Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

From molecules to organs : Microscopy and multi-scale nature of development

Morphogenesis is a phenomenon of intricate balance and dynamic interplay between processes occurring at a wide range of scales (spatial, temporal and energetic). During development, a variety of physical mechanisms are employed by tissues to simultaneously pattern, move, and differentiate based on information exchange between constituent cells, perhaps more than at any other time during an organism's life. To fully understand such events, a combined theoretical and experimental framework is required to assist in deciphering the correlations at both structural and functional levels at scales that include the intracellular and tissue levels as well as organs and organ systems. Microscopy, especially diffraction-limited light microscopy, has emerged as a central tool to capture the spatio-temporal context of life processes. Imaging has the unique advantage of watching biological events as they unfold over time at single-cell resolution in the intact animal. In this work I present a range of problems in morphogenesis, each unique in its requirements for novel quantitative imaging both in terms of the technique and analysis. Understanding the molecular basis for a developmental process involves investigating how genes and their products- mRNA and proteins-function in the context of a cell. Structural information holds the key to insights into mechanisms and imaging fixed specimens paves the first step towards deciphering gene function. The work presented in this thesis starts with the demonstration that the fluorescent signal from the challenging environment of whole-mount imaging, obtained by in situ hybridization chain reaction (HCR), scales linearly with the number of copies of target mRNA to provide quantitative sub-cellular mapping of mRNA expression within intact vertebrate embryos. The work then progresses to address aspects of imaging live embryonic development in a number of species. While processes such as avian cartilage growth require high spatial resolution and lower time resolution, dynamic events during zebrafish somitogenesis require higher time resolution to capture the protein localization as the somites mature. The requirements on imaging are even more stringent in case of the embryonic zebrafish heart that beats with a frequency of ~ 2-2.5 Hz, thereby requiring very fast imaging techniques based on two-photon light sheet microscope to capture its dynamics. In each of the hitherto-mentioned cases, ranging from the level of molecules to organs, an imaging framework is developed, both in terms of technique and analysis to allow quantitative assessment of the process in vivo. Overall the work presented in this thesis combines new quantitative tools with novel microscopy for the precise understanding of processes in embryonic development.

DEVELOPMENT OF MULTI-ANCHOR EARTH RETENTION SYSTEMS.

This paper discusses two projects, the first relating to tests on 'reinforced earth' conducted on the 1. 5 m radius centrifuge at U. M. I. S. T. and the second concerning a short pilot study on the T. R. R. L concept of 'anchored earth' carried out on the 5 m radius Cambridge Geotechnical Centrifuge. The paper proposes a role for centrifugal model testing in design evaluation, whether by the designer himself, his centrification authority, a rival patent holder, or a research worker.

Improving discharge characteristics of indirect integral collector storage systems with multi-element storage

Desired performance of unpressurized integral collector storage systems hinges on the appropriate selection of storage volume and the immersed heat exchanger. This paper presents analytical results expressing the relation between storage volume, number of heat exchanger transfer units and temperature limited performance. For a system composed of a single storage element, the limiting behavior of a perfectly stratified storage element is shown to be superior to a fully-mixed storage element, consistent with more general analysis of thermal storage. Since, however, only the fully-mixed limit is readily obtainable in a physical system, the present paper also examines a division of the storage volume into separate compartments. This multi-element storage system shows significantly improved discharge characteristics as a result of improved elemental area utilization and temperature variation between elements, comparable in many cases to a single perfectly-stratified storage element. In addition, the multi-element system shows increased robustness with respect to variations in heat exchanger effectiveness and initial storage temperature.

Supply network integration in multi-organisational network systems

This paper explores supply network integration in complex product service systems involving close collaboration between primes. Four case study networks are studied (aerospace, naval, power and telecoms), each involving equipment manufacture and service provision. Factors that support network integration, identified from the literature and refined in the in-depth pilot case, were used to explore which processes support integration of the extended enterprise. Results suggests that a select set of processes support integration of the extended enterprise and that the absence of a shared view on these critical enabling processes results from contextual complexity of the network rather than from competing commercial interests. Copyright © 2011 Inderscience Enterprises Ltd.

Multi-Modal Image Retrieval from Construction Databases and Model-Based Systems

In the modern and dynamic construction environment it is important to access information in a fast and efficient manner in order to improve the decision making processes for construction managers. This capability is, in most cases, straightforward with today’s technologies for data types with an inherent structure that resides primarily on established database structures like estimating and scheduling software. However, previous research has demonstrated that a significant percentage of construction data is stored in semi-structured or unstructured data formats (text, images, etc.) and that manually locating and identifying such data is a very hard and time-consuming task. This paper focuses on construction site image data and presents a novel image retrieval model that interfaces with established construction data management structures. This model is designed to retrieve images from related objects in project models or construction databases using location, date, and material information (extracted from the image content with pattern recognition techniques).

Tailored seeding geometries for the multi-fidelity design of compression systems

Design optimisation of compressor systems is a computationally expensive problem due to the large number of variables, complicated design space and expense of the analysis tools. One approach to reduce the expense of the process and make it achievable in industrial timescales is to employ multi-fidelity techniques, which utilise more rapid tools in conjunction with the highest fidelity analyses. The complexity of the compressor design landscape is such that the starting point for these optimisations can influence the achievable results; these starting points are often existing (optimised) compressor designs, which form a limited set in terms of both quantity and diversity of the design. To facilitate the multi-fidelity optimisation procedure, a compressor synthesis code was developed which allowed the performance attributes (e.g. stage loadings, inlet conditions) to be stipulated, enabling the generation of a variety of compressors covering a range of both design topology and quality to act as seeding geometries for the optimisation procedures. Analysis of the performance of the multi-fidelity optimisation system when restricting its exploration space to topologically different areas of the design space indicated little advantage over allowing the system to search the design space itself. However, comparing results from optimisations started from seed designs with different aerodynamic qualites indicated an improved performance could be achieved by starting an optimisation from a higher quality point, and thus that the choice of starting point did affect the final outcome of the optimisations. Both investigations indicated that the performance gains through the optimisation were largely defined by the early exploration of the design space where the multi-fidelity speedup could be exploited, thus extending this region is likely to have the greatest effect on performance of the optimisation system. © 2013 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

An approach to multi-fidelity optimization of aeroengine compression systems

The aerodynamic design of turbomachinery presents the design optimisation community with a number of exquisite challenges. Chief among these are the size of the design space and the extent of discontinuity therein. This discontinuity can serve to limit the full exploitation of high-fidelity computational fluid dynamics (CFD): such codes require detailed geometric information often available only sometime after the basic configuration of the machine has been set by other means. The premise of this paper is that it should be possible to produce higher performing designs in less time by exploiting multi-fidelity techniques to effectively harness CFD earlier in the design process, specifically by facilitating its participation in configuration selection. The adopted strategy of local multi-fidelity correction, generated on demand, combined with a global search algorithm via an adaptive trust region is first tested on a modest, smooth external aerodynamic problem. Speed-up of an order of magnitude is demonstrated, comparable to established techniques applied to smooth problems. A number of enhancements aimed principally at effectively evaluating a wide range of configurations quickly is then applied to the basic strategy, and the emerging technique is tested on a generic aeroengine core compression system. A similar order of magnitude speed-up is achieved on this relatively large and highly discontinuous problem. A five-fold increase in the number of configurations assessed with CFD is observed. As the technique places constraints neither on the underlying physical modelling of the constituent analysis codes nor on first-order agreement between those codes, it has potential applicability to a range of multidisciplinary design challenges. © 2012 by Jerome Jarrett and Tiziano Ghisu.