Dissertations / Theses on the topic 'Agricultural Engineering (General)'

The Alto Rio Lerma Irrigation District (ARLID), located in the state of Guanajuato in Mexico, is an agricultural area whose sustainability depends partially upon groundwater withdrawal for crop irrigation. Because of high pumping demands and current land-management practices, water levels in the regional groundwater aquifers have declined severely, resulting in aquifer overdraft. The potential adverse consequences of this overdraft cannot be overstated, as the long-term economic viability and environmental integrity of the region is threatened. In order to analyze this economic, environmental, and water use problems in this region, simulation of the agricultural system was performed and associated water use impacts quantified under different management scenarios. Linear programming identified the 12 optimal cropping patterns, and then multi-criteria decision-making methodologies were applied to rank and identify the best cropping pattern (satisficing solution). The GLEAMS model was used to simulate the amounts of water, nitrate, and pesticides in both runoff and percolation for each cropping pattern. In order to quantify the economic and environmental impacts of aquifer overdraft, two attributes were used; pumping costs and an aquifer exploitation coefficient. Three multiple criteria methods: Q-analysis, ELECTRE II, and the Range of Value Method, were evaluated and the latter method was selected to analyze the payoff matrix for the ARLID, where 12 alternatives, each with 13 attributes, were considered. The results show the best alternative for effectively balancing environmental with economic considerations was the farming practice, consisting of land leveling, growing vegetables such as red tomato, and controlled groundwater withdrawals to preserve aquifer sustainability. Low water availability does not necessarily reduce farmer's profits, if new water saving alternatives are applied, combined with more profitable crops. Given that ROV method only considers full compensation between objectives, this research contemplate an extension for the nonlinear case in order to assess the whole range of values of the objective function. The final findings suggest that the best methodology was to apply L1 in the lower levels and then L2 for the highest level in the hierarchy. In this manner, the partial compensation between objectives is considered and also the decrease in the uncertainty of alternatives selection.

Ammonia is the most prevalent alkaline gas in the atmosphere and plays an important role in environmental pollution through acidification and eutrophication. Livestock are the largest source of ammonia in the UK, mainly originating during storage and spreading of animal manure. The aim of this study was to validate the collection efficiency of recurved passive ammonia flux (PAF) samplers and the flux frame method to provide a robust methodology for measurement of distributed agricultural sources of ammonia outdoors. The collection efficiency of recurved PAF samplers was determined in a wind tunnel under controlled conditions of ammonia flux (0.771 - 13.49 mg NH3 m-2 s-1), and at angles of orientation to the flow direction (0, 30, 60, 70, 80, 90°). The samplers were effective up to a wind speed of 7 m s-1 and an angle of 80°, with a mean collection efficiency of 71%. The flux frame method had a mean collection efficiency of 87.4% when used with ground level point sources under controlled conditions in the Atmospheric Flow Laboratory. However, in controlled field releases, the efficiency fell to 56.4%. The flux frame method was also suitable for line sources, although assumptions must be made about the source homogeneity and plume dispersion. ADMS modelling was used to predict the collection efficiencies for the flux frame method and these agreed with measured collection efficiencies to within 37.3%. A comparison of source strengths determined using a full size flux frame and portions of the flux frame showed that a full size flux frame was unnecessary as one column of samplers produced a very similar estimate to that of the whole frame. The validated method was then used to measure ammonia emissions from free-range pigs. The amount of ammonia emitted from this source was very low and less than 0.16 g (kg of sow)-1 day-1.

Anaerobic digestion technology has not gained widespread acceptance on UK farms due mainly to the long return on investment periods involved. It has been suggested that co-digestion of agricultural and industrial wastes may enhance the economic viability of such installations. Batch and continuous digestion of cattle slurry and organic industrial wastes was carried out in specially constructed pilot plant digesters, to determine optimum mixtures of waste and digester loading rates. A total of 10 different wastes were tested, on a batch digestion basis, for their potential to co-digest with cattle slurry. Of these, 3 were chosen for continuous pilot plant trials, due to either a need to provide a disposal route for the waste, or positive effects of the waste on methane productivity. Chicken manure was found to slightly enhance methane productivity, but ammonia inhibition of methanogenic bacteria was noted over time. The organic fraction of municipal household waste (OFMSW) significantly enhanced digester methane productivity, while fish offal (FO) slightly enhanced methane productivity when added to the digester in small quantities, but quickly caused digester failure when added in larger amounts. An economic model of a digestion facility was developed and used to show the financial benefits of co-digestion.

Doctor of Philosophy
Department of Biological & Agricultural Engineering
Kyle Douglas-Mankin
Soil erosion is one of the most important of today’s global environmental problems. Over the past few decades, soil conservation practices were implemented to reduce soil erosion in the United States. However, excessive sediment still remains among the most prevalent water quality problems. Agricultural fields and in particular ephemeral gullies (EGs) are considered to be a major contributor of sediment. The overall goal of this study was to improve modeling utility to identify and quantify sources of sediment. Specific objectives were: (1) to develop and demonstrate a method of field-scale targeting using Soil and Water Assessment Tool (SWAT) and to use this method as a targeted, flexible approach to pay explicitly for sediment-yield reductions; (2) to evaluate topographic index models (Slope Area [SA], Compound Topographic Index [CTI], Slope Area Power [SAP] and Wetness Topographic Index [WTI]) and a physical-based model (Overland Flow Turbulent [OFT]) in predicting spatial EG location and lengths. Black Kettle Creek watershed was the focus of an innovative project to pay for modeled field sediment reductions. An Arc-Geographical Information System (GIS) tool bar was developed that post processed SWAT hydrologic response unit output to field boundaries and prepared maps of high-priority fields by sediment, total nitrogen, and total phosphorus and was demonstrated to be useful for field-scale targeting. Calibrated SWAT model was used to establish baseline sediment yields. Various Best Management Practices (BMPs) were simulated and payments to implement each BMP for a given field were calculated. This study helped to guide determination of appropriate farmer support payments and quantified the important influence of BMP type and site-specific conditions for use in targeting conservation practice funding to achieve maximum soil-loss reductions per dollar spent. Extreme care should be used in selecting the source of spatial model input data when using SWAT for field-level targeting. Automated geospatial models were developed in a GIS environment to spatially locate and derive length of EGs using topographic index and physical based models. EG predictions were better for the SA model among the four topographic index models tested. Individual calibration of topographic index model threshold for each application site was needed. An OFT model (physical based model), which utilized topography, precipitation, soil, landuse/landcover and SWAT-based runoff estimates, did not need individual site calibration, and may have broader applicability than empirical based models.

The well-known and widely accepted Penman combination equation was applied to climatic data collected in a desert environment to predict actual evapotranspiration if the desert region were developed into irrigated agriculture. The Penman evaporation estimates from desert climate data were compared to Bowen ratio ET measurements collected on irrigated alfalfa fields in the general vicinity. Six variations of the wind function in Penman's equation were tested. From these six the best fit-model was determined. surprisingly, Penman's original equation provided the best fit (in mean hourly units W m⁻²) as PLE₁ = 0.953LE + 43. The s.e. was 51 W⁻², r² = 0.953, and n = 298 hourly points. A calibrated wind function was developed and named 'Sonoran'. The Sonoran wind function PLE₆ = 0.954LE + 24, s.e. = 48.8 r² = 0.956 provided virtually imperceptible improvements over Penman's original wind function.

Doctor of Philosophy
Department of Grain Science and Industry
Keith C. Behnke
A series of experiments was conducted to compare methods used to evaluate the durability of animal feed pellets, as well as to investigate the potential for modeling the effects of formulation and processing factors on both pellet durability index (PDI) and pelleting energy consumption, measured in kilowatt hours per ton (kWh/ton). Seven different factors, including ground corn particle size, added fat level, inclusion of distillers dried grains with solubles (DDGS), feed rate, steam conditioning temperature, conditioner retention time, and pellet die thickness (L:D ratio) were examined. Each factor was evaluated at two levels, and treatments were developed in order that all factor to factor comparisons could be made. Pellet samples were analyzed according to the standard method as described in ASAE S269.4, a modification of this method, and by using the NHP100 pellet tester set to each of its four testing intervals (30, 60, 90, and 120 seconds). The standard method was found to provide the most consistent and repeatable determinations of pellet durability, and was found to correlate well with the modified method, as well as with the NHP100 results at 30 and 60 seconds. Physical attributes of feed pellets, such as pellet hardness, bulk density, and moisture content were found to have significant, but weak correlations with pellet quality. Pellet quality was found to be significantly influenced by all factors other than ground corn particle size and feed rate. Higher fat level, lower conditioning temperature, and the thinner pellet die most significantly lowered pellet quality, with increasing effect respectively. A regression model was developed that was able to predict pellet durability within an average of 1.1 PDI. Pelleting energy consumption was found to be significantly influenced by all seven factors, with the higher fat level, thinner pellet die, and higher conditioning temperature most improving efficiency, with increasing effect respectively. A regression model was developed that was able to predict energy consumption within an average of 0.3 kWh/ton. The successful creation of regression equations demonstrates that there is potential for modeling and optimizing pellet quality and energy consumption within a pelleting operation.

The original ARID (Algae Raceway Integrated Design) raceway was an effective method to increase temperature toward the optimal growth range. However, the energy input was high and flow mixing was poor. Thus, the ARID-HV (High Velocity Algae Raceway Integrated Design) raceway was developed to reduce energy input requirements and improve flow mixing. This was accomplished by improving pumping efficiency and using a serpentine flow pattern in which the water flows through channels instead of over barriers. A prototype ARID-HV system was installed in Tucson, Arizona, and the constructability, reliability of components, drainage of channels, and flow and energy requirements of the ARID-HV raceway were evaluated. Each of the electrical energy inputs to the raceway (air sparger, air tube blower, canal lift pump, and channel recirculation pump) was quantified, some by direct measurement and others by simulation. An algae growth model was used to determine the algae production rate vs. flow depth and time of year. Then the electrical energy requirement of the most effective flow depth was calculated. Channel hydraulics was evaluated with Manning's equation and the corner head loss equation. In this way, the maximum length of channels for several raceway slopes and mixing velocities were determined. Algae production in the ARID-HV raceway was simulated with a temperature and light growth model. An energy efficient design for the ARID-HV raceway was developed.

Master of Science
Department of Grain Science and Industry
Sajid Alavi
Texturized vegetable protein (TVP) based foods offer several advantages compared to animal protein, including lower costs and improved health benefits. Wheat gluten is often processed using extrusion to produce TVP. Processing aids, such as reducing agents (example, cysteine and sodium metabisulfite) and pH modifiers (example, tetra potassium phosphate) aid in texturization. Reduction of sulfhydryl groups, cleavage of disulfide bonds, and reformation of bonds between elongated protein molecules results in protein aggregation and texturization. This study focused on development of a fundamental understanding of these mechanisms for texturization using analytical tools such as the phase transition analyzer (PTA), in combination with lab- and pilot-scale extrusion. The abovementioned three chemicals were added to four varieties of gluten. The control treatment had no additives. PTA was used to understand the operative flow properties of gluten in an environment similar to an extrusion system. Addition of sulfite (0.18%) and cysteine (0.18%) lowered the thermal softening (Ts:36.6-44.1 °C) and thermal flow (Tf:79.6-105.6 °C) temperatures of all varieties of gluten as compared to the controls (Ts:38.8-48.2 °C; Tf:91.7-112.2 °C). Phosphate (3%) did not have the same lowering effect on Ts (40.2-47.0 °C) and Tf (96.2-108.2 °C), indicating a different mechanism. Extrusion studies were conducted to gain an understanding of the reformation of disulfide bonds and texturization. Two of the varieties of gluten, a “superior” one that texturizes well and an “inferior” gluten requiring texturizing aids, were processed on a lab-scale extruder. Pilot scale extrusion was used to process the other two glutens (“superior” varieties) to obtain commercial quality products, which were evaluated for degree of texturization (hydration rate, absorption index and integrity). During lab-scale extrusion, texturization was observed only in the case of phosphate and corresponded with an increase in specific mechanical energy (SME) as compared to the control, indicating disulfide bond reformation. Phosphate also led to significantly (p<0.05) better texturization during pilot-scale extrusion, although SME trends were different due to higher in-barrel moisture and a more ideal extrusion system. Fourier Transform Infrared Spectroscopy was used to examine protein structural changes and indicated a loss of α-helix structure in TVP with an increase in β-sheet formation.

Master of Science
Department of Biological & Agricultural Engineering
Naiqian Zhang
Mobile apps are useful tools for many different purposes. In agriculture, apps can be used to check the weather and markets, control irrigation, and monitor machine activity among other uses. This research project is a collaboration between Kansas State University and AGCO and includes the development of two apps, using MIT Application Inventor and Google App Engine. Kansas State University was responsible for developing the apps user interface and functionality while AGCO provide the data needs for the apps through Google App Engine. The first app is called Crop Maturity App and measures Growing Degree Days from a crops planting date. The second app is called Combine Efficiency App and determines the performance of a combine harvesting based on its speed. AGCO provided the server support for these apps from a weather service and their own combines that are connected. This project demonstrates the possibility of an open-source development environment with AGCO machine data.

Doctor of Philosophy
Department of Biological & Agricultural Engineering
James K. Koelliker
Small reservoirs catch and store water for long periods and they decrease streamflow and increase ground-water recharge. A field monitoring program provided the measured water depth for four years in several reservoirs in the Republican River Basin where there are concerns about their aggregate effects in the basin. The daily water budget operation for one reservoir was developed. Daily seepage rates were estimated by using precipitation, inflow and evaporation which was assumed equal to grass reference evapotranspiration (ET0), that average 120 to 150 cm/yr, along with the measured stage-storage and stage-surface area relationships. Two computer simulation modules, written in FORTRAN 95, were developed to estimate 1) overflow and gross seepage and 2) potential for ground-water recharge underneath the reservoir. Required daily input data are precipitation, ET0, and inflow from the watershed area. Required reservoir site characteristics include stage-storage and stage-surface area relationships, a standard seepage rate (S0) at 14 different levels in the reservoir, soil-water and plant-growth characteristics and a monthly crop-residue factor. The gross seepage module calculates water depth that determines daily overflow, the water-surface area for evaporation and the head of water on the 14 levels to cause seepage losses. If a level is not inundated, seepage is zero. If a level is inundated less than 0.3-m, S0 is used. When the water head (hL) on a level exceeds 0.3 m, the seepage rate (SL) is increased by, SL = S0 * (hL/0.3)0.25. This relationship was chosen after testing several exponent values between 0 and 1. The modules were calibrated on one reservoir and verified on two others in northwestern Kansas. Results showed runoff from the watersheds averaged about 1.2 to 1.6 cm/yr from the average annual precipitation of 46 to 62 cm. The three reservoirs reduced streamflow at the reservoir site by 74 to 97%, but 90 to 95% of the retained runoff was calculated to contribute to ground-water recharge. Several sensitivity analyses for model inputs were done. Results showed that, the ratio of the average annual inflow volume from the watershed area to the reservoir storage volume was the most sensitive input variable tested.

Relic periglacial solifluction features cover most of Britain, particularly the Midlands and the South, causing serious and continuing earthwork and construction problems. Although the engineering significance of the presence of periglacial solifluction deposits is widely appreciated, the mechanics of emplacement of these deposits has received surprisingly little attention. The principal objective of the research has been to investigate the freeze-thaw behaviour of some clay soils in Britain which have been exposed to periglacial conditions. The behaviour was examined using a Permafrost Oedometer or Permode, based on the apparatus used by Morgenstern and Smith, (1973). Tests have been carried out on Lias Clay, Weald Clay and Oxford Clay. In each test, a specimen was placed under an applied stress and subjected to 24 hour cycles of freezing and thawing. Freezing was mainly imposed from the top of the specimen downwards. The tests were carried out undrained. The pore water pressures were found to increase as a result of cyclic freeze-thaw conditions. Greater pore water pressures were generally recorded at the top than at the base of the specimen. This was considered to be due to moisture migration towards the freezing front during freezing, and impeded filtration, (due to underlying frozen material), during thaw. The significance of the additional pore water pressures in terms of slope stability was considered. A semi-infinite slope analysis model was used primarily, but reference was made to other, similar research. The analysis found that the predicted slope angle of failure is reduced significantly by relatively low increases in pore water pressure. Greater increases in pore water pressure are gained for soils of lower residual shear strength/higher plasticity. It was determined that the generation of excess pore water pressure and corresponding decrease in residual strength have considerable implications for the stability of slopes previously exposed to periglacial conditions.

The research demonstrates that Three-Dimensional Variable-Density Groundwater Flow models such as the SEAWAT model can be effectively used for design of subsurface drainage systems for controlling salt concentration in the root zone on salt affected irrigated land. The SEAWAT model was used to optimize subsurface drainage design to ensure that the salt concentration of the groundwater at the base of the root zone does not exceed pre determined levels instead of the conventional approach of maintaining the groundwater at a predetermined water table level. The study was carried out on a conceptual uniform homogenous block of irrigated flat field of shallow water table depth of 0.5 m and salt concentration of 7200 mg/l with impermeable layer at 20 m deep and impermeable field boundaries. Using the model, spacings were designed to be used as design criteria for subsurface drainage system to maintain salt concentrations of 6000, 5000 and 4000 mg/l at the base of the root zone and water table depth of 0.8 m from the soil surface. The results showed that over a wide range of irrigation water quality and aquifer hydraulic conductivity the optimum drain spacing using SEAWAT was, depending on irrigation water quality and aquifer hydraulic conductivity, wider by between 3 and 50 % and the amount of drain discharge reduced by 1 and 27 % than would be recommended using conventional design equations. It was concluded that Three-Dimensional Variable-Density Groundwater Flow models are better for designing effective drainage systems than Conventional drain spacing design equations such as Hooghoudt.

A small-scale physical modelling system was developed and employed to investigate the effects of tube sampling. Amorphous silica and an oil blend of matching refractive index were mixed to form a transparent soil. Black glass beads were embedded within the soil body on the vertical central plane. After consolidation in a Perspex box, a glass model sampler was pushed into the transparent soil. Movements within the soil body were recorded using digital photography; these images were later analysed by Particle Image Velocimetry. The centreline strain path (CSP) of the sample during tube penetration was calculated and compared to existing analytical and numerical models’ strain predictions, and some degree of correlation was observed. However, it is shown that the CSP is not constant throughout the sample, but varies with depth below the base of the borehole. It was also noticed that after tube penetration, significant residual extensive strains remain for soil on the centreline of the specimen. Different tube geometries were tested and a correlation was found between strain magnitudes and the Area Ratio, Inside Clearance Ratio and the Outer Cutting Edge Taper Angle. It was also found that samples taken in normally consolidated soils were more heavily disturbed than those in lightly overconsolidated soils. After removal from the soil model, samples were stored for six months and volumetric strains within them, set up by a redistribution of pore fluid pressures, were found to be small, typically less than 1%. Soil at the edge of the sampler wall reduced in volume, while the centre swelled. Specimens were thereafter extruded from the sampling tube and the strain path created by this step was quantified. It was found that extrusion compresses the soil while still inside the tube, with soil closest to the extruder more significantly affected. All of these parts of the sampling process contribute to the overall sample disturbance and can therefore have an effect on the sample’s measured properties.

This thesis looks directly into the controversial subject of the microwave field effect by the production of a versatile prototype isothermal microwave reactor for the investigation of enzymatic and microbiological reactions. The observed results from the prototype reactor and experiments conducted conclude that there is a nonthermal, nonlinear response between the exposure microwave power and rate and yield of cellulose saccharification. The nature of the nonthermal response is controversial and may be dependent on the definition of "nonthermal,' leading to ambiguity of exact mechanism. Enzymatic and microbial conversion of cellulosic material to ethanol is a highly desirable industrial process. Whether the demand is for the mitigation of climate change, political obligations or energy independence, the use of arable land for energy crops limits the available glucose carbon sources for conversion to bioproducts. To prevent this limitation, cellulose (~-l,4-linked glucose polymers) are touted as the "silver bullet" to prevent carbon exhaustion or impinging on food crops. The technical constraint for the industrialization of cellulose based processing is the rate limitation in the cellulase enzymatic action on cellulose. The enzyme rate is limited by feedback cycles and limited mechanical freedom, therefore a relatively high enzyme concentration is required to speed up the process. To date, the associated enzyme production costs and infrastructure prevents bulk volume exploitation. Biomolecular advances (amino acid substitutions, recombination of expression vectors etc) have gone some way to increase either enzymatic rate or enzyme concentration. The work presented in this thesis differs by increasing the rate of the enzyme without molecular modification. Using a microwave field, the work presented shows that by separating the system into its base units, irradiation of the enzyme/substrate complex in an aqueous environment can increase both the initial enzyme rate and the saccharification yield without alteration of the temperature set point. This study shows that the rate increase is not proportional to the microwave field power. An optimal power in each study is either found or suggested. The results cited show that in the three systems (Endoglucanase and cellobiohydrolase with cellulose, endoglucanase and cellobiohydrolase and ~- glucosidase with cellulose, and ~-glucosidase with cellobiose) the initial rates can be increased by 201 %, 65.5% and 69% respectively. In the total hydrolytic process (endoglucanase and cellobiohydrolase and ~-glucosidase on a cellulose substrate) the final glucose yield was increased by 43% in comparison to the conventional thermal control reaction. This is shown in Figure 1. 10.000 1 9.000 1 8.000 j 7.000 6.000 o 20 40 60 80 100 120 140 160 180 I I 1 I U 5.000 r:: o u 4.000 3.000 2.000 j i t t , f 1.000 0.000 Time (hours) =->=OOOW Glucose' °012W Glucose ?p025W Glucose ~050W Glucose ·075W Glucose Figure 1. Microwave irradiated "cellulase" enzymes with cellulose substrate I For development into an industrial system and looking towards simultaneous saccharification and fermentation (SSF), the yeast Saccharomyces cerevisiae was subjected to irradiated microwave fermentations on a glucose substrate. Although inconclusive in terms of rate increase, cell density 1 was comparable across the power range showing that the irradiation does not have a derogatory effect. ! The natural evolution of the conclusions drawn would be development of the system into a SSF or SSCF configuration for bio-product formation is possible with irradiation up to SOW. ii The novelty of the experiments conducted is twofold. Firstly, the reactor has been designed to ensure that the microwave irradiation is independent of the bulk temperature therefore allowing the exploration of the microwave field effect independently to the thermal effect. Secondly, the microwave source is a continuous microwave irradiation (none pulse irradiation) ensuring that the reaction is subjected to the microwave field for the entire reaction.

Biodegradable mulch may offer the benefits of polyethylene mulch for crop production with the added benefit of biodegradability. Four studies were carried out in Mount Vernon, WA to evaluate biodegradable mulch for tomato (Solanum lycopersicum L.) and broccoli (Brassica oleracea var. italica) production. The first study compared four biodegradable mulch treatments: BioAgri, BioTelo, WeedGuardPlus (cellulose product), and SB-PLA-10/11/12 (experimental, non-woven fabric), to polyethylene mulch and bare ground in high tunnels and in the open field for tomato yield and fruit quality over three growing seasons. Biodegradable plastic films produced yields and fruit quality comparable to polyethylene. Moreover, high tunnels increased total and marketable fruit weight five and eight times, respectively, compared to the open field.

The second study quantified relationships among visual assessment parameters and mulch mechanical properties. Visual assessments and mechanical property tests of polyethylene, BioAgri, BioTelo, WeedGuardPlus, and SB-PLA-10/11/12, were made over three growing seasons. Regression analyses found the strongest relationship overall (r² = 0.41) to be between the percent of initial breaking force in the machine direction and log ₁₀ of percent visual deterioration. However, evaluating mulch products individually and increasing sample frequency are recommended for future research.

The third study evaluated three biodegradable mulch products, BioAgri, Crown 1, and SB-PLA-11, after soil-incorporation. The average area of recovered mulch fragments decreased for all mulch products over time. The number of mulch fragments initially increased for all mulch products, with the greatest number of Crown 1 and BioAgri fragments recovered 132 and 299 days after incorporation, respectively. At 397 days after soil-incorporation, the total area of recovered fragments of Crown 1 and BioAgri was 0% and 34% of the theoretical maximum area, respectively.

The fourth study used the diffusion of innovations framework to study perceptions about biodegradable mulch and employed the concept of "tactile space" to create sensuously rich learning environments wherein participants could interact with each other and the environment to evaluate biodegradable plastic mulch. Participants' perceptions about biodegradable mulch and attitudes toward adoption improved. Employing tactile space as a diffusion strategy may encourage non-representational learning to supplement and reinforce the knowledge claims being made at outreach/education events.

The disposal of biosolids poses a major environmental and economic problem. Agricultural use is generally regarded as the best means of disposal. Although the impact on soil ecosystems remains uncertain. Biosolids can improve soil properties by supplying nutrients and increasing organic matter content but there is also a potentially negative impact arising from the introduction of heavy metal contaminants into soils. It is widely acknowledged that the bioavailable fraction, rather than total metal content, is indicative of plant metal uptake and toxicity. The bioavailable metal fraction in turn is dependent on soil properties. Therefore, the overall aim of this work was to determine the bio-geochemical factors that control the dynamics of trace element bioavailability in soils that have been subject to the disposal of sewage sludge for over 100 years. Three main investigations were undertaken. In order to determine the current metal composition of the site and identifying the geochemical factors that control the dynamics of metals bioavailability, thirty -eight fields, from a dedicated sewage sludge disposal site for over 100 years, were sampled for both soil (bulk and rhizosphere) and plant. Special attention was devoted to determining soil properties that govern metal partitioning between different metal pools (i.e. total, isotopically exchangeable, Ca(NO3)2-extractable and free ion activity). In order to identify the best estimate of plant uptake and toxic response, a pot experiment was carried out to compare the effects of Zn on plant growth in soils recently spiked with Zn and soils historically amended with biosolids to identify soil properties that best predict metal uptake and subsequent phytotoxicity. The effect of biosolids on soil microorganisms was assessed. Terminal restriction fragment length polymorphism, a fingerprint molecular technique, in combination with multivariate data analysis were used to relate soil microbial diversity and community structure to metal accumulation and bioavailability. High levels of contamination, exceeding the current limits for the use of biosolids in agriculture, were observed in the studied soils reflecting extensive long-term biosolid application. Enrichment factors in relation to background levels in the area were greater than 5 and followed the trend Cd>Cu>Zn>Pb>Ni. Copper and Cd exhibited extremely high enrichment levels, up to 106 and 151 respectively. Except for Pb, the isotopically exchangeable pool of the studied metals (E-value) was mainly controlled by the total metal content in soil, accounting for more than 90% of the variation in E-values. Lead lability was primarily controlled by the total P, LOI and Fe oxides. Metal labilities expressed as % of total metal content were < 40% for the five studied elements following decreasing order of Cu > Cd > Zn ≈ Ni > Pb. Apart from Pb, all the bioavailability estimates (total, E-values, Ca(NO3)2-extractable and free ion activity) correlated strongly with metal concentration in plant, accounting for more than 70% of the variation in plant concentrations. Ca(NO3)2-extractable provided the best estimate out of the four measures of bioavailability, accounting for 87, 77, 87 and 83% of the variation in plant concentration of Ni, Cu, Zn and Cd respectively. The results of the pot trial showed that 67-90% of the added Zn remained isotopically exchangeable after 3 months of Zn addition, suggesting that rapid adsorption processes take place, followed by a slow aging process that cannot be detected over the period of the experiment (3 months). The speciation of soil solution showed that Zn was present mainly (80% on average) as free ion indicating the low affinity of this metal to complexation by dissolved organic matter. An antagonistic relationship was observed between Zn and Cd suggesting that greater Zn availability suppressed Cd uptake by plant. Although Zn addition increased Cd concentration in the soil solution, Cd transfer factor was simultaneously inversely correlated with Zn concentration in soil solution. The free ion activity model (FIAM), based on the biotic ligand model (BLM), accounted for 94% of the variation Zn concentration in plant. Cadmium appeared to play an important role in competing with Zn for uptake. A simple regression model utilising soil total Zn, soil organic matter and soil pH accounted for 88% of the variation in plant uptake. This indicates the possibility of using soil properties that are measured routinely as input for prediction of plant uptake. The results of the Zn phytotoxicity test indicated that the intensity of the exposure (i.e. free ion activity) was the key quantity in the context of predicting plant toxic response, describing 80% of the variation in the response of barley growth to Zn toxicity. Only labile Zn from the quantity based extraction was able to describe the toxic response explaining only 46% of the variation. The study of the effect of biosolids on soil microorganisms showed that soil total Zn concentration could be adopted as a good indicator of the overall (historical) biosolids loading. A biosolids loading, equivalent to 700 – 1000 mg kg-1 Zn appeared to be optimal for maximum bacterial and fungal diversity. This markedly exceeds the maximum soil Zn concentration of 300 mg kg-1permitted under the current UK Sludge (use in agriculture) Regulations. Redundancy analysis (RDA) suggested that the soil microbial communities had been altered in response to the accumulation of trace metals, especially Zn, Cd, and Cu. Based on the findings of this thesis, it can be concluded that (i) the estimation of metal speciation, both in the solution and solid phase is a key factor in determining the bioavailability and thus, has greater chemical and biological significance than soil total metal content; (ii) the maximum beneficial effect of biosolids on soil microbial diversity occurred at a metal (Zn) concentration well in excess of current regulations governing application of biosolids to agricultural land. This indicates that soil microbial diversity is unlikely to be determining factor for regulatory limits for biosolids disposal to agricultural lands.

A cleaner use of fossil fuels supported by Carbon Capture and Storage (CCS) techniques is considered to be one of the main short-term strategies for addressing the global climate change problem. However, potential CO2 or CO2/SO2 seepage during some of the phases of a CCS project not only reduces its performing efficiency, but also impacts the local environment, which could have further impacts on human health. It is therefore essential to assess the potential risks and provide evidence that the impacts are well understood. Moreover, studying the effects of CO2 leakage is useful for identifying monitoring parameters if the leakage does happen, leading to the development of new approaches in detecting CO2 leaks. Accordingly, this research is carried out to assess the relevant impacts on the local environment of CO2 leakage, focusing on the environmental impacts caused by CO2 seepage associated with various soil types, mostly on the soil geochemical changes, which is currently lacked. As a cost effective approach, this research was carried out with two types of well controlled laboratory experiments: Stage I- Closed reactor experiments and Stage II- A flow through column system (designed by the author). As a supplementary study to the research of the ASGARD site, Stage I experiments were carried out with soil samples collected from the ASGARD site and gave directions for Stage II column system design. Stage II experiments were carried out with two contrasting mono-mineral sediments considering sensitivity to CO2 gas, Trucal 5 and Trucal 6 (limestone sand of different particle size) and silica sand. Certain limitations of this research have to be considered. Firstly, highly idealised samples were used in the experiments instead of true soils and there was no heterogeneity in the samples used, which is not representative of the full complexity of a natural system. Secondly, the scale limitation of the laboratory work would lead to a higher gas/mineral ratio compared with field conditions. Therefore, results from the laboratory work cannot simply represent all the soils in the field, except the specific soil related problem and the results are better to be used to demonstrate the conditions where the soils/sediments are surrounded by high levels of CO2, such as the ones nearby a leaking injection well or along a fracture/fault. Nevertheless, this study is believed to provide a step towards understanding the potential impacts of CO2 seepage in soil, and potentially to be useful as a mean of identifying indicators of related problems when applying to the full-scale design, leading to the development of new approaches in detecting CO2 leaks. Throughout the experiments, the experimental apparatus (the continuous column system) newly designed by the author was run successfully, providing an alternative way in respect to the majority of soil-column studies for assessing issues of CO2 seepage. The main impact of CO2 emissions on soil properties is to drop the pH which triggers metals mobilisation from soils (all within safety limits to plant growth). The change of pH associated with both limestone and silica sand indicates that pH is an excellent parameter to indicate the CO2 intrusion into sediments once the background is set. The response of calcium (Ca) to CO2 flux highlights that carbonate minerals are sensitive to CO2 increase and could possibly be used as a parameter to monitor CO2 leakage once the baseline for the pre-injection concentration is set.

This thesis develops a participatory modelling process to study improvement in the management of irrigation efficiency, including physical and social dimensions in the context of arid and semi-arid regions of Iran. This study develops an interdisciplinary and participatory method to understand and strengthen collective decision-making in local Iranian farming systems. Specific attention is given to groundwater irrigated agricultural practices under the Iranian governance system to provide wider context. Kashan City, in central Iran is selected as a case study area for specific reasons, such as historical water use, the farmers’ rich indigenous knowledge, and successful agricultural practices under conditions of water scarcity. The accessibility and willingness of local farmers to engage in a participatory modelling process are considered. The thesis suggests the first use of role-play simulation for irrigation management practices in Iran, is an effective and insightful method of achieving adaptive management solutions. The application of an innovative participatory simulation modelling with farmers revealed their main incentives for collective irrigation practices, their capabilities to learn and evaluate the system. It is argued that management decisions have major impacts on farmers’ livelihoods and therefore it is essential to integrate farmers’ perspectives in local governance to sustain agricultural productivity.

Phytoremediation is a green technique used to restore polluted sites through plant-initiated biochemical processes. Its effectiveness, however, depends on the successful establishment of plants in the contaminated soil. Soils that are contaminated with polycyclic aromatic hydrocarbons (PAHs), especially low molecular weight, mobile PAHs such as naphthalene pose a significant challenge to this. Plant roots growing in these soils exhibit changes to their structure, physiology and growth patterns. Tall fescue (Festuca arundinacea) roots grown in sand contaminated with either petroleum crude oil (10.8g total extractable hydrocarbons kg-1 sand dw) or naphthalene (0.8g kg-1 sand dw) exhibited a temporary inhibition in elongation with accelerated lateral growth (p<0.01), whilst also showing a deviation from the normal root orientation responses to gravity. Scanning electron micrographs (SEM) revealed that the stele in the contaminated roots was located much further away from the root epidermis, because the cortex was larger (p<0.001) due to the cells being more isodiametric in shape. Once past the initial acclimatisation period of 2.5-3.0 months, no visual differences were observed between control and treated plants, but the root ultrastructural modifications persisted. The fluorescent hydrophobic probe „Nile red‟ was applied to the epidermis of a living root to mimic and visualise the uptake of naphthalene into the root through the transpiration stream. The root sections were also stained with 0.1% (w/v) berberine hemisulphate in order to stain Casparian bands. Overlaying images obtained with the use of Texas red HYQ filter (wavelength 589-615nm) and UV illumination (wavelength 345-458nm) revealed the presence of passage cells in the endodermis and uptake of Nile red into protoxylem vessels beyond the endodermis of control roots. On the other hand, the path of Nile red was blocked at the endodermis of naphthalene- treated roots. The cell walls in the endodermis of naphthalene-treated roots were prominently thickened (p<0.001) and lacked passage cells. The treated roots also possessed a well-formed exodermis (p<0.01). The results suggest that the well-formed endodermis lacking passage cells, the well-formed exodermis as well as the increased cortex zone provided an effective barrier to the flux of hydrophobic xenobiotics towards the inner core of the roots, if previously exposed to the contaminants. The SEM images of naphthalene-treated as well as crude oil-treated roots showed partial collapse in the cortex zone, presumably due to water stress, but the treated plants withstood drought stress better than the control plants. The underlying physiological changes responsible for the adaptive responses of tall fescue to the exposure to naphthalene contamination were studied through metabolic profiling of plant roots and shoots. The results indicated synergistic interactions between sugars or sugar- like compounds and phenolic compounds may assist to create an integrated redox system and contribute to stress tolerance in naphthalene-treated tall fescue. The signal for a compound speculated to be indole acetic acid (IAA) was either subdued or absent in the tissues of naphthalene-treated tall fescue, suggesting the existence of a detoxification mechanism/ defence pathway in the treated plants. The ultra-structural and molecular modifications, resulting from PAH stress enabled tall fescue to resist tougher challenges.

Processes and mechanisms of bank erosion on the non-tidal, navigable River Thames were identified and investigated using site specific monitoring and extensive geomorphic surveys. As a lowland, impounded river the Thames has little potential for bank erosion associated with reach-scale morphological channel adjustments. In fact, erosion is closely related to local conditions at the bank and significant processes and mechanisms include fluvial entrainment, slumping, and weakening and weathering of in situ bank material. Approximately 38.5km of eroding bankline was measured (-10% of the total length). Average rates of bank erosion monitored ranged from 0.05ni/yr to -0.5m/yr. The relative contribution to bank retreat of each process or mechanism depends on local conditions such as the use of the bank, the type of bank material and the bank geometry and the type of vegetation. Analysis of the causes of bank retreat at 147 sites along the River Thames revealed that erosion was generally influenced by a combination of factors. Navigation related activities contribute to the bank erosion at nearly all sites (-90%) but is solely responsible for erosion at only about 12%. Factors related to the use of the bank and adjacent land contribute to erosion along -65% of the total length of eroding bank but are the sole influence at only -5%. Channel planform and geometry contribute to -53% of observed bank erosion, but are the sole influence at less than <1% of the erosion sites. A review of selected of erosion control techniques applied on the River Thames suggested that solutions tend to be over-engineered and that strategies adopted were not necessarily appropriate for the causes and consequences of the bank erosion. Furthermore, whilst mitigation measures are often incorporated into the solutions, environmental enhancements are rarely included. Assessment of the causes and consequences of erosion has led to the development of a bank erosion management strategy for the River Thames based on geomorphological and sustainability principles. The strategy is presented as a transferable tool through which to achieve sustainable river management.

The study of behaviour is vital for animal welfare assessment in animal husbandry systems, exploring mechanisms of underlying diverse forms of behaviours and animal physiological and ecological interaction. Understanding animal behaviour is used in a systematic way to unlock and explore underlying functionalities of the brain which is one of the biggest challenges to science. This thesis introduces four novel applications for computational intelligence in human and animal behaviours. The four applications are: horse transport stress prediction system, human activity recognition, fish behaviour tracking and detection, and intelligent interactive fish feeding system. In the first application of human gait recognition, a practical, accurate and novel supervised learning system is proposed to recognize human activities. The proposed system uses single accelerometer device which makes the system practical to use and capable of being integrated with many commercially available devices. This work proposes highly accurate and practical human gait recognition system. In the second application of horse transport, a novel system is proposed to predict horse stress episodes during transport which enables a potential solution of horse stress by interfering at a suitable time. Dynamic nonlinear neural network is trained to predict horse stress time series given travel route and driving style time series. Horse transport is one of the most routinely stressful procedures in equine industry. In the third application of horse transport, a novel system for automatic fish tracking and behaviour recognition system is proposed. Fish are the second most popular experimental model behind mice in pharmaceuticals and biological research. Fish anxious behaviour could confound experiment outcomes. Fish behaviour could also be affected by invasive or non-invasive experiments in addition to other possible causes of distress. The proposed system consists of 3d real-time fish tracking, behaviour quantifying and recognition algorithms. Fish behaviour is estimated through fish swimming patterns. The system showed high accuracy recognition of fish behaviour in experiment where fish were exposed to a variety of external stimuli. In the fourth application of horse transport, an innovative smart fish feeding system is proposed. The fourth application of computational intelligence techniques addresses one of the major challenges in the fastest growing food sector industry worldwide, aquaculture industry. Most conventional fish feeding techniques are inefficient, cause environmental damage and fish losses, raise concerns regarding fish welfare and lead to non-uniform fish growth. Addressing these problems is a necessity for this industry to continue its growth. The novel feeding system is built based on fish behaviour which recognises, and assesses fish behaviours and interacts with fish to optimise the feeding process. Fish showed quick adaptation to this novel low-cost feeding system which proves the feasibly of implementing this system. The proposed system is expected to reduce food competition and environmental impact because of its responsive nature. Through novel applications of computational intelligence, this thesis has provided successful solutions for human and animal behaviour analysis research problems.

Master of Science
Department of Civil Engineering
Steven K. Starrett
Current aquaponic technology ranges from backyard hobbyist to technologically advanced commercial production. A single source for protein (fish) and nutrients/vitamins (vegetables), development of a technologically simplified commercial-scale system is a realistic solution for many impoverished nations. This study develops a simplified aquaponic facility to be implemented in rural northern Uganda. Research objectives were to: (1) identify simplified commercial-scale system design components, (2) establish a water quality baseline, (3) identify plant/tilapia production ratios, (4) identify construction materials available in northern Uganda, (5) integrate culturally familiar elements, (6) complete preliminary facility design, and (7) calculate facility water balance. The study established that a viable simplified design achieves: (1) water circulation with weir gravity flow and one return pump, (2) tank cleaning with strategically sloped floors and manual waste siphoning, and (3) breeding control with raised bottom fishnets. Submerged aeration is critical to optimal fish growth, and cannot be eliminated despite surface aeration’s low energy appeal. Baseline water quality parameter values of DO > 3 mg/L, pH > 5.5, and TAN > 3 mg/L (2 mg/L average) were established for the pilot study configuration and hydraulic retention time (HRT). A plant/tilapia ratio of 2.5 ft[superscript]2/lb was identified for the proposed facility’s design. The simplified design was assessed compatible with concrete block construction local to northern Uganda. Incorporating the following culturally familiar elements will facilitate technology adoption: utilize native fish (tilapia) and vegetable crops identified in community markets, replace commercially produced plant tank raft components with woven matting from locally available natural materials, and identify the unfamiliar proposed tank design with newly adopted raceway culture techniques at a well-known Ugandan national fishery institute. A proposed facility preliminary design represents local materials, identified plant/tilapia ratio, minimum HRT, and simplified design components for tilapia densities ranging from 12 to 3 gal/lb. With the facility supplied by both rainwater and groundwater, corresponding water balances for 12 to 3 gal/lb densities ranged from a 9,735 gal/yr well supply demand to a 10,984 gal/yr rainwater surplus.

Food and energy security are two key environmental challenges currently faced by mankind. The principles behind organic farming are to promote environmental sustainability; however within the organic standards the use of renewable energy is only a suggested method with which to achieve this. If organic farmers can successfully utilise anaerobic digesters, they could contribute towards the provision of both food and energy security using one holistic system. Within this thesis, the suitability of anaerobic digesters on organic farms was explored using methods from ecological, sociological and environmental sciences. This enabled both the practical and theoretical issues behind the question of whether it is suitable for anaerobic digesters to be used on organic farms to be addressed. Field and laboratory experiments were used to compare the effects digestate and slurry had on earthworms, grass and weeds. Digestate and slurry had species dependent effects on earthworms during both LD50 / LT50 experiments and behavioural bioassays; Lumbricus terrestris survived longer in slurry and showed a behavioural preference towards slurry over digestate, whereas Eisenia fetida showed the opposite responses. Fertiliser application rates over 170 kg N ha-1 were found to be harmful to both species of earthworm. Suppressed germination effects were seen on thistles treated with digestate compared with no treatment (F0.56,19.66 =4.66, P < 0.01), whilst grass fertilised with digestate had a greater total mass than grass fertilised with slurry or left unfertilised (F2,27 =17.92, P < 0.001). Questionnaires and interviews were used to obtain a better understanding of the opinions farmers had about anaerobic digesters. Organic farmers believed renewable energy generation fitted well within organic principles, but using an anaerobic digester on an organic farm was less practical than on a conventional farm. This was due to multiple reasons including lack of information, poor associated finances, and that existing digesters are currently unsuitable for small organic farms. There was also support for anaerobic digesters to be on dairy farms- this was regardless of whether the farm was organic or conventional. Two case-study farms were used to assess the impact an anaerobic digester would have on the farms total GHG emissions. An anaerobic digester on the dairy farm was calculated to reduce GHG emissions by up to 24%, while for the mixed farm, the maximum reduction was by 20%. This was primarily due to the fact that the dairy farm benefitted from a higher volume of feedstock and proposed to use the biogas in a more energy efficient manner by producing electricity rather than vehicle fuel. Due to the high emissions associated with keeping livestock, both case studies needed to import additional feedstock if the farms were to achieve zero net GHG emissions. The answer to whether anaerobic digesters can be suitable for organic farms was judged on how well they complimented or conflicted with IFOAM’s definition of organic farming. Three main aspects of their definition were chosen and evidence from each chapter used to address the main question of the thesis. In conclusion, anaerobic digesters are theoretically suitable for use on organic farms, but are generally more practical for use on conventional farm systems. Across both farm systems the most suitable enterprises to adopt anaerobic digesters are dairy farms. This highlights the need for suitability of new systems to be assessed on a case-by-case scenario when trying to maximise positive impacts from new technologies.

Doctor of Philosophy
Department of Industrial and Manufacturing Systems Engineering
Zhijian Pei
Donghai Wang
The U.S. economy has been depending on petroleum-based liquid transportation fuels (such as gasoline, diesel, and jet fuels). Currently, about 50% of petroleum used in the U.S. is imported. Petroleum is a finite and non-renewable energy source and its use emits greenhouse gases. Therefore, it is extremely important to develop domestic sustainable alternatives for petroleum-based liquid transportation fuels. Ethanol produced from cellulosic biomass can be such an alternative. However, several technical barriers have hindered large-scale, cost-effective manufacturing of cellulosic ethanol. One such barrier is related to the low density of cellulosic feedstocks, causing high cost in their transportation and storage. Another barrier is low efficiency in conversion of cellulose to fermentable sugar (pretreatment and enzymatic hydrolysis are two major conversion processes), causing high cost in pretreatment and enzymatic hydrolysis of cellulosic biomass. Ultrasonic vibration-assisted (UV-A) pelleting increases both density and sugar yield of cellulosic feedstocks. Incorporating UV-A pelleting into cellulosic ethanol manufacturing may help realize cost-effective manufacturing of cellulosic ethanol. This PhD dissertation consists of 13 chapters. An introduction is given in Chapter 1. Chapter 2 presents a literature review on related topics. Experimental studies regarding effects of input parameters (such as particle size, pressure, and ultrasonic power) on output parameters (density, durability, stability, and sugar yield) are presented in Chapters 3–4. In Chapters 5–6, comparisons are made between UV-A pelleting and ring-die pelleting (a traditional pelleting method) in terms of pellet properties (density and durability), power consumption, and sugar yield under different conditions. Next, effects of input parameters (such as biomass type, particle size, moisture content, pelleting pressure, and ultrasonic power) on power consumption are studied in Chapters 7–9. Chapter 10 presents an investigation on biomass temperature in UV-A pelleting. Chapter 11 presents an investigation on effects of UV-A pelleting on sugar yield and chemical composition of cellulosic biomass. Chapter 12 presents an investigation on influence of UV-A pelleting on biomass characteristics (such as crystallinity index, thermal properties, and morphological structure). Finally, conclusions are presented in Chapter 13.

Doctor of Philosophy
Department of Grain Science and Industry
Praveen V. Vadlani
As the world population continues to grow and the uncertainty of petroleum and food availability transpires, alternative resources will be needed to meet our demands. Single cell oil (SCO) from oleaginous yeast is a renewable noncrop-based resource that can be used for the production of petroleum counterparts. Currently, commercial production is limited, mainly due to high production costs and competition from cheaper alternatives. As a result, improved fermentation techniques, utilization of low-valued feedstocks and efficient downstream processing would be highly valuable. The major objectives of this study were to: 1) optimize fermentation conditions for the development of a novel fed-batch fermentation to enhance oil production using Lipomyces starkeyi, 2) determine the major lipids produced by L. starkeyi, 3) utilize low-valued hemicellulose-rich feedstocks for oil production, and 4) demonstrate the use of 2-methyltetrahydrofuran (2-MeTHF) and cyclopentyl methyl ether (CPME) as greener solvents for oil extraction. Under optimized fermentation conditions, the oil yield increased from 78 to 157 mg oil/g sugar when supplying xylose rather than glucose as the major carbon source. A novel repeated fed-batch fermentation supplying glucose for growth and xylose for lipid accumulation generated the highest oil yield of 171 mg oil/g sugar, oil content of 60% (dry mass basis) and oil productivity of 143 mg oil/L/hr. Oleic acid accounted for 70% of the total fatty acid profile indicating that oil from L. starkeyi is a naturally high source of oleic acid; an added benefit for the biofuel, cosmetic, food, and oleochemical industries. Hemicellulose-rich corn bran and wheat bran were successfully used to produce oil; oil yields of 125 and 71 mg oil/g sugar were reported for whole and de-starched bran hydrolysates, respectively. Compared to traditional methods, biphasic oil extraction systems of 2-MeTHF and CPME had an 80 and 53% extraction efficiency and 64 and 49% selectivity, respectively. The information from this study will be useful for the development of an integrated approach to improve the viability of SCO biochemical platforms for the production of advanced biofuels and renewable chemicals.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008.
Source: Dissertation Abstracts International, Volume: 69-11, Section: B, page: 6956. Adviser: Vijay Singh. Includes bibliographical references (leaves 110-118) Available on microfilm from Pro Quest Information and Learning.