花岗岩风化土微观结构及其工程地质特性研究

Saprolite is the residual soil resulted from completely weathered or highly weathered granite and with corestones of parent rock. It is widely distributed in Hong Kong. Slope instability usually happens in this layer of residual soil and thus it is very important to study the engineering geological properties of Saprolite. Due to the relic granitic texture, the deformation and strength characteristics of Saprolite are very different from normal residual soils. In order to investigate the effects of the special microstructure on soil deformation and strength, a series of physical, chemical and mechanical tests were conducted on Saprolite at Kowloon, Hong Kong. The tests include chemical analysis, particle size analysis, mineral composition analysis, mercury injection, consolidation test, direct shear test, triaxial shear test, optical analysis, SEM & TEM analysis, and triaxial shear tests under real-time CT monitoring.Based on the testing results, intensity and degree of weathering were classified, factors affecting and controlling the deformation and strength of Saprolite were identified, and the interaction between those factors were analyzed.The major parameters describing soil microstructure were introduced mainly based on optical thin section analysis results. These parameters are of importance and physical meaning to describe particle shape, particle size distribution (PSD), and for numerical modeling of soil microstructure. A few parameters to depict particle geometry were proposed or improved. These parameters can be used to regenerate the particle shape and its distribution. Fractal dimension of particle shape was proposed to describe irregularity of particle shapes and capacity of space filling quantitatively. And the effect of fractal dimension of particle shape on soil strength was analyzed. At the same time, structural coefficient - a combined parameter which can quantify the overall microstructure of rock or soil was introduced to study Saprolite and the results are very positive. The study emphasized on the fractal characteristics of PSD and pore structure by applying fractal theory and method. With the results from thin section analysis and mercury injection, it was shown that at least two fractal dimensions Dfl(DB) and Df2 (Dw), exist for both PSD and pore structure. The reasons and physical meanings behind multi-fractal dimensions were analyzed. The fractal dimensions were used to calculate the formation depth and weathering rate of granite at Kowloon. As practical applications, correlations and mathematical models for fractal dimensions and engineering properties of soil were established. The correlation between fractal dimensions and mechanical properties of soil shows that the internal friction angle is mainly governed by Dfl 9 corresponding to coarse grain components, while the cohesion depends on Df2 , corresponding to fine grain components. The correlations between the fractal dimension, friction angle and cohesion are positive linear.Fractal models of PSD and pore size distribution were derived theoretically. Fragmentation mechanism of grains was also analyzed from the viewpoint of fractal. A simple function was derived to define the theoretical relationship between the water characteristic curve (WCC) and fractal dimension, based on a number of classical WCC models. This relationship provides a new analytical tool and research method for hydraulic properties in porous media and solute transportation. It also endues fractal dimensions with new physical meanings and facilitates applications of fractal dimensions in water retention characteristics, ground water movement, and environmental engineering.Based on the conclusions from the fractal characteristics of Saprolite, size effect on strength was expressed by fractal dimension. This function is in complete agreement with classical Weibull model and a simple function was derived to represent the relationship between them.In this thesis, the phenomenon of multi-fractal dimensions was theoretically analyzed and verified with WCC and saprolite PSD results, it was then concluded that multi-fractal can describe the characteristics of one object more accurately, compared to single fractal dimension. The multi-fractal of saprolite reflects its structural heterogeneity and changeable stress environment during the evolution history.

Olympic Robot Building Manual

The 1989 AI Lab Winter Olympics will take a slightly different twist from previous Olympiads. Although there will still be a dozen or so athletic competitions, the annual talent show finale will now be a display not of human talent, but of robot talent. Spurred on by the question, "Why aren't there more robots running around the AI Lab?", Olympic Robot Building is an attempt to teach everyone how to build a robot and get them started. Robot kits will be given out the last week of classes before the Christmas break and teams have until the Robot Talent Show, January 27th, to build a machine that intelligently connects perception to action. There is no constraint on what can be built; participants are free to pick their own problems and solution implementations. As Olympic Robot Building is purposefully a talent show, there is no particular obstacle course to be traversed or specific feat to be demonstrated. The hope is that this format will promote creativity, freedom and imagination. This manual provides a guide to overcoming all the practical problems in building things. What follows are tutorials on the components supplied in the kits: a microprocessor circuit "brain", a variety of sensors and motors, a mechanical building block system, a complete software development environment, some example robots and a few tips on debugging and prototyping. Parts given out in the kits can be used, ignored or supplemented, as the kits are designed primarily to overcome the intertia of getting started. If all goes well, then come February, there should be all kinds of new members running around the AI Lab!

Quantitative Inference in a Mechanical Design Compiler

This paper presents the ideas underlying a program that takes as input a schematic of a mechanical or hydraulic power transmission system, plus specifications and a utility function, and returns catalog numbers from predefined catalogs for the optimal selection of components implementing the design. It thus provides the designer with a high level "language" in which to compose new designs, then performs some of the detailed design process for him. The program is based on a formalization of quantitative inferences about hierarchically organized sets of artifacts and operating conditions, which allows design compilation without the exhaustive enumeration of alternatives.

Calibração e validação de sensor dielétrico para estimativa de teor de água em solos do Cerrado.

2008

An Autonomous Sailing Robot for Ocean Observation

Sauze, C. and Neal, M. 'An Autonomous Sailing Robot for Ocean Observation', in proceedings of TAROS 2006, Guildford, UK, Sept 4-6th 2006, pages 190-197.

Rainfall infiltration and soil hydrological characteristics below ancient forest, planted forest, and grassland in a temperate northern climate

How rainfall infiltration rate and soil hydrological characteristics develop over time under forests of different ages in temperate regions is poorly understood. In this study, infiltration rate and soil hydrological characteristics were investigated under forests of different ages and under grassland. Soil hydraulic characteristics were measured at different scales under a 250 year old grazed grassland (GL), a six (6 yr) and 48 (48 yr) year old Scots pine (Pinus sylvestris) plantation, remnant 300 year old individual Scots pines (OT) and a 4000 year old Caledonian Forest (AF). In-situ field saturated hydraulic conductivity (Kfs) was measured and visible root:soil area was estimated from soil pits. Macroporosity, pore structure, and macropore connectivity were estimated from X-ray tomography of soil cores, and from water-release characteristics. At all scales the median values for Kfs, root fraction, macro-porosity and connectivity values tended to AF > OT > 48 yr > GL > 6 yr, indicating that infiltration rates and water storage increased with forest age. The remnant Caledonian Forest had a huge range of Kfs (12 to > 4922 mm h-1), with maximum Kfs values 7 to 15 times larger than 48-year-old Scots pine plantation, suggesting that undisturbed old forests, with high rainfall and minimal evapotranspiration in winter, may act as important areas for water storage and sinks for storm rainfall to infiltrate and transport to deeper soil layers via preferential flow. The importance of the development of soil hydrological characteristics under different aged forests is discussed.

Tectonics Inversions & Emerald Deposits

In spite of the great amount of emerald deposits throughout the world, the priorities in quality and volume of extracted rough material are the sites of Colombia (Muzo and Chivor emerald belts). This sites are know even before the Spanish conquistadores. Emeralds were extracted from Somondoco mine (today Chivor) since 1537 and from Muzo in 1567. Contrariwise to the majority of the emerald deposits of the world, which are associated with granitic rocks, the Colombian emerald deposits are associated with hydrofracturing (the main factor controlling emerald mineralization) and hydrothermal fluids, rich in beryl, chrome and vanadium, induced by a tectonic inversion of the deep Mesozoic backarc basin, which is also responsible of the majority of the petroleum systems of the foredeep and foldbelt areas (maturation of the source-rocks andcreation of structural traps). The host rocks of the emeralds are carbonaceous calsiltites (calcareous schists) rich in organic matter of Lower Cretaceous age, which are cut by calcite veins, which, often, contain emeralds, particularly when they are folded. Indeed, since long time (Cheilletz, A. and Giulliani, G., 1996) suggested a two-stage model for the formation of the Colombian emeralds : (i) Stage I is characterized by décollement planes (early compressional tectonic regime) within the carbonaceous calsiltites, hydrothermal fluid infiltration and wall-rock metasomatic alteration ; (ii) Stage II (late tectonic regime) deforms the previous veins by thrust-related folds (development of stratiform and hydraulic breccia), which are synchronous of the emerald mineralization. The resulting tectonic structures are complex fold patterns characterized by propagation anticlines with emerald veins and emerald hydraulic breccia in the apexes, as in Quipama, Tendenquema and Chivor mines. Otherwise stated, since all emerald exploitations are, presently underground, exhaustive geological and particularly structural studies are required to reduce the probability of disappointments. The color of emeralds is from light green to thick green with obvious pleochroism. They appears with different colors when observed at different angles, especially with polarized light. The emeralds from Coscuez deposits have a homogeneous intensive color and bluish tone. At Muzo deposit, the emeralds have middle or dark green color with yellowish tone. At the Chivor deposits, the emeralds have less intensive green color with slight bluish tone. The typical inclusions are albite and pyrite, as well as long bubbles with three phase-inclusions according the zones of growth and along the crystal shapes.

Integrated magnetic components for high-power high-current dc-dc converters

This thesis is focused on the design and development of an integrated magnetic (IM) structure for use in high-power high-current power converters employed in renewable energy applications. These applications require low-cost, high efficiency and high-power density magnetic components and the use of IM structures can help achieve this goal. A novel CCTT-core split-winding integrated magnetic (CCTT IM) is presented in this thesis. This IM is optimized for use in high-power dc-dc converters. The CCTT IM design is an evolution of the traditional EE-core integrated magnetic (EE IM). The CCTT IM structure uses a split-winding configuration allowing for the reduction of external leakage inductance, which is a problem for many traditional IM designs, such as the EE IM. Magnetic poles are incorporated to help shape and contain the leakage flux within the core window. These magnetic poles have the added benefit of minimizing the winding power loss due to the airgap fringing flux as they shape the fringing flux away from the split-windings. A CCTT IM reluctance model is developed which uses fringing equations to accurately predict the most probable regions of fringing flux around the pole and winding sections of the device. This helps in the development of a more accurate model as it predicts the dc and ac inductance of the component. A CCTT IM design algorithm is developed which relies heavily on the reluctance model of the CCTT IM. The design algorithm is implemented using the mathematical software tool Mathematica. This algorithm is modular in structure and allows for the quick and easy design and prototyping of the CCTT IM. The algorithm allows for the investigation of the CCTT IM boxed volume with the variation of input current ripple, for different power ranges, magnetic materials and frequencies. A high-power 72 kW CCTT IM prototype is designed and developed for use in an automotive fuelcell-based drivetrain. The CCTT IM design algorithm is initially used to design the component while 3D and 2D finite element analysis (FEA) software is used to optimize the design. Low-cost and low-power loss ferrite 3C92 is used for its construction, and when combined with a low number of turns results in a very efficient design. A paper analysis is undertaken which compares the performance of the high-power CCTT IM design with that of two discrete inductors used in a two-phase (2L) interleaved converter. The 2L option consists of two discrete inductors constructed from high dc-bias material. Both topologies are designed for the same worst-case phase current ripple conditions and this ensures a like-for-like comparison. The comparison indicates that the total magnetic component boxed volume of both converters is similar while the CCTT IM has significantly lower power loss. Experimental results for the 72 kW, (155 V dc, 465 A dc input, 420 V dc output) prototype validate the CCTT IM concept where the component is shown to be 99.7 % efficient. The high-power experimental testing was conducted at General Motors advanced technology center in Torrence, Los Angeles. Calorific testing was used to determine the power loss in the CCTT IM component. Experimental 3.8 kW results and a 3.8 kW prototype compare and contrast the ferrite CCTT IM and high dc-bias 2L concepts over the typical operating range of a fuelcell under like-for-like conditions. The CCTT IM is shown to perform better than the 2L option over the entire power range. An 8 kW ferrite CCTT IM prototype is developed for use in photovoltaic (PV) applications. The CCTT IM is used in a boost pre-regulator as part of the PV power stage. The CCTT IM is compared with an industry standard 2L converter consisting of two discrete ferrite toroidal inductors. The magnetic components are compared for the same worst-case phase current ripple and the experimental testing is conducted over the operation of a PV panel. The prototype CCTT IM allows for a 50 % reduction in total boxed volume and mass in comparison to the baseline 2L option, while showing increased efficiency.

Biomethane production from food waste and organic residues

Anaerobic digestion (AD) of biodegradable waste is an environmentally and economically sustainable solution which incorporates waste treatment and energy recovery. The organic fraction of municipal solid waste (OFMSW), which comprises mostly of food waste, is highly degradable under anaerobic conditions. Biogas produced from OFMSW, when upgraded to biomethane, is recognised as one of the most sustainable renewable biofuels and can also be one of the cheapest sources of biomethane if a gate fee is associated with the substrate. OFMSW is a complex and heterogeneous material which may have widely different characteristics depending on the source of origin and collection system used. The research presented in this thesis investigates the potential energy resource from a wide range of organic waste streams through field and laboratory research on real world samples. OFMSW samples collected from a range of sources generated methane yields ranging from 75 to 160 m3 per tonne. Higher methane yields are associated with source segregated food waste from commercial catering premises as opposed to domestic sources. The inclusion of garden waste reduces the specific methane yield from household organic waste. In continuous AD trials it was found that a conventional continuously stirred tank reactor (CSTR) gave the highest specific methane yields at a moderate organic loading rate of 2 kg volatile solids (VS) m-3 digester day-1 and a hydraulic retention time of 30 days. The average specific methane yield obtained at this loading rate in continuous digestion was 560 ± 29 L CH4 kg-1 VS which exceeded the biomethane potential test result by 5%. The low carbon to nitrogen ratio (C: N <14:1) associated with canteen food waste lead to increasing concentrations of volatile fatty acids in line with high concentrations of ammonia nitrogen at higher organic loading rates. At an organic loading rate of 4 kg VS m-3day-1 the specific methane yield dropped considerably (381 L CH4 kg-1 VS), the pH rose to 8.1 and free ammonia (NH3 ) concentrations reached toxicity levels towards the end of the trial (ca. 950 mg L-1). A novel two phase AD reactor configuration consisting of a series of sequentially fed leach bed reactors connected to an upflow anaerobic sludge blanket (UASB) demonstrated a high rate of organic matter decay but resulted in lower specific methane yields (384 L CH4 kg-1 VS) than the conventional CSTR system.

Resonant power conversion topologies for inductive charging of electrical vehicle batteries

This thesis is concerned with inductive charging of electric vehicle batteries. Rectified power form the 50/60 Hz utility feeds a dc-ac converter which delivers high-frequency ac power to the electric vehicle inductive coupling inlet. The inlet configuration has been defined by the Society of Automotive Engineers in Recommended Practice J-1773. This thesis studies converter topologies related to the series resonant converter. When coupled to the vehicle inlet, the frequency-controlled series-resonant converter results in a capacitively-filtered series-parallel LCLC (SP-LCLC) resonant converter topology with zero voltage switching and many other desirable features. A novel time-domain transformation analysis, termed Modal Analysis, is developed, using a state variable transformation, to analyze and characterize this multi-resonant fourth-orderconverter. Next, Fundamental Mode Approximation (FMA) Analysis, based on a voltage-source model of the load, and its novel extension, Rectifier-Compensated FMA (RCFMA) Analysis, are developed and applied to the SP-LCLC converter. The RCFMA Analysis is a simpler and more intuitive analysis than the Modal Analysis, and provides a relatively accurate closed-form solution for the converter behavior. Phase control of the SP-LCLC converter is investigated as a control option. FMA and RCFMA Analyses are used for detailed characterization. The analyses identify areas of operation, which are also validated experimentally, where it is advantageous to phase control the converter. A novel hybrid control scheme is proposed which integrates frequency and phase control and achieves reduced operating frequency range and improved partial-load efficiency. The phase-controlled SP-LCLC converter can also be configured with a parallel load and is an excellent option for the application. The resulting topology implements soft-switching over the entire load range and has high full-load and partial-load efficiencies. RCFMA Analysis is used to analyze and characterize the new converter topology, and good correlation is shown with experimental results. Finally, a novel single-stage power-factor-corrected ac-dc converter is introduced, which uses the current-source characteristic of the SP-LCLC topology to provide power factor correction over a wide output power range from zero to full load. This converter exhibits all the advantageous characteristics of its dc-dc counterpart, with a reduced parts count and cost. Simulation and experimental results verify the operation of the new converter.

Magnetic materials and soft-switched topologies for high-current DC-DC converters

The thesis is focused on the magnetic materials comparison and selection for high-power non-isolated dc-dc converters for industrial applications or electric, hybrid and fuel cell vehicles. The application of high-frequency bi-directional soft-switched dc-dc converters is also investigated. The thesis initially outlines the motivation for an energy-efficient transportation system with minimum environmental impact and reduced dependence on exhaustible resources. This is followed by a general overview of the power system architectures for electric, hybrid and fuel cell vehicles. The vehicle power sources and general dc-dc converter topologies are discussed. The dc-dc converter components are discussed with emphasis on recent semiconductor advances. A novel bi-directional soft-switched dc-dc converter with an auxiliary cell is introduced in this thesis. The soft-switching cell allows for the MOSFET's intrinsic body diode to operate in a half-bridge without reduced efficiency. The converter's mode-by-mode operation is analysed and closed-form expressions are presented for the average current gain of the converter. The design issues are presented and circuit limitations are discussed. Magnetic materials for the main dc-dc converter inductor are compared and contrasted. Novel magnetic material comparisons are introduced, which include the material dc bias capability and thermal conductivity. An inductor design algorithm is developed and used to compare the various magnetic materials for the application. The area-product analysis is presented for the minimum inductor size and highlights the optimum magnetic materials. Finally, the high-flux magnetic materials are experimentally compared. The practical effects of frequency, dc-bias, and converters duty-cycle effect for arbitrary shapes of flux density, air gap effects on core and winding, the winding shielding effect, and thermal configuration are investigated. The thesis results have been documented at IEEE EPE conference in 2007 and 2008, IEEE APEC in 2009 and 2010, and IEEE VPPC in 2010. A 2011 journal has been approved by IEEE Transactions on Power Electronics.

High-current inductors for high-power automotive DC-DC converters

This thesis is focused on the investigation of magnetic materials for high-power dcdc converters in hybrid and fuel cell vehicles and the development of an optimized high-power inductor for a multi-phase converter. The thesis introduces the power system architectures for hybrid and fuel cell vehicles. The requirements for power electronic converters are established and the dc-dc converter topologies of interest are introduced. A compact and efficient inductor is critical to reduce the overall cost, weight and volume of the dc-dc converter and optimize vehicle driving range and traction power. Firstly, materials suitable for a gapped CC-core inductor are analyzed and investigated. A novel inductor-design algorithm is developed and automated in order to compare and contrast the various magnetic materials over a range of frequencies and ripple ratios. The algorithm is developed for foil-wound inductors with gapped CC-cores in the low (10 kHz) to medium (30 kHz) frequency range and investigates the materials in a natural-convection-cooled environment. The practical effects of frequency, ripple, air-gap fringing, and thermal configuration are investigated next for the iron-based amorphous metal and 6.5 % silicon steel materials. A 2.5 kW converter is built to verify the optimum material selection and thermal configuration over the frequency range and ripple ratios of interest. Inductor size can increase in both of these laminated materials due to increased airgap fringing losses. Distributing the airgap is demonstrated to reduce the inductor losses and size but has practical limitations for iron-based amorphous metal cores. The effects of the manufacturing process are shown to degrade the iron-based amorphous metal multi-cut core loss. The experimental results also suggest that gap loss is not a significant consideration in these experiments. The predicted losses by the equation developed by Reuben Lee and cited by Colonel McLyman are significantly higher than the experimental results suggest. Iron-based amorphous metal has better preformance than 6.5 % silicon steel when a single cut core and natural-convection-cooling are used. Conduction cooling, rather than natural convection, can result in the highest power density inductor. The cooling for these laminated materials is very dependent on the direction of the lamination and the component mounting. Experimental results are produced showing the effects of lamination direction on the cooling path. A significant temperature reduction is demonstrated for conduction cooling versus natural-convection cooling. Iron-based amorphous metal and 6.5% silicon steel are competitive materials when conduction cooled. A novel inductor design algorithm is developed for foil-wound inductors with gapped CC-cores for conduction cooling of core and copper. Again, conduction cooling, rather than natural convection, is shown to reduce the size and weight of the inductor. The weight of the 6.5 % silicon steel inductor is reduced by around a factor of ten compared to natural-convection cooling due to the high thermal conductivity of the material. The conduction cooling algorithm is used to develop high-power custom inductors for use in a high power multi-phase boost converter. Finally, a high power digitally-controlled multi-phase boost converter system is designed and constructed to test the high-power inductors. The performance of the inductors is compared to the predictions used in the design process and very good correlation is achieved. The thesis results have been documented at IEEE APEC, PESC and IAS conferences in 2007 and at the IEEE EPE conference in 2008.

A kinesin motor in a force-producing conformation.

BACKGROUND: Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states. RESULTS: Here we show that mutation of a single residue in the kinesin-14 Ncd causes the motor to release ADP and hydrolyze ATP faster than wild type, but move more slowly along microtubules in gliding assays, uncoupling nucleotide hydrolysis from force generation. A crystal structure of the motor shows a large rotation of the stalk, a conformation representing a force-producing stroke of Ncd. Three C-terminal residues of Ncd, visible for the first time, interact with the central beta-sheet and dock onto the motor core, forming a structure resembling the kinesin-1 neck linker, which has been proposed to be the primary force-generating mechanical element of kinesin-1. CONCLUSIONS: Force generation by minus-end Ncd involves docking of the C-terminus, which forms a structure resembling the kinesin-1 neck linker. The mechanism by which the plus- and minus-end motors produce force to move to opposite ends of the microtubule appears to involve the same conformational changes, but distinct structural linkers. Unstable ADP binding may destabilize the motor-ADP state, triggering Ncd stalk rotation and C-terminus docking, producing a working stroke of the motor.

Electron tomography of cryofixed, isometrically contracting insect flight muscle reveals novel actin-myosin interactions.

BACKGROUND: Isometric muscle contraction, where force is generated without muscle shortening, is a molecular traffic jam in which the number of actin-attached motors is maximized and all states of motor action are trapped with consequently high heterogeneity. This heterogeneity is a major limitation to deciphering myosin conformational changes in situ. METHODOLOGY: We used multivariate data analysis to group repeat segments in electron tomograms of isometrically contracting insect flight muscle, mechanically monitored, rapidly frozen, freeze substituted, and thin sectioned. Improved resolution reveals the helical arrangement of F-actin subunits in the thin filament enabling an atomic model to be built into the thin filament density independent of the myosin. Actin-myosin attachments can now be assigned as weak or strong by their motor domain orientation relative to actin. Myosin attachments were quantified everywhere along the thin filament including troponin. Strong binding myosin attachments are found on only four F-actin subunits, the "target zone", situated exactly midway between successive troponin complexes. They show an axial lever arm range of 77°/12.9 nm. The lever arm azimuthal range of strong binding attachments has a highly skewed, 127° range compared with X-ray crystallographic structures. Two types of weak actin attachments are described. One type, found exclusively in the target zone, appears to represent pre-working-stroke intermediates. The other, which contacts tropomyosin rather than actin, is positioned M-ward of the target zone, i.e. the position toward which thin filaments slide during shortening. CONCLUSION: We present a model for the weak to strong transition in the myosin ATPase cycle that incorporates azimuthal movements of the motor domain on actin. Stress/strain in the S2 domain may explain azimuthal lever arm changes in the strong binding attachments. The results support previous conclusions that the weak attachments preceding force generation are very different from strong binding attachments.

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.