Predicting structural disruption of proteins caused by crossover

We present a machine learning model that predicts a structural disruption score from a protein’s primary structure. SCHEMA was introduced by Frances Arnold and colleagues as a method for determining putative recombination sites of a protein on the basis of the full (PDB) description of its structure. The present method provides an alternative to SCHEMA that is able to determine the same score from sequence data only. Circumventing the need for resolving the full structure enables the exploration of yet unresolved and even hypothetical sequences for protein design efforts. Deriving the SCHEMA score from a primary structure is achieved using a two step approach: first predicting a secondary structure from the sequence and then predicting the SCHEMA score from the predicted secondary structure. The correlation coefficient for the prediction is 0.88 and indicates the feasibility of replacing SCHEMA with little loss of precision. ©2005 IEEE

An automated failure mode and effect analysis based on high-level design specificication with behavior trees

Formal methods have significant benefits for developing safety critical systems, in that they allow for correctness proofs, model checking safety and liveness properties, deadlock checking, etc. However, formal methods do not scale very well and demand specialist skills, when developing real-world systems. For these reasons, development and analysis of large-scale safety critical systems will require effective integration of formal and informal methods. In this paper, we use such an integrative approach to automate Failure Modes and Effects Analysis (FMEA), a widely used system safety analysis technique, using a high-level graphical modelling notation (Behavior Trees) and model checking. We inject component failure modes into the Behavior Trees and translate the resulting Behavior Trees to SAL code. This enables us to model check if the system in the presence of these faults satisfies its safety properties, specified by temporal logic formulas. The benefit of this process is tool support that automates the tedious and error-prone aspects of FMEA.

Design and characterisation of novel blends of poly(lactic acid)

This thesis is concerned with the effect of polymer structure on miscibility of the three component blends based on poly(lactic acid) (PLA) with using blending techniques. The examination of novel PLA homologues (pre-synthesised poly(a-esters)), including a range of aliphatic and aromatic poly(a-esters) is an important aspect of the work. Because of their structural simplicity and similarity to PLA, they provide an ideal system to study the effect of polyester structures on the miscibility of PLA polymer blends. The miscibility behaviour of the PLA homologues is compared with other aliphatic polyesters (e.g. poly(e-caprolactone) (PCL), poly(hydroxybutyrate hydroxyvalerate) (P(HB-HV)), together with a series of cellulose-based polymers (e.g. cellulose acetate butyrate (CAB)). The work started with the exploration the technique used for preliminary observation of the miscibility of blends referred to as “a rapid screening method” and then the miscibility of binary blends was observed and characterised by percent transmittance together with the Coleman and Painter miscibility approach. However, it was observed that symmetrical structures (e.g. a1(dimethyl), a2(diethyl)) promote the well-packing which restrict their chains from intermingling into poly(L-lactide) (PLLA) chains and leads the blends to be immiscible, whereas, asymmetrical structures (e.g. a4(cyclohexyl)) behave to the contrary. a6(chloromethyl-methyl) should interact well with PLLA because of the polar group of chloride to form interactions, but it does not. It is difficult to disrupt the helical structure of PLLA. PLA were immiscible with PCL, P(HB-HV), or compatibiliser (e.g. G40, LLA-co-PCL), but miscible with CAB which is a hydrogen-bonded polymer. However, these binary blends provided a useful indication for the exploration the novel three component blends. In summary, the miscibility of the three-component blends are miscible even if only two polymers are miscible. This is the benefit for doing the three components blend in this thesis, which is not an attempt to produce a theoretical explanation for the miscibility of three components blend system.

Design of improved membrane protein production experiments:quantitation of the host response

Eukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial-and-error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high-performance bioreactors under tightlydefined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly-controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels of FPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology. Copyright © 2005 The Protein Society.

Design and implementation of graphical user interfaces for complex simulations

The development of increasingly powerful computers, which has enabled the use of windowing software, has also opened the way for the computer study, via simulation, of very complex physical systems. In this study, the main issues related to the implementation of interactive simulations of complex systems are identified and discussed. Most existing simulators are closed in the sense that there is no access to the source code and, even if it were available, adaptation to interaction with other systems would require extensive code re-writing. This work aims to increase the flexibility of such software by developing a set of object-oriented simulation classes, which can be extended, by subclassing, at any level, i.e., at the problem domain, presentation or interaction levels. A strategy, which involves the use of an object-oriented framework, concurrent execution of several simulation modules, use of a networked windowing system and the re-use of existing software written in procedural languages, is proposed. A prototype tool which combines these techniques has been implemented and is presented. It allows the on-line definition of the configuration of the physical system and generates the appropriate graphical user interface. Simulation routines have been developed for the chemical recovery cycle of a paper pulp mill. The application, by creation of new classes, of the prototype to the interactive simulation of this physical system is described. Besides providing visual feedback, the resulting graphical user interface greatly simplifies the interaction with this set of simulation modules. This study shows that considerable benefits can be obtained by application of computer science concepts to the engineering domain, by helping domain experts to tailor interactive tools to suit their needs.

Applications of Reissner's principle to structural dynamics

The analysis and prediction of the dynamic behaviour of s7ructural components plays an important role in modern engineering design. :n this work, the so-called "mixed" finite element models based on Reissnen's variational principle are applied to the solution of free and forced vibration problems, for beam and :late structures. The mixed beam models are obtained by using elements of various shape functions ranging from simple linear to complex cubic and quadratic functions. The elements were in general capable of predicting the natural frequencies and dynamic responses with good accuracy. An isoparametric quadrilateral element with 8-nodes was developed for application to thin plate problems. The element has 32 degrees of freedom (one deflection, two bending and one twisting moment per node) which is suitable for discretization of plates with arbitrary geometry. A linear isoparametric element and two non-conforming displacement elements (4-node and 8-node quadrilateral) were extended to the solution of dynamic problems. An auto-mesh generation program was used to facilitate the preparation of input data required by the 8-node quadrilateral elements of mixed and displacement type. Numerical examples were solved using both the mixed beam and plate elements for predicting a structure's natural frequencies and dynamic response to a variety of forcing functions. The solutions were compared with the available analytical and displacement model solutions. The mixed elements developed have been found to have significant advantages over the conventional displacement elements in the solution of plate type problems. A dramatic saving in computational time is possible without any loss in solution accuracy. With beam type problems, there appears to be no significant advantages in using mixed models.

Problem solving in architectural design

This thesis is presented in two parts. The first part is an attempt to set out a framework of factors influencing the problem solving stage of the architectural design process. The discussion covers the nature of architectural problems and some of the main ways in which they differ from other types of design problems. The structure of constraints that both the problem and the architect impose upon solutions are seen as of great importance in defining the type of design problem solving situation. The problem solver, or architect, is then studied. The literature of the psychology of thinking is surveyed for relevant work . All of the traditional schools of psychology are found wanting in terms of providing a comprehensive theory of thinking. Various types of thinking are examined, particularly structural and productive thought, for their relevance to design problem solving. Finally some reported common traits of architects are briefly reviewed. The second section is a report of u~o main experiments which model some aspects of architectural design problem solving. The first experiment examines the way in which architects come to understand the structure of their problems. The performances of first and final year architectural students are compared with those of postgraduate science students and sixth form pupils. On the whole these groups show significantly different results and also different cognitive strategies. The second experiment poses design problems which involve both subjective and objective criteria, and examines the way in which final year architectural students are able to relate the different types of constraint produced. In the final section the significance of all the results is suggested. Some educational and methodological implications are discussed and some further experiments and investigations are proposed.

The design of novel antifolates against pneumocystis carinii

The pneumonia caused by Pneumocystis carinii is ultimately responsible for the death of many acquired immunodeficiency syndrome (AIDS) patients. Large doses of trimethoprim and pyrimethamine in combination with a sulphonamide and/or pentamidine suppress the infection but produce serious side-effects and seldom prevent recurrence after treatment withdrawal. However, the partial success of the aforementioned antifolates, and also trimetrexate used alone, does suggest dihydrofolate reductase (DHFR) as a target for the development of antipneumocystis agents. From the DHFR inhibitory activities of 3'-substituted pyrimethamine analogues it was suggested that the 3'-(3'',3''-dimethyltriazen-1''-yl) substituent may be responsible for the greater activity for the P.carinii over the mammalian enzyme. Crystallographic and molecular modeling studies revealed considerable geometrical and electronic differences between the triazene and the chemically related formamidine functions that may account for the differences in DHFR inhibitory profiles. Structural and electronic parameters calculated for a series of 3'-(3'',3''-disubstitutedtriazen-1''-yl) pyrimethamine analogues did not correlate with the DHFR inhibitory activities. However, the in vitro screening against P.carinii DHFR revealed that the 3''-hydroxyethyl-3''-benzyl analogue was the most active and selective. Models of the active sites of human and P.carinii DHFRs were constructed using DHFR sequence and structural homology data which had identified key residues involved in substrate and cofactor binding. Low energy conformations of the 3'',3''-dimethyl and 3''-hydroxyethyl-3''-benzyle analogues, determined from nuclear magnetic resonance studies and theoretical calculations, were docked by superimposing the diaminopyrimidine fragment onto a previously docked pyrimethamine analogue. Enzyme kinetic data supported the 3''-hydroxyethyl-3''-benzyl moiety being located in the NADPH binding groove. The 3''-benzyl substituent was able to locate to within 3 AA of a valine residue in the active site of P.carinii DHFR thereby producing a hydrophobic contact. The equivalent residue in human DHFR is threonine, more hydrophilic and less likely to be involved in such a contact. This difference may account for the greater inhibitory activity this analogue has for P.carinii DHFR and provide a basis for future drug design. From an in vivo model of PCP in immunosuppressed rats it was established that the 3"-hydroxyethyl-3"-benzyl analogue was able to reduce the.P.carinii burden more effectively with increasing doses, without causmg any visible signs of toxicity. However, equivalent doses were not as effective as pentamidine, a current treatment of choice for Pneumocystis carinii pneumonia.

Some aspects of the dynamic performance of machine tool structural joints

The work presented in this thesis is concerned with the dynamic behaviour of structural joints which are both loaded, and excited, normal to the joint interface. Since the forces on joints are transmitted through their interface, the surface texture of joints was carefully examined. A computerised surface measuring system was developed and computer programs were written. Surface flatness was functionally defined, measured and quantised into a form suitable for the theoretical calculation of the joint stiffness. Dynamic stiffness and damping were measured at various preloads for a range of joints with different surface textures. Dry clean and lubricated joints were tested and the results indicated an increase in damping for the lubricated joints of between 30 to 100 times. A theoretical model for the computation of the stiffness of dry clean joints was built. The model is based on the theory that the elastic recovery of joints is due to the recovery of the material behind the loaded asperities. It takes into account, in a quantitative manner, the flatness deviations present on the surfaces of the joint. The theoretical results were found to be in good agreement with those measured experimentally. It was also found that theoretical assessment of the joint stiffness could be carried out using a different model based on the recovery of loaded asperities into a spherical form. Stepwise procedures are given in order to design a joint having a particular stiffness. A theoretical model for the loss factor of dry clean joints was built. The theoretical results are in reasonable agreement with those experimentally measured. The theoretical models for the stiffness and loss factor were employed to evaluate the second natural frequency of the test rig. The results are in good agreement with the experimentally measured natural frequencies.

The structural properties of glassfibre reinforced plastics

The research work described in this thesis is concerned with the development of glassfibre reinforced plastics for structural uses in Civil Engineering construction. The first stage was primarily concerned with the design of GRP lamintes with structura1 properties and method of manufacture suitable for use with relatively large structural components. A cold setting, pressure moulding technique was developed which proved to be efficient in reducing the void content in the composite and minimising the exothermic effect due to curing. The effect of fibre content and fibre arrangement on strength and stiffness of the cornposite was studied and the maximum amount of' fibre content that could be reached by the adopted type of moulding technique was determined. The second stage of the project was concerned with the introduction of steel-wire "sheets" into the GRP cornposites, to take advantage of the high modulus of steel wire to improve the GRP stiffness and to reduce deformation. The experimental observations agreed reasonably well with theoretical predictions in both first and second stages of the work. The third stage was concerned with studying the stability of GRP flat rectangular plates subjected to uniaxial compression or pure shear, to simulate compression flanges or shear webs respectively. The investigation was concentrated on the effect of fibre arrangement in the plate on buckling load. The effect of the introduction of steel-wire sheets on the plate stability in compression was also investigated. The boundary conditions were chosen to be close to those usually assumed in built-up box-sections for both compression flanges and webs. The orthotropic plate and the mid-plane symmetric were used successfully in predicting the buckling load theoretically. In determining the buckling load experimentally, two methods were used. The Southwell plot method and electrical strain gauge method. The latter proved to be more reliable in predicting the buckling load than the former, especially for plates under uniaxial compression. Sample design charts for GRP plates that yield and buckle simultaneously under compression are also presented in the thesis. The final stage of the work dealt with the design and test of GRP beams. The investigation began by finding the optimum cross-section for a GRP beam. The cross-section which was developed was a thin walled corrugated section which showed higher stiffness than other cross-sections for the same cross-sectional area (i.e. box, I, and rectangular sections). A cold setting, hand layings technique was used in manufacturing these beams wbich were of nine types depending on the type of glass reinforcement employed and the arrangement of layers in the beam. The simple bending theory was used in the beam design and proved to be satisfactory in predicting the stresses and deflections. A factor of safety of 4 was chosen for design purposes and considered to be suitable for long term use under static load. Because of its relatively low modulus, GRP beams allowable deflection was limited to 1/120th of the span which was found to be adequate for design purposes. A general discussion of the behaviour of GRP composites and their place relative to the more conventional structural material was also presented in the thesis.

Design of an expandable manufacturing simulator through the application of object-oriented principles

In analysing manufacturing systems, for either design or operational reasons, failure to account for the potentially significant dynamics could produce invalid results. There are many analysis techniques that can be used, however, simulation is unique in its ability to assess detailed, dynamic behaviour. The use of simulation to analyse manufacturing systems would therefore seem appropriate if not essential. Many simulation software products are available but their ease of use and scope of application vary greatly. This is illustrated at one extreme by simulators which offer rapid but limited application whilst at the other simulation languages which are extremely flexible but tedious to code. Given that a typical manufacturing engineer does not posses in depth programming and simulation skills then the use of simulators over simulation languages would seem a more appropriate choice. Whilst simulators offer ease of use their limited functionality may preclude their use in many applications. The construction of current simulators makes it difficult to amend or extend the functionality of the system to meet new challenges. Some simulators could even become obsolete as users, demand modelling functionality that reflects the latest manufacturing system design and operation concepts. This thesis examines the deficiencies in current simulation tools and considers whether they can be overcome by the application of object-oriented principles. Object-oriented techniques have gained in popularity in recent years and are seen as having the potential to overcome any of the problems traditionally associated with software construction. There are a number of key concepts that are exploited in the work described in this thesis: the use of object-oriented techniques to act as a framework for abstracting engineering concepts into a simulation tool and the ability to reuse and extend object-oriented software. It is argued that current object-oriented simulation tools are deficient and that in designing such tools, object -oriented techniques should be used not just for the creation of individual simulation objects but for the creation of the complete software. This results in the ability to construct an easy to use simulator that is not limited by its initial functionality. The thesis presents the design of an object-oriented data driven simulator which can be freely extended. Discussion and work is focused on discrete parts manufacture. The system developed retains the ease of use typical of data driven simulators. Whilst removing any limitation on its potential range of applications. Reference is given to additions made to the simulator by other developers not involved in the original software development. Particular emphasis is put on the requirements of the manufacturing engineer and the need for Ihe engineer to carrv out dynamic evaluations.