Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 x 10(11) possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 angstrom r.m.s. deviation of C alpha atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes.

Probabilistic world modelling for distributed team planning

This paper describes an application of decoupled probabilistic world modeling to achieve team planning. The research is based on the principle that tbe action selection mechanism of a member in a robot team cm select am effective action if a global world model is available to all team members. In the real world, the sensors are imprecise, and are individual to each robot, hence providing each robot a partial and unique view about the environment. We address this problem by creating a probabilistic global view on each agent by combining the perceptual information from each robot. This probsbilistie view forms the basis for selecting actions to achieve the team goal in a dynamic environment. Experiments have been carried ont to investigate the effectiveness of this principle using custom-built robots for real world performance, in addition, to extensive simulation results. The results show an improvement in team effectiveness when using probabilistic world modeling based on perception sharing for team planning.

A study of business user based information systems development, and modelling success factors

This thesis describes research into business user involvement in the information systems application building process. The main interest of this research is in establishing and testing techniques to quantify the relationships between identified success factors and the outcome effectiveness of 'business user development' (BUD). The availability of a mechanism to measure the levels of the success factors, and quantifiably relate them to outcome effectiveness, is important in that it provides an organisation with the capability to predict and monitor effects on BUD outcome effectiveness. This is particularly important in an era where BUD levels have risen dramatically, user centred information systems development benefits are recognised as significant, and awareness of the risks of uncontrolled BUD activity is becoming more widespread. This research targets the measurement and prediction of BUD success factors and implementation effectiveness for particular business users. A questionnaire instrument and analysis technique has been tested and developed which constitutes a tool for predicting and monitoring BUD outcome effectiveness, and is based on the BUDES (Business User Development Effectiveness and Scope) research model - which is introduced and described in this thesis. The questionnaire instrument is designed for completion by 'business users' - the target community being more explicitly defined as 'people who primarily have a business role within an organisation'. The instrument, named BUD ESP (Business User Development Effectiveness and Scope Predictor), can readily be used with survey participants, and has been shown to give meaningful and representative results.

A semantic modelling approach to knowledge based statistical software

The topic of this thesis is the development of knowledge based statistical software. The shortcomings of conventional statistical packages are discussed to illustrate the need to develop software which is able to exhibit a greater degree of statistical expertise, thereby reducing the misuse of statistical methods by those not well versed in the art of statistical analysis. Some of the issues involved in the development of knowledge based software are presented and a review is given of some of the systems that have been developed so far. The majority of these have moved away from conventional architectures by adopting what can be termed an expert systems approach. The thesis then proposes an approach which is based upon the concept of semantic modelling. By representing some of the semantic meaning of data, it is conceived that a system could examine a request to apply a statistical technique and check if the use of the chosen technique was semantically sound, i.e. will the results obtained be meaningful. Current systems, in contrast, can only perform what can be considered as syntactic checks. The prototype system that has been implemented to explore the feasibility of such an approach is presented, the system has been designed as an enhanced variant of a conventional style statistical package. This involved developing a semantic data model to represent some of the statistically relevant knowledge about data and identifying sets of requirements that should be met for the application of the statistical techniques to be valid. Those areas of statistics covered in the prototype are measures of association and tests of location.

Modelling e-business processes:a component-based simulation approach

With new and emerging e-business technologies to transform business processes, it is important to understand how those technologies will affect the performance of a business. Will the overall business process be cheaper, faster and more accurate or will a sub-optimal change have been implemented? The use of simulation to model the behaviour of business processes is well established, and it has been applied to e-business processes to understand their performance in terms of measures such as lead-time, cost and responsiveness. This paper introduces the concept of simulation components that enable simulation models of e-business processes to be built quickly from generic e-business templates. The paper demonstrates how these components were devised, as well as the results from their application through case studies.

Modelling and simulation of biomass gasification in a circulating fluidized bed reactor

Computational Fluid Dynamics (CFD) has found great acceptance among the engineering community as a tool for research and design of processes that are practically difficult or expensive to study experimentally. One of these processes is the biomass gasification in a Circulating Fluidized Bed (CFB). Biomass gasification is the thermo-chemical conversion of biomass at a high temperature and a controlled oxygen amount into fuel gas, also sometime referred to as syngas. Circulating fluidized bed is a type of reactor in which it is possible to maintain a stable and continuous circulation of solids in a gas-solid system. The main objectives of this thesis are four folds: (i) Develop a three-dimensional predictive model of biomass gasification in a CFB riser using advanced Computational Fluid Dynamic (CFD) (ii) Experimentally validate the developed hydrodynamic model using conventional and advanced measuring techniques (iii) Study the complex hydrodynamics, heat transfer and reaction kinetics through modelling and simulation (iv) Study the CFB gasifier performance through parametric analysis and identify the optimum operating condition to maximize the product gas quality. Two different and complimentary experimental techniques were used to validate the hydrodynamic model, namely pressure measurement and particle tracking. The pressure measurement is a very common and widely used technique in fluidized bed studies, while, particle tracking using PEPT, which was originally developed for medical imaging, is a relatively new technique in the engineering field. It is relatively expensive and only available at few research centres around the world. This study started with a simple poly-dispersed single solid phase then moved to binary solid phases. The single solid phase was used for primary validations and eliminating unnecessary options and steps in building the hydrodynamic model. Then the outcomes from the primary validations were applied to the secondary validations of the binary mixture to avoid time consuming computations. Studies on binary solid mixture hydrodynamics is rarely reported in the literature. In this study the binary solid mixture was modelled and validated using experimental data from the both techniques mentioned above. Good agreement was achieved with the both techniques. According to the general gasification steps the developed model has been separated into three main gasification stages; drying, devolatilization and tar cracking, and partial combustion and gasification. The drying was modelled as a mass transfer from the solid phase to the gas phase. The devolatilization and tar cracking model consist of two steps; the devolatilization of the biomass which is used as a single reaction to generate the biomass gases from the volatile materials and tar cracking. The latter is also modelled as one reaction to generate gases with fixed mass fractions. The first reaction was classified as a heterogeneous reaction while the second reaction was classified as homogenous reaction. The partial combustion and gasification model consisted of carbon combustion reactions and carbon and gas phase reactions. The partial combustion considered was for C, CO, H2 and CH4. The carbon gasification reactions used in this study is the Boudouard reaction with CO2, the reaction with H2O and Methanation (Methane forming reaction) reaction to generate methane. The other gas phase reactions considered in this study are the water gas shift reaction, which is modelled as a reversible reaction and the methane steam reforming reaction. The developed gasification model was validated using different experimental data from the literature and for a wide range of operating conditions. Good agreement was observed, thus confirming the capability of the model in predicting biomass gasification in a CFB to a great accuracy. The developed model has been successfully used to carry out sensitivity and parametric analysis. The sensitivity analysis included: study of the effect of inclusion of various combustion reaction; and the effect of radiation in the gasification reaction. The developed model was also used to carry out parametric analysis by changing the following gasifier operating conditions: fuel/air ratio; biomass flow rates; sand (heat carrier) temperatures; sand flow rates; sand and biomass particle sizes; gasifying agent (pure air or pure steam); pyrolysis models used; steam/biomass ratio. Finally, based on these parametric and sensitivity analysis a final model was recommended for the simulation of biomass gasification in a CFB riser.

Optimisation of two-stage raman converter based on phosphosilicate core fibre:Modelling and experiment

Parameter optimization of a two-stage Raman fibre converters (RFC) based on phosphosilicate core fiber was presented. The optimal operational regime was determined and tolerance of the converter against variations of laser parameters was analyzed. Converter was pumped by ytterbium-doped double-clad fibre laser with a maximum output power of 3.8W at 1061 nm. A phosphosilicate-core RFC with enhanced performance was fabricated using the results of numerical modelling.

Conceptual Building Information Modelling Framework for Whole‐house Refurbishment based on LCC and LCA

The UK government aims at achieving 80% CO2 emission reduction by 2050 which requires collective efforts across all the UK industry sectors. In particular, the housing sector has a large potential to contribute to achieving the aim because the housing sector alone accounts for 27% of the total UK CO2 emission, and furthermore, 87% of the housing which is responsible for current 27% CO2 emission will still stand in 2050. Therefore, it is essential to improve energy efficiency of existing housing stock built with low energy efficiency standard. In order for this, a whole‐house needs to be refurbished in a sustainable way by considering the life time financial and environmental impacts of a refurbished house. However, the current refurbishment process seems to be challenging to generate a financially and environmentally affordable refurbishment solution due to the highly fragmented nature of refurbishment practice and a lack of knowledge and skills about whole‐house refurbishment in the construction industry. In order to generate an affordable refurbishment solution, diverse information regarding costs and environmental impacts of refurbishment measures and materials should be collected and integrated in right sequences throughout the refurbishment project life cycle among key project stakeholders. Consequently, various researchers increasingly study a way of utilizing Building Information Modelling (BIM) to tackle current problems in the construction industry because BIM can support construction professionals to manage construction projects in a collaborative manner by integrating diverse information, and to determine the best refurbishment solution among various alternatives by calculating the life cycle costs and lifetime CO2 performance of a refurbishment solution. Despite the capability of BIM, the BIM adoption rate is low with 25% in the housing sector and it has been rarely studied about a way of using BIM for housing refurbishment projects. Therefore, this research aims to develop a BIM framework to formulate a financially and environmentally affordable whole‐house refurbishment solution based on the Life Cycle Costing (LCC) and Life Cycle Assessment (LCA) methods simultaneously. In order to achieve the aim, a BIM feasibility study was conducted as a pilot study to examine whether BIM is suitable for housing refurbishment, and a BIM framework was developed based on the grounded theory because there was no precedent research. After the development of a BIM framework, this framework was examined by a hypothetical case study using BIM input data collected from questionnaire survey regarding homeowners’ preferences for housing refurbishment. Finally, validation of the BIM framework was conducted among academics and professionals by providing the BIM framework and a formulated refurbishment solution based on the LCC and LCA studies through the framework. As a result, BIM was identified as suitable for housing refurbishment as a management tool, and it is timely for developing the BIM framework. The BIM framework with seven project stages was developed to formulate an affordable refurbishment solution. Through the case study, the Building Regulation is identified as the most affordable energy efficiency standard which renders the best LCC and LCA results when it is applied for whole‐house refurbishment solution. In addition, the Fabric Energy Efficiency Standard (FEES) is recommended when customers are willing to adopt high energy standard, and the maximum 60% of CO2 emissions can be reduced through whole‐house fabric refurbishment with the FEES. Furthermore, limitations and challenges to fully utilize BIM framework for housing refurbishment were revealed such as a lack of BIM objects with proper cost and environmental information, limited interoperability between different BIM software and limited information of LCC and LCA datasets in BIM system. Finally, the BIM framework was validated as suitable for housing refurbishment projects, and reviewers commented that the framework can be more practical if a specific BIM library for housing refurbishment with proper LCC and LCA datasets is developed. This research is expected to provide a systematic way of formulating a refurbishment solution using BIM, and to become a basis for further research on BIM for the housing sector to resolve the current limitations and challenges. Future research should enhance the BIM framework by developing more detailed process map and develop BIM objects with proper LCC and LCA Information.

Reliability modelling and verification of manufacturing processes based on process knowledge management

Reliability modelling and verification is indispensable in modern manufacturing, especially for product development risk reduction. Based on the discussion of the deficiencies of traditional reliability modelling methods for process reliability, a novel modelling method is presented herein that draws upon a knowledge network of process scenarios based on the analytic network process (ANP). An integration framework of manufacturing process reliability and product quality is presented together with a product development and reliability verification process. According to the roles of key characteristics (KCs) in manufacturing processes, KCs are organised into four clusters, that is, product KCs, material KCs, operation KCs and equipment KCs, which represent the process knowledge network of manufacturing processes. A mathematical model and algorithm is developed for calculating the reliability requirements of KCs with respect to different manufacturing process scenarios. A case study on valve-sleeve component manufacturing is provided as an application example of the new reliability modelling and verification procedure. This methodology is applied in the valve-sleeve component manufacturing processes to manage and deploy production resources.

Evaluation of climate change scenarios based on aquatic food web modelling

In the years 2004 and 2005 we collected samples of phytoplankton, zooplankton and macroinvertebrates in an artificial small pond in Budapest. We set up a simulation model predicting the abundance of the cyclopoids, Eudiaptomus zachariasi and Ischnura pumilio by considering only temperature as it affects the abundance of population of the previous day. Phytoplankton abundance was simulated by considering not only temperature, but the abundance of the three mentioned groups. This discrete-deterministic model could generate similar patterns like the observed one and testing it on historical data was successful. However, because the model was overpredicting the abundances of Ischnura pumilio and Cyclopoida at the end of the year, these results were not considered. Running the model with the data series of climate change scenarios, we had an opportunity to predict the individual numbers for the period around 2050. If the model is run with the data series of the two scenarios UKHI and UKLO, which predict drastic global warming, then we can observe a decrease in abundance and shift in the date of the maximum abundance occurring (excluding Ischnura pumilio, where the maximum abundance increases and it occurs later), whereas under unchanged climatic conditions (BASE scenario) the change in abundance is negligible. According to the scenarios GFDL 2535, GFDL 5564 and UKTR, a transition could be noticed.

Analysis of climate change scenarios based on modelling of the seasonal dynamics of a Danubian copepod species

Climate change is one of the most crucial ecological problems of our age with great influence. Seasonal dynamics of aquatic communities are — among others — regulated by the climate, especially by temperature. In this case study we attempted the simulation modelling of the seasonal dynamics of a copepod species, Cyclops vicinus, which ranks among the zooplankton community, based on a quantitative database containing ten years of data from the Danube’s Göd area. We set up a simulation model predicting the abundance of Cyclops vicinus by considering only temperature as it affects the abundance of population. The model was adapted to eight years of daily temperature data observed between 1981 and 1994 and was tested successfully with the additional data of two further years. The model was run with the data series of climate change scenarios specified for the period around 2070- 2100. On the other hand we looked for the geographically analogous areas with the Göd region which are mostly similar to the future climate of the Göd area. By means of the above-mentioned points we can get a view how the climate of the region will change by the end of the 21st century, and the way the seasonal dynamics of a chosen planktonic crustacean species may follow this change. According to our results the area of Göd will be similar to the northern region of Greece. The maximum abundance of the examined species occurs a month to one and a half months earlier, moreover larger variances are expected between years in respect of the abundance. The deviations are expected in the direction of smaller or significantly larger abundance not observed earlier.