基于软粘土微观特性的非线性固结理论研究

The land subsidence of soft clay is including natural and man-made content, which leads to the research on the mechanism of land subsidence constituted by two different aspects, which are studied by geological engineers and geologist. The main major research is focused on the effects of engineering. The land subsidence engineering of soil mechanics is caused by the consolidation and compression of soft clay, the content of which is including the micro-structural characteristics, the stress - strain constitutive relation, porous law, and consolidation theory. In this paper, it is discussed the nonlinear consolidation and compression theory of soft clay. The main studies and conclusions of this thesis are as follows. （1）The micro-structure and its stability are closely related to the engineering characters of soft clay. The stiffness and force connection status of micro-structure plays a controlling influence to its stability. （2）Under saturated state, clay particles remain in a non-full contact or non-contact status, so it is needed to modify the Terzaghi effective stress principle. With the discharge of pore water, the effective stress is increasing, and part of weakly bound-water begins flow, while the porosity and permeability are became lower. （3）It exist non-linear flow in soft clay, which is caused by the shear flow situation of weakly bounded-water. In this case, permeability coefficient is a nonlinear function of hydraulic gradient. （4）In the initial consolidation stage of soft clay in the initial stage, the porous flow is mainly caused by the excretion of free water. With the decrease of free water content, combined bonded-water start to supply free water. At the later stage of consolidation, the flow of fluid is mainly consisted by weakly bounded-water. The exchange between bonded-water and free water is played a role, which slows down the consolidation process.

煤层气储层工程的地下水行为研究

The practice of coalbed methane development from home and abroad demonstrated Hydrogeological factor is one of the important geological factors influencing the coalbed methane productivity. The grasp of groundwater behavior feature is the prerequisite to success development of coalbed methane. Through researching the mechanism by which hydrodynamics factors control the storage and transportation of coalfen methane, the ground- water behavior reflecting the feature of coalbed, and mathematics model describing the production process of coalbed methane, this paper devoted to finding the law of groundwater behavior during the course of storage and production and gave hydrogeology theoretical support to the development of coalbed methane. This paper firstly studied hydrodynamic factors influencing the productivity of coalbed methane, based on the analysis of the relative feature of coalbed methane and that of it's reservoir. The productivity of coalbed methane is controlled by reservoir pressure、permeability and recharge conditions. Reservoir pressure, the key factor controlling gas content of coalbed, is ruled by the history of hydrodynamic and current hydrogeological conditions. It indirectly controls the poductivity through influencing the permeability. The permeability of coalbed is the direct factor controlling the productivity. The recharge conditions controls the productivity through influencing initial reservoir pressure and the descend of reservoir pressure during development of coalbed methane. The field of hydrodynamic and the field of hydrochemistry can be used to identified the flow model of groundwater and the coalbed feature can be deducted by the hydraulic gradient、pressure compartment and hydrochemistry. The production of coalbed methane is a complex physical process which including the mutual action between water、solid and gas. This paper studied the mechanism of water-solid action and that of water-gas action, conducted the controlling equation describing the complex process and gave the corresponding mathematics model with its solution by finite-Element method. Finally, this paper analysised the prospective of coalbed methane development of the south section of Hongguo area in Yizikong basin and put emphasis on the analysis of productivity of liangshan and jingzhuping blocks.

抽水引起岩溶塌陷的机理及非线性预测研究

Karst collapse is one of the most important engineering geology hazards in Karst district, which seriously endangers the living of humankind and the environment around us, as well as the natural resources. Generally speaking, there exist three processes of overburden karst collapse:the formation of soil cavity, the expansion of soil cavity and the fall of the cavity roof. During these processes, groundwater is always the most active factor and plays a key role. Pumping will bring into the great change of groundwater in flow state, flowrate, frequency of fluctuation as well as hydraulic gradient and will speed the fall. Statistics shows that most of the man-made karst collapse are induced by pumping, so studying the mechanism of Karst collapse induced by pumping will provide theoretical base for the prediction and precaution of collapse. By theoretically studying the initial condition for the forming and expanding of a soil cavity, Spalling step by step the essential mechanism of Karst collapse induced by pumping is put forward. The catastrophe model for the collapse induced by pumping is set up to predict the fall probability of a cavity roof, and the criterion for the collapse is determined. Simultaneously, Karst collapse induced by pumping is predicted with manmade neural network theory. Finally, the appropriate precaution measurements for the collapse induced by pumping are provided. The creative opinions of the paper is following: The initial condition of forming a soil cavity is put forwarded as formula (4-1-5), (4-1-24),(4-1-25) and (4-1-27); which provide theoretical base for foreclosing the formation of a soil cavity and defending collapse. Spaliing step by step as the essential mechanism of Karst collapse induced by pumping is put forward. The spaliing force is defined as formula (4-2-15). The condition for the expanding of a soil cavity is that spaliing force is greater than tensile strength of soil. The stability of a soil cavity is first studied with catastrophe theory. It is concluded that the process of development up to ground collapse of a small cavity is continuous, however, the process of a big cavity is catastrophic. It is feasibility that the Karst collapse be predicted with manmade neural network theory as a new way.

华南震旦纪-寒武纪两期成磷事件及其地球动力学意义

Phosphorus is an important biological and ecological element that to a certain degree constrains ecological environment and nutrient (including carbon) cycling. Marine sedimentary phosphorites are the principal phosphorus supply of the mankind. In the eastern to southern margins of the Yangtze Craton, South China, there are two phosphogenetic events at the Doushantuo stage of the Late Sinian and the Meishucun stage of the Early Cambrian respectively, corresponding two explosion events of life across the Precambrian\Cambrian boundary. Phosphorus ores from the Sinian and Cambrian phosphate in South China can be classified roughly into two categories, namely, grained and non-grained phosphorites. Grained phosphorites, hosted in dolostone type of phosphogenetic sequences and with larger industrial values, occur mainly in margins of the Upper Yangtze Platform, formed in shallow-water environments with high hydraulic energy and influenced by frequent sea-level change. Non-grained phosphorites, hosted principally in black-shale type of phosphogenetic sequences and with smaller industrial values, are distributed mainly in the Jiangnan region where deeper-water sub-basins with low hydraulic energy were prevailing at the time of phosphogenesis. Secular change ofδ~(13)C, δ~(18) O, ~(86)Sr/~(87)Sr values of carbonates from Sinian and Cambrian sequences were determined. A negative abnormal ofδ~(13)C, δ~(18)O values and positive abnormal of 86Sr/87Sr values from the fossiliferous section of the Lowest Cambrian Meishucun Formation implies life depopulation and following explosion of life across the PrecambriamCambrian boundary. Based on a lot of observations, this paper put forward a six-stage genetic model describing the whole formational process of industrial phosphorites: 1) Phosphorus was transported from continental weathering products and stored in the ocean; 2) dissolved phosphates in the seawater were enriched in specific deep seawater layer; 3) coastal upwelling currents took this phosphorus-rich seawater to a specific coastal area where phosphorus was captured by oceanic microbes; 4) clastic sediments in this upwelling area were enriched in phosphorus because of abundant phosphorus-rich organic matters and because of phosphorus absorption on grain surfaces; 5) during early diagenesis, the phosphorus enriched in the clastic sediments was released into interstitial water by decomposition and desorption, and then transported to the oxidation-reduction interface where authigenic phosphates were deposited and enriched; 6) such authigenic phosphate-rich layers were scoured, broken up, and winnowed in shallow-water environments resulting in phosphate enrichment. The Sinian-Cambrian phosphorites in South China are in many aspects comparable with coastal-upwelling phosphorites of younger geological ages, especially with phosphorites from modern coastal upwelling areas. That implies the similarities between the Sinian-Cambrian ocean and the modern ocean. Although Sinian-Cambrian oceanic life was much simpler than modern one, but similar oceanic planktons prevail, because oceanic planktons (particularly phytoplanktons) are crucial for phosphate enrichment related to coastal upwelling. It implies also a similar seawater-layering pattern between the Sinian-Cambrian ocean and the modern ocean. The two global phosphate-forming events and corresponding life-explosion events at the Sinian and Cambrian time probably resulted from dissolved-phosphate accumulation in seawater over a critical concentration during the Earth's evolution. Such an oceanic system with seawater phosphorus supersaturation is evidently unstable, and trends to return to normal state through phosphate deposition. Accordingly, this paper put forward a new conception of "normal state <=> phosphorus-supersaturation state" cycling of oceanic system. Such "normal state <=> phosphorus-supersaturation state" cycling was not only important for the three well-known global phosphate-forming events, also related to the critical moments of life evolution on the Earth. It might be of special significance. The favorable paleo-oceanic orientation in regard to coastal-upwelling phosphorite formation suggests a different orientation of the Yangtze Craton between the Sinian time and the present time (with a 135° clockwise difference), and a 25° anti-clockwise rotation of the Yangtze Craton from late Sinian to early Cambrian. During the Sinian-Cambrian time, the Yangtze Craton might be separated from the Cathaysia Block, but might be still associated with the North China Craton.

溶蚀岩体渗透水力学特性研究

Seepage control in karstic rock masses is one of the most important problems in domestic hydroelectric engineering and mining engineering as well as traffic engineering. At present permeability assessment and leakage analysis of multi-layer karstic rock masses are mainly qualitative, while seldom quantitative. Quantitative analyses of the permeability coefficient and seepage amount are conducted in this report, which will provide a theoretical basis for the study of seepage law and seepage control treatment of karstic rocks. Based on the field measurements in the horizontal grouting galleries of seepage control curtains on the left bank of the Shuibuya Hydropower Project on the Qingjiang river, a hydraulic model is established in this report, and the computation results will provide a scientific basis for optimization of grouting curtain engineering. Following issues are addressed in the report. (1) Based on the in-situ measurements of fissures and karstic cavities in grouting galleries, the characteristics of karstic rock mass is analyzed, and a stochastic structural model of karstic rock masses is set up, which will provide the basis for calculation of the permeability and leakage amount of karstic rock mass. (2) According to the distribution of the measured joints in the grouting galleries and the stochastic results obtained from the stochastic structural model of karstic rock mass between grouting galleries, a formula for computation of permeability tensor of fracturing system is set up, and a computation program is made with Visual Basic language. The computation results will be helpful for zoning of fissured rock masses and calculation of seepage amount as well as optimization of seepage control curtains. (3) Fractal theory is used to describe quantitatively the roughness of conduit walls of karstic systems and the sinuosity of karstic conduits. It is proposed that the roughness coefficient of kastic caves can be expressed by both fractal dimension Ds and Dr that represent respectively the extension sinuosity of karstic caves and the roughness of the conduit walls. The existing formula for calculating the seepage amount of karstic conduits is revised and programmed. The seepage amount of rock masses in the measured grouting galleries is estimated under the condition that no seepage control measures are taken before reservoir impoundment, and the results will be helpful for design and construction optimization of seepage curtains of the Shuibuya hydropower project. This report is one part of the subject "Karstic hydrogeology and the structural model and seepage hydraulics of karstic rock masses", a sub-program of "Study on seepage hydraulics of multi-layer karstic rock masses and its application in seepage control curtain engineering", which is financially supported by the Hubei Provincial key science and technology programme.

水库滑坡复活机理及其发展趋势预测研究

Various numbers of ancient landslides of various scales are frequently distributed on both banks of reservoirs, especially large reservoirs, both in China and abroad. During inundation and operation of theses reservoirs, some of the landslides are reactivated, which caused losses of people's lives and properties to various extents, some even disasters. Systematic studies are, however, very few on the reservoir-induced reactivation mechanism and development tendency prediction. Based on investigation of reservoir-induced reactivation phenomena of ancient landslides and relevant existing research problems, a systematic study is carried out on the field identification, induced reactivation mechanism, development tendency prediction, risk decision-making and treatment of reservoir-related ancient landslides, through analysis of large numbers of engineering geological investigation results, scientific experimental and research results, in combination with prevention and treatment practices of reservoir-related landslides both in China and abroad, and a series of research results have been obtained. 1. On the basis of study of the distribution features, genesis mechanism of ancient landslides on river banks, a set of scientific methods are summarized on field identification of ancient landslides, and a significant method named "lithologic sequence method" or "indicator layer method", is proposed, which is proved to be very useful. 2. A detail study is made on the reservoir-induced hydraulic effects and material mechanic effects (or softening effects) on the ancient landslide through model and case studies, which concludes that the magnitude and properties of reservoir-induced hydraulic effects are related to the shapes of sliding planes, water content and permeability of landslide materials and variation rate and magnitude of reservoir levels; the magnitude of material mechanic effects are related to the material composition (including mineral composition and grain size), natural water content and saturation state of sliding zones. Also a sensitive analysis is made on the factors that are related to the stabilities of the landslides, which indicate that the stability of a landslide is more sensitive to the groundwater head h_w in the slides and the inner friction angleψof sliding zones than others. 3. The joint inducing mechanism of rainfall and reservoir is also discussed in the paper through model analysis and case study, which proves that reservoir inundation increases firstly the sensitivity of a landslides to rainfall through reduction of its stability or cracking deformation which will increase the rainfall infiltration to the slide body, and then rainfall triggers reactivation or intensifies the reservoir-induced deformation of a landslide. 4. Based on rheologic test results of sliding zones of several reservoir-related ancient landslides, the rheologic characteristics of sliding zones have been discussed in detail and several typical rheologic models have been set up, which well explains the dynamic process of slide deformation. The response types to reservoir inundation and development tendency of reservoir -related ancient landslide are discussed in the paper based on field investigation results. And prediction methods for reservoir-related landslides have been studied based on the Mate-Synthetic principle of quantitative and qualitative analysis, as well as combination of computation and internal mechanism analysis, and a rheologic analytical method is proposed which is proved very useful for prediction of the landslide development tendency. 6. In disaster-prevention and treatment of reservoir-related landslides, risk decision-making has been proved very significant both in engineering and economics. Based on the practices in disaster-prevention and treatment of reservoir-related landslides both in China and abroad, the disaster-prevention risk decision-making for reservoir-related landslides has been proposed in terms of philosophy, methods and procedures, and well put into practice. A summary is also made through case study of the experiences of treatment of reservoir-related landslides both in China and abroad in terms of principle, methods and technical lines. 7 A detail study is made as a case study of the reactivated Maoping ancient landslide on the left bank of the Geheyan Reservoir on Qingjiang river in Hubei province, China, including its field identification features, reservoir-induced reactivation characteristics and mechanism, development tendency prediction and proposed counter measures based on risk analysis.

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.

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

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.

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.

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.

Conversion of natural forests to managed forest plantations decreases tree resistance to prolonged droughts

© 2015 Published by Elsevier B.V.Throughout the southern US, past forest management practices have replaced large areas of native forests with loblolly pine plantations and have resulted in changes in forest response to extreme weather conditions. However, uncertainty remains about the response of planted versus natural species to drought across the geographical range of these forests. Taking advantage of a cluster of unmanaged stands (85-130year-old hardwoods) and managed plantations (17-20year-old loblolly pine) in coastal and Piedmont areas of North Carolina, tree water use, cavitation resistance, whole-tree hydraulic (Ktree) and stomatal (Gs) conductances were measured in four sites covering representative forests growing in the region. We also used a hydraulic model to predict the resilience of those sites to extreme soil drying. Our objectives were to determine: (1) if Ktree and stomatal regulation in response to atmospheric and soil droughts differ between species and sites; (2) how ecosystem type, through tree water use, resistance to cavitation and rooting profiles, affects the water uptake limit that can be reached under drought; and (3) the influence of stand species composition on critical transpiration that sets a functional water uptake limit under drought conditions. The results show that across sites, water stress affected the coordination between Ktree and Gs. As soil water content dropped below 20% relative extractable water, Ktree declined faster and thus explained the decrease in Gs and in its sensitivity to vapor pressure deficit. Compared to branches, the capability of roots to resist high xylem tension has a great impact on tree-level water use and ultimately had important implications for pine plantations resistance to future summer droughts. Model simulations revealed that the decline in Ktree due to xylem cavitation aggravated the effects of soil drying on tree transpiration. The critical transpiration rate (Ecrit), which corresponds to the maximum rate at which transpiration begins to level off to prevent irreversible hydraulic failure, was higher in managed forest plantations than in their unmanaged counterparts. However, even with this higher Ecrit, the pine plantations operated very close to their critical leaf water potentials (i.e. to their permissible water potentials without total hydraulic failure), suggesting that intensively managed plantations are more drought-sensitive and can withstand less severe drought than natural forests.

Deficiencias hídricas inducidas en un cultivo de maíz : efectos sobre las propiedades hidráulicas del suelo

p.203-210