Bacteriophage genomes show pervasive mosaicism, indicating that horizontal gene exchange plays a crucial role in their evolution. Phage genomes represent unique combinations of modules, each of them with a different phylogenetic history. Thus, a web-like, rather than a hierarchical scheme is needed for an appropriate representation of phage evolutionary relationships. Part of the virology community has long recognized this fact and calls for changing the traditional taxonomy that classifies tailed phages according to the type of genetic materials and phage tail and head/capsid morphologies. Moreover, based on morphological features, the current system depends on inspection of phage virions under the electron microscope and cannot directly classify prophages. With the genomic era, many phages have been sequenced that are not classified, calling for development of an automatic classification procedure that can cope with the sequencing pace. The ACLAME database provides a classification of phage proteins into families and assigns the families with at least 3 members to one or several functions. In the first contribution of this work, the relative contribution of those different protein families to the similarities between the phages is assessed using pair-wise similarity matrices. The modular character of phage genomes is readily visualized using heatmaps, which differ depending on the function of the proteins used to measure the similarity. Next, I propose a framework that allows for a reticulate classification of phages based on gene content (with statistical assessment of the significance of number of shared genes). Starting from gene/protein families, we built a weighted graph, where nodes represent phages and edges represent phage-phage similarities in terms of shared families. The topology of the network shows that most dsDNA phages form an interconnected group, confirming that dsDNA phages share a common gene pool, as proposed earlier. Differences are observed between temperate and virulent phages in the values of several centrality measures, which may correlate with different constraints to rampant recombination dictated by the phage lifestyle, and thus with a distinct evolutionary role in the phage population. To this graph I applied a two-step clustering method to generate a fuzzy classification of phages. Using this methodology, each phage is associated with a membership vector, which quantitatively characterizes the membership of the phage to the clusters. Alternatively, genes were clustered based on their ‘phylogenetic profiles’ to define ‘evolutionary cohesive modules’. Phages can then be described as composite of a set of modules from the collection of modules of the whole phage population. The relationships between phages define a network based on module sharing. Unlike the first network built from statistical significant number of shared genes, this second network allows for a direct exploration of the nature of the functions shared between the connected phages. This functionality of the module-based network runs at the expense of missing links due to genes that are not part of modules, but which are encoded in the first network. These approaches can easily focus on pre-defined modules for tracing one or several traits across the population. They provide an automatic and dynamic way to study relationships within the phage population. Moreover, they can be extended to the representation of populations of other mobile genetic elements or even to the entire mobilome. Finally, to enrich the phage sequence space, which in turn allows for a better assessment of phage diversity and evolution, I devise a prophage prediction tool. With this methodology, approximately 800 prophages are predicted in 266 among 800 replicons screened. The comparison of a subset of these predictions with a manually annotated set shows a sensitivity of 79% and a positive predictive value of 91%, this later value suggesting that the procedure makes few false predictions. The preliminary analysis of the predicted prophages indicates that many may constitute novel phage types. This work allows tracing guidelines for the classification and analysis of other mobile genetic elements. One can foresee that a pool of putative mobile genetic elements sequences can be extracted from the prokaryotic genomes and be further broken down in groups of related elements and evolutionary conserved modules. This would allow widening the picture of the evolutionary and functional relationships between these elements.

In predicting the likely behaviour of precast prestressed concrete flooring systems in fire using advanced finite element methods, an improved numerical model using the non-linear finite element program SAFIR has been developed in order to investigate the effects and the interaction of the surrounding structures and has been used extensively throughout this thesis. Note that fire induced spalling is not included in the analysis. In the numerical investigation of the new model, the reinforced concrete topping is modelled as part of the beam elements in order to predict the behaviour of single hollowcore concrete slabs, with various support conditions, under a Standard ISO fire. It is shown that the current approach using tendons that are anchored into the supporting beams leads to a major problem for precast prestressed flooring systems. In order to resolve this problem, a multi-spring connection model has been developed to include the old and new connection systems corresponding to the New Zealand Concrete Standard NZS 3101. The connection model with hollowcore slabs is validated against a published fire test. The investigation on restrained hollowcore floors is performed with various parameters and boundary support conditions. Numerical studies on various boundary support conditions show that the behaviour of hollowcore floors in fire is very sensitive to the existence of side beams. Further investigations on the effects of fire emergency beams, which reduce the transverse curvature of floors to improve fire resistance, are made on 4x1 multi-bay hollowcore floors with different arrangements of theses beams. The numerical studies show that fire emergency beams significantly increase the fire resistance. Code based equations which can calculate the shear resistance and splitting resistance are then introduced. The Eurocode equation can be modified with high temperature material properties to estimate the shear capacity of a hollowcore slab. The modified Eurocode equation which is fit to fire situations validated against the published literature with respect to shear tests in fire. The structural behaviour of single tee slabs having different axial restraint stiffness as well as the variation of axial thrust in fire is then studied. SAFIR analyses of single tee slabs show that fire performance can increase when a web support type is used that has high axial restraint stiffness. A series of test results on prestressed flat slabs conducted in United States are used to validate a simply supported numerical model. The application of multi-spring connection elements is also investigated in order to examine the feasibility of continuity.

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This thesis essentially presents the experimental investigation of the fundamental phenomena of electric fuse element disintegration and its causation and influence on the subsequent fragmentation of the fuse elements when subjected to excessive fault currents. The basis of the study involved experimental observation of disintegration of fuse elements and the analysis of the dynamic responses of current-carrying conductors, which precipitate disintegration. The experimental techniques employed utilised commercially available video cameras to capture images of element disruptions during disintegration of fuse elements subjected to low short-circuit and high overload currents. Specialist experimental image capturing techniques and hardware implementations were developed to enable investigation of element disintegration caused by high short-circuit fault currents. Disintegration phenomena of fuse elements for all fault cases were compared within different time domains, which included specialist techniques to investigate disintegration of elements in sand and against glass substrates. Disintegration phenomena of elements in unconfined media such as air and water also constituted the studies. The studies diverged, finally, into experimental observations of the temporal development of arc initiation and extinction phenomena of fault current limiting of HBC fuses using spectroscopic analysis of the arc light radiation. The range of studies covered have led to new understandings of fundamental current limiting behaviour of HBC and open type fuses which contribute, in a small way, to the knowledge base of the subject and hopefully will be an aid to improved designs and development of new types of electric fuse.

Advection-dispersion is generally solved numerically with methods that treat the problem from one of three perspectives. These are described as the Eulerian reference, the Lagrangian reference or a combination of the two that will be referred to as Eulerian-Lagrangian. Methods that use the Eulerian-Lagrangian approach incorporate the computational power of the Lagrangian treatment of advection with the simplicity of the fixed Eulerian grid. A modified version of a relatively new adaptive Eulerian-Lagrangian finite element method is presented for the simulation of advection-dispersion. Advection is solved by an adaptive technique that automatically chooses a local solution technique based upon a criterion involving the spatial variation of the gradient of the concentration. Moving particles (the method of characteristics; MOC) are used to define the concentration field in areas with significant variation of the concentration gradient. A modified method of characteristics (MMOC) called single-step reverse particle tracking is used to treat advection in areas with fairly uniform concentration gradients. As the simulation proceeds, the adaptive technique, as needed to maintain solution accuracy and optimal simulation efficiency, adjusts the advection solution process by inserting and deleting moving particles to shift between MMOC and MOC. Dispersion is simulated by a finite element formulation that involves only symmetric and diagonal matrices. Despite evidence from other investigators that diagonalization of the mass matrix may lead to poor solutions to advection-dispersion problems, this method seems to allow "lumping" of the mass matrix by essentially decoupling advection and dispersion. Based on tests of problems with analytical solutions, the method seems capable of reliably simulating the entire range of Peclet numbers with Courant numbers that range to 15.

This research is an investigation into two different aspects of the faulting process. The first part of the study focuses on the initial stages of fault formation, while the second analyzes the deformation produced by an existing fault. The section on fault formation is an attempt to determine whether slip on an existing fault has a significant effect on the formation of subsequent faults. A two-dimensional elastic finite element technique is used to examine the system of stresses produced by slip on an initial fault, assuming that deformation occurs either elastically or by brittle failure. A Mohr-Coulomb failure criterion is used to determine the most likely region of secondary fault initiation. A strain energy criterion is then used to find the preferred direction of fault propagation. The study on fault formation is subdivided into two sections representing two idealized tectonic environments: purely extensional and purely compressional. The section on extensional fault formation explains the prevalence of grabens in extensional tectonic regimes as a consequence of the stress perturbations due to slip on an initial normal fault. Slip on the initial fault produces a region of high proximity to failure at the surface of the downthrown block. A secondary fault would be expected to initiate in this region. The direction of propagation of this fault that most effectively relieves the shear stress (and therefore minimizes the total strain energy) is toward the initial fault, resulting in an antithetic orientation, or graben. The width of the graben is found to be controlled by the depth of the initial normal fault, rather than the depth to a change in material properties. The study of compressional fault formation indicates that, except for steeply-dipping faults, the presence of an initial thrust fault tends to suppress the formation of other faults in its vicinity. However, if a secondary fault initiates near an initial thrust fault, the direction in which it propagates will be influenced by the presence of the initial fault. The way in which it is influenced is dependent on the fault dip. The final part of this study examines the deformation produced by repeated earthquake cycles on the San Andreas fault in southern California. A three-dimensional, time-dependent kinematic finite element model is used to investigate the influence of slip distribution and rheological parameters on the predicted horizontal and vertical deformation. The models include depth-varying rheological properties and power-law viscoelastic behavior. The predicted deformation patterns are fairly sensitive to the parameters used in this study. Of particular importance is the calculation of vertical uplift rate since, in many cases, models that cannot be distinguished from each other on the basis of horizontal deformation may produce distinctive vertical uplift patterns.

This project investigates the heat flow from the rock into ventilating airways by studying various parameters. Two approaches have been used: laboratory measurement of thermal properties to study their variation, and analytic and numerical models to study the effect of these variations on the heat flow. Access to a heat-flux system and special treatment of contact resistance has provided the opportunity to study thermal conductivity as a function of moisture contained in rock specimens. For porous sandstone, tuff, and concretes, thermal conductivity can double when the specimens are soaked; the functional dependence of conductivity on moisture for the first two cases is definitely non-linear. Five previous models for conductivity as a function of porosity are shown not to explain this new phenomenon. A preliminary finite element model is proposed which explains the key features. Other variations of conductivity with applied pressure, location, constituents, weathering or other damage, and anisotropy have been measured. In the second phase of the research, analytical and numerical methods have been employed to consider the effects of the variation in the thermal properties plus the use of insulation on the heat flow from the rock into the ventilated and cooled airways. Temperature measurements taken in drill holes at a local mine provide confirmation for some of the models. Results have been provided in a sensitivity analysis mode so that engineers working on other projects can see which parameters would require more detailed consideration. The thermal conductivity of the rock close to the airways is a key factor in affecting heat loads. Dewatering and the use of insulation, such as lightweight foamed shotcretes, are recommended.

A finite element formulation, based on assumed stress functions, is developed for the linear elastic analysis of the stresses in two-dimensional elasticity problems, including multiply-connected regions and flat plate bending. For planar analysis the Airy stress function is utilized. The physical significance of the Airy stress function and its normal derivatives are brought out. A new technique is introduced to account for traction type boundary conditions. A family of rectangular finite elements, which enables the direct insertion of stress type boundary conditions, and two higher-order rectangular elements which enable continuous stress variations along the interelement boundaries are constructed using blending function interpolants. In addition, a C° continuous triangular plate bending element is adapted for use as a plate stretching element. The Southwell stress function is employed for the analysis of flat plates in bending. A computer program is developed to substantiate the proposed methodology. The formulations are evaluated through the comparison of solutions obtained from the proposed method with classical solutions and solutions obtained from the assumed displacement finite element method. The elements are evaluated by solving the same example problem with different element types. Extensions of the proposed method to account for body forces, initial stresses, material nonlinearities, and shells are briefly discussed. It is demonstrated that the proposed method can directly be integrated with minimal modifications into existing general purpose finite element programs.