Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.

Modelling tribology of slider and disk in a computer hard drive system

Issues of wear and tribology are increasingly important in computer hard drives as slider flying heights are becoming lower and disk protective coatings thinner to minimise spacing loss and allow higher areal density. Friction, stiction and wear between the slider and disk in a hard drive were studied using Accelerated Friction Test (AFT) apparatus. Contact Start Stop (CSS) and constant speed drag tests were performed using commercial rigid disks and two different air bearing slider types. Friction and stiction were captured during testing by a set of strain gauges. System parameters were varied to investigate their effect on tribology at the head/disk interface. Chosen parameters were disk spinning velocity, slider fly height, temperature, humidity and intercycle pause. The effect of different disk texturing methods was also studied. Models were proposed to explain the influence of these parameters on tribology. Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) were used to study head and disk topography at various test stages and to provide physical parameters to verify the models. X-ray Photoelectron Spectroscopy (XPS) was employed to identify surface composition and determine if any chemical changes had occurred as a result of testing. The parameters most likely to influence the interface were identified for both CSS and drag testing. Neural Network modelling was used to substantiate results. Topographical AFM scans of disk and slider were exported numerically to file and explored extensively. Techniques were developed which improved line and area analysis. A method for detecting surface contacts was also deduced, results supported and explained observed AFT behaviour. Finally surfaces were computer generated to simulate real disk scans, this allowed contact analysis of many types of surface to be performed. Conclusions were drawn about what disk characteristics most affected contacts and hence friction, stiction and wear.

Analysis and simulation of computer controlled cellular mobile radio systems

Cellular mobile radio systems will be of increasing importance in the future. This thesis describes research work concerned with the teletraffic capacity and the canputer control requirements of such systems. The work involves theoretical analysis and experimental investigations using digital computer simulation. New formulas are derived for the congestion in single-cell systems in which there are both land-to-mobile and mobile-to-mobile calls and in which mobile-to-mobile calls go via the base station. Two approaches are used, the first yields modified forms of the familiar Erlang and Engset formulas, while the second gives more complicated but more accurate formulas. The results of computer simulations to establish the accuracy of the formulas are described. New teletraffic formulas are also derived for the congestion in multi -cell systems. Fixed, dynamic and hybrid channel assignments are considered. The formulas agree with previously published simulation results. Simulation programs are described for the evaluation of the speech traffic of mobiles and for the investigation of a possible computer network for the control of the speech traffic. The programs were developed according to the structured progranming approach leading to programs of modular construction. Two simulation methods are used for the speech traffic: the roulette method and the time-true method. The first is economical but has some restriction, while the second is expensive but gives comprehensive answers. The proposed control network operates at three hierarchical levels performing various control functions which include: the setting-up and clearing-down of calls, the hand-over of calls between cells and the address-changing of mobiles travelling between cities. The results demonstrate the feasibility of the control netwvork and indicate that small mini -computers inter-connected via voice grade data channels would be capable of providing satisfactory control

Distributed control of computer communication systems

Flow control in Computer Communication systems is generally a multi-layered structure, consisting of several mechanisms operating independently at different levels. Evaluation of the performance of networks in which different flow control mechanisms act simultaneously is an important area of research, and is examined in depth in this thesis. This thesis presents the modelling of a finite resource computer communication network equipped with three levels of flow control, based on closed queueing network theory. The flow control mechanisms considered are: end-to-end control of virtual circuits, network access control of external messages at the entry nodes and the hop level control between nodes. The model is solved by a heuristic technique, based on an equivalent reduced network and the heuristic extensions to the mean value analysis algorithm. The method has significant computational advantages, and overcomes the limitations of the exact methods. It can be used to solve large network models with finite buffers and many virtual circuits. The model and its heuristic solution are validated by simulation. The interaction between the three levels of flow control are investigated. A queueing model is developed for the admission delay on virtual circuits with end-to-end control, in which messages arrive from independent Poisson sources. The selection of optimum window limit is considered. Several advanced network access schemes are postulated to improve the network performance as well as that of selected traffic streams, and numerical results are presented. A model for the dynamic control of input traffic is developed. Based on Markov decision theory, an optimal control policy is formulated. Numerical results are given and throughput-delay performance is shown to be better with dynamic control than with static control.

Emulation of dynamic computer models with multivariate output

This preliminary report describes work carried out as part of work package 1.2 of the MUCM research project. The report is split in two parts: the ?rst part (Sections 1 and 2) summarises the state of the art in emulation of computer models, while the second presents some initial work on the emulation of dynamic models. In the ?rst part, we describe the basics of emulation, introduce the notation and put together the key results for the emulation of models with single and multiple outputs, with or without the use of mean function. In the second part, we present preliminary results on the chaotic Lorenz 63 model. We look at emulation of a single time step, and repeated application of the emulator for sequential predic- tion. After some design considerations, the emulator is compared with the exact simulator on a number of runs to assess its performance. Several general issues related to emulating dynamic models are raised and discussed. Current work on the larger Lorenz 96 model (40 variables) is presented in the context of dimension reduction, with results to be provided in a follow-up report. The notation used in this report are summarised in appendix.

An Investigation into the adoption and implementation of computer aided production management systems:using the Rogers model of adoption and implementation and a social constuctionist account of technology

The research investigates the processes of adoption and implementation, by organisations, of computer aided production management systems (CAPM). It is organised around two different theoretical perspectives. The first part is informed by the Rogers model of the diffusion, adoption and implementation of innovations, and the second part by a social constructionist approach to technology. Rogers' work is critically evaluated and a model of adoption and implementation is distilled from it and applied to a set of empirical case studies. In the light of the case study data, strengths and weaknesses of the model are identified. It is argued that the model is too rational and linear to provide an adequate explanation of adoption processes. It is useful for understanding processes of implementation but requires further development. The model is not able to adequately encompass complex computer based technologies. However, the idea of 'reinvention' is identified as Roger's key concept but it needs to be conceptually extended. Both Roger's model and definition of CAPM found in the literature from production engineering tend to treat CAPM in objectivist terms. The problems with this view are addressed through a review of the literature on the sociology of technology, and it is argued that a social constructionist approach offers a more useful framework for understanding CAPM, its nature, adoption, implementation, and use. CAPM it is argued, must be understood on terms of the ways in which it is constituted in discourse, as part of a 'struggle for meaning' on the part of academics, professional engineers, suppliers, and users.

Computer aided manufacturing of geometric models

As systems for computer-aided-design and production of mechanical parts have developed, there has arisen a need for techniques for the comprehensive description of the desired part, including its 3-D shape. The creation and manipulation of shapes is generally known as geometric modelling. It is desirable that links be established between geometric modellers and machining programs. Currently, unbounded APT and some bounded geometry systems are being widely used in manufacturing industry for machining operations such as: milling, drilling, boring and turning, applied mainly to engineering parts. APT systems, however, are presently only linked to wire-frame drafting systems. The combination of a geometric modeller and APT will provide a powerful manufacturing system for industry from the initial design right through part manufacture using NC machines. This thesis describes a recently developed interface (ROMAPT) between a bounded geometry modeller (ROMULUS) and an unbounded NC processor (APT). A new set of theoretical functions and practical algorithms for the computer aided manufacturing of 3D solid geometric model has been investigated. This work has led to the development of a sophisticated computer program, ROMAPT, which provides a new link between CAD (in form of a goemetric modeller ROMULUS) and CAM (in form of the APT NC system). ROMAPT has been used to machine some engineering prototypes successfully both in soft foam material and aluminium. It has been demonstrated above that the theory and algorithms developed by the author for the development of computer aided manufacturing of 3D solid modelling are both valid and applicable. ROMAPT allows the full potential of a solid geometric modeller (ROMULUS) to be further exploited for NC applications without requiring major investment in new NC processor. ROMAPT supports output in APT-AC, APT4 and the CAM-I SSRI NC languages.

Computer integrated monitoring

Computer integrated monitoring is a very large area in engineering where on-line, real time data acquisition with the aid of sensors is the solution to many problems in the manufacturing industry as opposed to the old data logging method by graphics analysis. The raw data which is collected this way however is useless in the absence of a proper computerized management system. The transfer of data between the management and the shop floor processes has been impossible in the past unless all the computers in the system were totally compatible with each other. This limits the efficiency of the systems because they get governed by the limitations of the computers. General Motors of U.S.A. have recently started research on a new standard called the Manufacturing Automation Protocol (MAP) which is expected to allow data transfer between different types of computers. This is still in early development stages and also is currently very expensive. This research programme shows how such a shop floor data acquisition system and a complete management system on entirely different computers can be integrated together to form a single system by achieving data transfer communications using a cheaper but a superior alternative to MAP. Standard communication character sets and hardware such as ASCII and UARTs have been used in this method but the technique is so powerful that totally incompatible computers are shown to run different programs (in different languages) simultaneously and yet receive data from each other and process in their own CPUs with no human intervention.

Computer-assisted production scheduling, planning and control in foundries

The present study describes a pragmatic approach to the implementation of production planning and scheduling techniques in foundries of all types and looks at the use of `state-of-the-art' management control and information systems. Following a review of systems for the classification of manufacturing companies, a definitive statement is made which highlights the important differences between foundries (i.e. `component makers') and other manufacturing companies (i.e. `component buyers'). An investigation of the manual procedures which are used to plan and control the manufacture of components reveals the inherent problems facing foundry production management staff, which suggests the unsuitability of many manufacturing techniques which have been applied to general engineering companies. From the literature it was discovered that computer-assisted systems are required which are primarily `information-based' rather than `decision based', whilst the availability of low-cost computers and `packaged-software' has enabled foundries to `get their feet wet' without the financial penalties which characterized many of the early attempts at computer-assistance (i.e. pre-1980). Moreover, no evidence of a single methodology for foundry scheduling emerged from the review. A philosophy for the development of a CAPM system is presented, which details the essential information requirements and puts forward proposals for the subsequent interactions between types of information and the sub-system of CAPM which they support. The work developed was oriented specifically at the functions of production planning and scheduling and introduces the concept of `manual interaction' for effective scheduling. The techniques developed were designed to use the information which is readily available in foundries and were found to be practically successful following the implementation of the techniques into a wide variety of foundries. The limitations of the techniques developed are subsequently discussed within the wider issues which form a CAPM system, prior to a presentation of the conclusions which can be drawn from the study.

Computer integrated manufacturing control

Many manufacturing companies have long endured the problems associated with the presence of `islands of automation'. Due to rapid computerisation, `islands' such as Computer-Aided Design (CAD), Computer-Aided Manufacturing (CAM), Flexible Manufacturing Systems (FMS) and Material Requirement Planning (MRP), have emerged, and with a lack of co-ordination, often lead to inefficient performance of the overall system. The main objective of Computer-Integrated Manufacturing (CIM) technology is to form a cohesive network between these islands. Unfortunately, a commonly used approach - the centralised system approach, has imposed major technical constraints and design complication on development strategies. As a consequence, small companies have experienced difficulties in participating in CIM technology. The research described in this thesis has aimed to examine alternative approaches to CIM system design. Through research and experimentation, the cellular system approach, which has existed in the form of manufacturing layouts, has been found to simplify the complexity of an integrated manufacturing system, leading to better control and far higher system flexibility. Based on the cellular principle, some central management functions have also been distributed to smaller cells within the system. This concept is known, specifically, as distributed planning and control. Through the development of an embryo cellular CIM system, the influence of both the cellular principle and the distribution methodology have been evaluated. Based on the evidence obtained, it has been concluded that distributed planning and control methodology can greatly enhance cellular features within an integrated system. Both the cellular system approach and the distributed control concept will therefore make significant contributions to the design of future CIM systems, particularly systems designed with respect to small company requirements.

Computer integrated manufacturing (CIM) and the principle of business control

In response to the increasing international competitiveness, many manufacturing businesses are rethinking their management strategies and philosophies towards achieving a computer integrated environment. The explosive growth in Advanced Manufacturing Technology (AMI) has resulted in the formation of functional "Islands of Automation" such as Computer Aided Design (CAD), Computer Aided Manufacturing (CAM), Computer Aided Process Planning (CAPP) and Manufacturing Resources Planning (MRPII). This has resulted in an environment which has focussed areas of excellence and poor overall efficiency, co-ordination and control. The main role of Computer Integrated Manufacturing (CIM) is to integrate these islands of automation and develop a totally integrated and controlled environment. However, the various perceptions of CIM, although developing, remain focussed on a very narrow integration scope and have consequently resulted in mere linked islands of automation with little improvement in overall co-ordination and control. This thesis, that is the research described within, develops and examines a more holistic view of CIM, which is based on the integration of various business elements. One particular business element, namely control, has been shown to have a multi-facetted and underpinning relationship with the CIM philosophy. This relationship impacts various CIM system design aspects including the CIM business analysis and modelling technique, the specification of systems integration requirements, the CIM system architectural form and the degree of business redesign. The research findings show that fundamental changes to CIM system design are required; these are incorporated in a generic CIM design methodology. The affect and influence of this holistic view of CIM on a manufacturing business has been evaluated through various industrial case study applications. Based on the evidence obtained, it has been concluded that this holistic, control based approach to CIM can provide a greatly improved means of achieving a totally integrated and controlled business environment. This generic CIM methodology will therefore make a significant contribution to the planning, modelling, design and development of future CIM systems.

A study of thermodynamic characteristics and predictive computer modelling of an air to water heat pump system

A study on heat pump thermodynamic characteristics has been made in the laboratory on a specially designed and instrumented air to water heat pump system. The design, using refrigerant R12, was based on the requirement to produce domestic hot water at a temperature of about 50 °C and was assembled in the laboratory. All the experimental data were fed to a microcomputer and stored on disk automatically from appropriate transducers via amplifier and 16 channel analogue to digital converters. The measurements taken were R12 pressures and temperatures, water and R12 mass flow rates, air speed, fan and compressor input powers, water and air inlet and outlet temperatures, wet and dry bulb temperatures. The time interval between the observations could be varied. The results showed, as expected, that the COP was higher at higher air inlet temperatures and at lower hot water output temperatures. The optimum air speed was found to be at a speed when the fan input power was about 4% of the condenser heat output. It was also found that the hot water can be produced at a temperature higher than the appropriate R12 condensing temperature corresponding to condensing pressure. This was achieved by condenser design to take advantage of discharge superheat and by further heating the water using heat recovery from the compressor. Of the input power to the compressor, typically about 85% was transferred to the refrigerant, 50 % by the compression work and 35% due to the heating of the refrigerant by the cylinder wall, and the remaining 15% (of the input power) was rejected to the cooling medium. The evaporator effectiveness was found to be about 75% and sensitive to the air speed. Using the data collected, a steady state computer model was developed. For given input conditions s air inlet temperature, air speed, the degree of suction superheat , water inlet and outlet temperatures; the model is capable of predicting the refrigerant cycle, compressor efficiency, evaporator effectiveness, condenser water flow rate and system Cop.

The development of a computer aided system for adaptive budgeting in a confectionery manufacturing firm

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Air traffic controller reactions to computer assistance

The research was instigated by the Civil Aviation Authority (CAA) to examine the implications for air traffic controllers' (ATCO) job satisfaction of the possible introduction of systems incorporating computer-assisted decision making. Additional research objectives were to assess the possible costs of reductions in ATCO job satisfaction, and to recommend appropriate task allocation between ATCOs and computer for future systems design (Chapter 1). Following a review of the literature (Chapter 2) it is argued that existing approaches to systems and job design do not allow for a sufficiently early consideration of employee needs and satisfactions in the design of complex systems. The present research develops a methodology for assessing affective reactions to an existing system as a basis for making reommendations for future systems design (Chapter 3). The method required analysis of job content using two techniques: (a) task analysis (Chapter 4.1) and (b) the Job Diagnostic Survey (JDS). ATCOs' affective reactions to the several operational positions on which they work were investigated at three levels of detail: (a) Reactions to positions, obtained by ranking techniques (Chapter 4.2); (b) Reactions to job characteristics, obtained by use of JDS (Chapter 4.3); and (c) Reactions to tasks, obtained by use of Repertory Grid technique (Chapter 4.4). The conclusion is drawn that ATCOs' motivation and satisfaction is greatly dependent on the presence of challenge, often through tasks requiring the use of decision making and other cognitive skills. Results suggest that the introduction of systems incorporating computer-assisted decision making might result in financial penalties for the CAA and significant reductions in job satisfaction for ATCOs. General recommendations are made for allocation of tasks in future systems design (Chapter 5).