present if a ventilation reversal occurs. It also briefly examines simulation of use of the inertisation to assist in mine recovery. Mine fires are recognised across the world as a major hazard issue. New approaches allowing improvement in understanding their consequences have been developed as an aid in handling this complex area.

JKSimFloat V6: Improving flotation circuit performance and understanding

Methods of analysing and optimising flotation circuits have improved significantly over the last 15 years. Mineral flotation is now generally better understood through major advances in measuring and modelling the sub-processes within the flotation system. JKSimFloat V6 is a user-friendly Windows-based software package incorporating simulation, mass balancing, and, currently under development, liberation data viewing and model fitting. This paper presents an overview of the development of the program up to its current status, and the plans established for the future. The application of the simulator, in particular, at various operations is also discussed with emphasis on the use of the program in improving flotation circuit performance.

A learning approach for performance evaluation of local network

In this paper, a novel approach is developed to evaluate the overall performance of a local area network as well as to monitor some possible intrusion detections. The data is obtained via system utility 'ping' and huge data is analyzed via statistical methods. Finally, an overall performance index is defined and simulation experiments in three months proved the effectiveness of the proposed performance index. A software package is developed based on these ideas.

A survey of continuous improvement practices in the United Kingdom and Mexico

With the advent of globalisation companies all around the world must improve their performance in order to survive. The threats are coming from everywhere, and in different ways, such as low cost products, high quality products, new technologies, and new products. Different companies in different countries are using various techniques and using quality criteria items to strive for excellence. Continuous improvement techniques are used to enable companies to improve their operations. Therefore, companies are using techniques such as TQM, Kaizen, Six-Sigma, Lean Manufacturing, and quality award criteria items such as Customer Focus, Human Resources, Information & Analysis, and Process Management. The purpose of this paper is to compare the use of these techniques and criteria items in two countries, Mexico and the United Kingdom, which differ in culture and industrial structure. In terms of the use of continuous improvement tools and techniques, Mexico formally started to deal with continuous improvement by creating its National Quality Award soon after the Americans began the Malcolm Baldrige National Quality Award. The United Kingdom formally started by using the European Quality Award (EQA), modified and renamed as the EFQM Excellence Model. The methodology used in this study was to undertake a literature review of the subject matter and to study some general applications around the world. A questionnaire survey was then designed and a survey undertaken based on the same scale, about the same sample size, and the about the same industrial sector within the two countries. The survey presents a brief definition of each of the constructs to facilitate understanding of the questions. The analysis of the data was then conducted with the assistance of a statistical software package. The survey results indicate both similarities and differences in the strengths and weaknesses of the companies in the two countries. One outcome of the analysis is that it enables the companies to use the results to benchmark themselves and thus act to reinforce their strengths and to reduce their weaknesses.

The effects of relocation on Royal Air Force families

This doctoral research project examines the effects that geographical transience has on Royal Air Force families. The methodology employed in this exploratory and qualitative study consisted largely of open-ended interview questions but also included a series of demographic variables. In total, 29 RAF personnel without families, 33 RAF personnel with families, 33 RAF spouses, and 15 RAF children participated in this research (N = 110). All respondents volunteered to take part in the study and were based in the United Kingdom at the time of data collection. The interviews were transcribed and content coded according to six major relocation themes arising from the literature (change, tasks, support, coping, difficulty, and outcome). QSR NVIVO 2.0, a qualitative data analysis software package, was used to facilitate the process. Through the utilisations of qualitative methodology, the researcher was able to offer various novel and reoccurring variables that appear to play an important role (at least subjectively) in relocation. Additionally, frequencies associated with these factors were presented. The findings were integrated with those from the literature in order to offer an initial comparison and differentiation between civilian and military samples. The main theoretical contributions were the introduction of the concept of mobile mentality, the creation of a novel relocation model that takes familial interaction into account, and the development of a taxonomy for the classification of relocation outcomes. Finally, additional observations, recommendations for future research, and practical implications are reviewed.

Neural network enhanced self tuning adaptive control application for non-linear control of dynamic systems

The main theme of research of this project concerns the study of neutral networks to control uncertain and non-linear control systems. This involves the control of continuous time, discrete time, hybrid and stochastic systems with input, state or output constraints by ensuring good performances. A great part of this project is devoted to the opening of frontiers between several mathematical and engineering approaches in order to tackle complex but very common non-linear control problems. The objectives are: 1. Design and develop procedures for neutral network enhanced self-tuning adaptive non-linear control systems; 2. To design, as a general procedure, neural network generalised minimum variance self-tuning controller for non-linear dynamic plants (Integration of neural network mapping with generalised minimum variance self-tuning controller strategies); 3. To develop a software package to evaluate control system performances using Matlab, Simulink and Neural Network toolbox. An adaptive control algorithm utilising a recurrent network as a model of a partial unknown non-linear plant with unmeasurable state is proposed. Appropriately, it appears that structured recurrent neural networks can provide conveniently parameterised dynamic models for many non-linear systems for use in adaptive control. Properties of static neural networks, which enabled successful design of stable adaptive control in the state feedback case, are also identified. A survey of the existing results is presented which puts them in a systematic framework showing their relation to classical self-tuning adaptive control application of neural control to a SISO/MIMO control. Simulation results demonstrate that the self-tuning design methods may be practically applicable to a reasonably large class of unknown linear and non-linear dynamic control systems.

Computer interpretation of engineering drawings as solid models

Much of the geometrical data relating to engineering components and assemblies is stored in the form of orthographic views, either on paper or computer files. For various engineering applications, however, it is necessary to describe objects in formal geometric modelling terms. The work reported in this thesis is concerned with the development and implementation of concepts and algorithms for the automatic interpretation of orthographic views as solid models. The various rules and conventions associated with engineering drawings are reviewed and several geometric modelling representations are briefly examined. A review of existing techniques for the automatic, and semi-automatic, interpretation of engineering drawings as solid models is given. A new theoretical approach is then presented and discussed. The author shows how the implementation of such an approach for uniform thickness objects may be extended to more general objects by introducing the concept of `approximation models'. Means by which the quality of the transformations is monitored, are also described. Detailed descriptions of the interpretation algorithms and the software package that were developed for this project are given. The process is then illustrated by a number of practical examples. Finally, the thesis concludes that, using the techniques developed, a substantial percentage of drawings of engineering components could be converted into geometric models with a specific degree of accuracy. This degree is indicative of the suitability of the model for a particular application. Further work on important details is required before a commercially acceptable package is produced.

GIS linked environmental process models

In recent years there has been a great effort to combine the technologies and techniques of GIS and process models. This project examines the issues of linking a standard current generation 2½d GIS with several existing model codes. The focus for the project has been the Shropshire Groundwater Scheme, which is being developed to augment flow in the River Severn during drought periods by pumping water from the Shropshire Aquifer. Previous authors have demonstrated that under certain circumstances pumping could reduce the soil moisture available for crops. This project follows earlier work at Aston in which the effects of drawdown were delineated and quantified through the development of a software package that implemented a technique which brought together the significant spatially varying parameters. This technique is repeated here, but using a standard GIS called GRASS. The GIS proved adequate for the task and the added functionality provided by the general purpose GIS - the data capture, manipulation and visualisation facilities - were of great benefit. The bulk of the project is concerned with examining the issues of the linkage of GIS and environmental process models. To this end a groundwater model (Modflow) and a soil moisture model (SWMS2D) were linked to the GIS and a crop model was implemented within the GIS. A loose-linked approach was adopted and secondary and surrogate data were used wherever possible. The implications of which relate to; justification of a loose-linked versus a closely integrated approach; how, technically, to achieve the linkage; how to reconcile the different data models used by the GIS and the process models; control of the movement of data between models of environmental subsystems, to model the total system; the advantages and disadvantages of using a current generation GIS as a medium for linking environmental process models; generation of input data, including the use of geostatistic, stochastic simulation, remote sensing, regression equations and mapped data; issues of accuracy, uncertainty and simply providing adequate data for the complex models; how such a modelling system fits into an organisational framework.

A combination of cyclone and vert techniques for the management of construction projects

Many planning and control tools, especially network analysis, have been developed in the last four decades. The majority of them were created in military organization to solve the problem of planning and controlling research and development projects. The original version of the network model (i.e. C.P.M/PERT) was transplanted to the construction industry without the consideration of the special nature and environment of construction projects. It suited the purpose of setting up targets and defining objectives, but it failed in satisfying the requirement of detailed planning and control at the site level. Several analytical and heuristic rules based methods were designed and combined with the structure of C.P.M. to eliminate its deficiencies. None of them provides a complete solution to the problem of resource, time and cost control. VERT was designed to deal with new ventures. It is suitable for project evaluation at the development stage. CYCLONE, on the other hand, is concerned with the design and micro-analysis of the production process. This work introduces an extensive critical review of the available planning techniques and addresses the problem of planning for site operation and control. Based on the outline of the nature of site control, this research developed a simulation based network model which combines part of the logics of both VERT and CYCLONE. Several new nodes were designed to model the availability and flow of resources, the overhead and operating cost and special nodes for evaluating time and cost. A large software package is written to handle the input, the simulation process and the output of the model. This package is designed to be used on any microcomputer using MS-DOS operating system. Data from real life projects were used to demonstrate the capability of the technique. Finally, a set of conclusions are drawn regarding the features and limitations of the proposed model, and recommendations for future work are outlined at the end of this thesis.

Ophthalmic engineering:the development of novel instrumentation to further research in the field

The principle theme of this thesis is the advancement and expansion of ophthalmic research via the collaboration between professional Engineers and professional Optometrists. The aim has been to develop new and novel approaches and solutions to contemporary problems in the field. The work is sub divided into three areas of investigation; 1) High technology systems, 2) Modification of current systems to increase functionality, and 3) Development of smaller more portable and cost effective systems. High Technology Systems: A novel high speed Optical Coherence Tomography (OCT) system with integrated simultaneous high speed photography was developed achieving better operational speed than is currently available commercially. The mechanical design of the system featured a novel 8 axis alignment system. A full set of capture, analysis, and post processing software was developed providing custom analysis systems for ophthalmic OCT imaging, expanding the current capabilities of the technology. A large clinical trial was undertaken to test the dynamics of contact lens edge interaction with the cornea in-vivo. The interaction between lens edge design, lens base curvature, post insertion times and edge positions was investigated. A novel method for correction of optical distortion when assessing lens indentation was also demonstrated. Modification of Current Systems: A commercial autorefractor, the WAM-5500, was modified with the addition of extra hardware and a custom software and firmware solution to produce a system that was capable of measuring dynamic accommodative response to various stimuli in real time. A novel software package to control the data capture process was developed allowing real time monitoring of data by the practitioner, adding considerable functionality of the instrument further to the standard system. The device was used to assess the accommodative response differences between subjects who had worn UV blocking contact lens for 5 years, verses a control group that had not worn UV blocking lenses. While the standard static measurement of accommodation showed no differences between the two groups, it was determined that the UV blocking group did show better accommodative rise and fall times (faster), thus demonstrating the benefits of the modification of this commercially available instrumentation. Portable and Cost effective Systems: A new instrument was developed to expand the capability of the now defunct Keeler Tearscope. A device was developed that provided a similar capability in allowing observation of the reflected mires from the tear film surface, but with the added advantage of being able to record the observations. The device was tested comparatively with the tearscope and other tear film break-up techniques, demonstrating its potential. In Conclusion: This work has successfully demonstrated the advantages of interdisciplinary research between engineering and ophthalmic research has provided new and novel instrumented solutions as well as having added to the sum of scientific understanding in the ophthalmic field.

An overall profit Malmquist productivity index with fuzzy and interval data

Although crisp data are fundamentally indispensable for determining the profit Malmquist productivity index (MPI), the observed values in real-world problems are often imprecise or vague. These imprecise or vague data can be suitably characterized with fuzzy and interval methods. In this paper, we reformulate the conventional profit MPI problem as an imprecise data envelopment analysis (DEA) problem, and propose two novel methods for measuring the overall profit MPI when the inputs, outputs, and price vectors are fuzzy or vary in intervals. We develop a fuzzy version of the conventional MPI model by using a ranking method, and solve the model with a commercial off-the-shelf DEA software package. In addition, we define an interval for the overall profit MPI of each decision-making unit (DMU) and divide the DMUs into six groups according to the intervals obtained for their overall profit efficiency and MPIs. We also present two numerical examples to demonstrate the applicability of the two proposed models and exhibit the efficacy of the procedures and algorithms. © 2011 Elsevier Ltd.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).