Doctor of Philosophy / Department of Biological and Agricultural Engineering / Wenqiao Yuan / Biodiesel production and utilization has been increasing rapidly worldwide in recent years. A main challenge in the commercialization and public acceptance of biodiesel is its quality control. This work reports the use of infrared spectroscopy to monitor biodiesel quality through the development of models to predict (1) the blending level of biodiesel in biodiesel-diesel mixtures, (2) the fatty acid profile of biodiesel fuels derived from various lipids, and (3) the concentration of most common impurities present in biodiesel including water, glycerol, methanol and triglycerides. Regressions based on near-infrared (NIR) spectroscopy were developed for relatively inexpensive and rapid on-line measurement of the concentration and specific gravity of biodiesel-diesel blends. Methyl esters of five different oils—soybean oil, canola oil, palm oil, waste cooking oil, and coconut oil—and two different brands of commercial-grade No. 2 on-highway diesel and one brand of off-road No. 2 diesel were used in the calibration and validation processes. The predicted concentration and specific gravity of the biodiesel-diesel blends were compared with the actual values. The maximum and average root-mean-square errors of prediction (RMSEP) of biodiesel concentration were 5.2% and 2.9%, respectively, from the biodiesel type-specific regression. For the general regression, the RMSEP were 3.2% and 0.002 for biodiesel concentration and specific gravity predictions, respectively. Five different models were developed to determine the concentration of methyl palmitate (C16:0), methyl stearate (C18:0), methyl oleate (C18:1), methyl linoleate (C18:2), and methyl linolenate (18:3) present in biodiesel. Using the NIR range a set of models based on four different types of biodiesel was developed. The maximum RMSEP was 0.553% when the models were validated with biodiesel samples that were used in the calibration, however, prediction accuracy of the model under external samples was poor, therefore, a new set of models was proposed. For this case, six different types of biodiesel were used. The models developed for C18:1, C18:2 and C18:3 presented good accuracy on prediction. However, for C16:0 and C18:0, additional work was necessary to reach reasonable accuracy in prediction. Three sub models for specific ranges of concentration (low, medium, and high) were developed. The RMSEP was reduced from 2.98% to 1.51% for the C16:0 and from 2.33% to 0.56% for C18:0, when the sub-models were validated under internal and external samples. Similar procedures were followed to develop regression models based on mid infrared (MIR) spectra. The RMSEP for C16:0, C18:0, C18:1, C18:2, and C18:3 were 0.83%, 0.37%, 1.45%, 1.59%, and 0.84%, respectively. Predictions using MIR spectroscopy models were better than those obtained with NIR spectroscopy models for the C16:0 and C18:0 models. The most common impurities present in biodiesel from production processes, including methanol, free glycerol, triglycerides, and water, were determined by infrared methods using NIR and MIR spectra and partial least square regression (PLSR) methods. The models were developed in two different approaches, one was when a single impurity was present and the other was when all impurities were present. In the single impurity models, the maximum RMSEP obtained in the NIR and MIR models were 647 mg kg[superscript]-1 and 206 mg kg[superscript]-1, respectively. The models for methanol, glycerol, and water performed better using the NIR data. For the triglycerides model, MIR worked better. Only NIR data were used to develop the models for samples with all impurities. Data pre-treatment (Savitzky-Golay second derivative) was necessary to achieve reasonable accuracy in the predictions in this type of models. The maximum RMSEP was 932 mg kg[superscript]-1 presented in the model for triglycerides. The best performance was obtained in the model developed to predict methanol concentration in biodiesel with RMSEP of 177 mg kg[superscript]-1 when all listed impurities were presented. The feasibility of using NIR and MIR spectroscopy to monitor biodiesel quality was demonstrated in this work. The developed method was accurate, rapid, convenient, yet inexpensive to determine some important characteristics of biodiesel, such as biodiesel blending level in biodiesel-diesel mixtures, the fatty acid profile of biodiesel, and impurities present in the fuel.

Doctor of Philosophy / Department of Biological & Agricultural Engineering / Naiqian Zhang / A two-tier wireless data communication system was developed to remotely monitor sediment concentration in streams in real time. The system used wireless motes and other devices to form a wireless sensor network to acquire data from multiple sensors. The system also used a Stargate, a single-board computer, as a gateway to manage and control data flow and wireless data transfer. The sensor signals were transmitted from an AirCard on the Stargate to an Internet server through the General Packet Radio Service (GPRS) provided by a commercial GSM cellular carrier. Various types of antennas were used to boost the signal level in a radio-hostile environment. Both short- and long-distance wireless data communications were achieved. Power supplies for the motes, Stargate, and AirCard were improved for reliable and robust field applications. The application software was developed using Java, C, nesC, LabView, and SQL to ensure seamless data transfer and enable both on-site and remote monitoring. Remote field tests were carried out at different locations with different GPRS signal strengths and a variety of landscapes. A three-tier wireless sensor network was then developed and deployed at three military installations around the country – Fort Riley in Kansas, Fort Benning in Georgia, and Aberdeen Proving Ground in Maryland - to remotely monitor sediment concentration and movement in real time. Sensor nodes, gateway stations, repeater stations, and central stations were strategically deployed to insure reliable signal transmissions. Radio signal strength was tested to analyze effects of distance, vegetation, and topographical barriers. Omni- and Yagi-directional antennas with different gains were tested to achieve robust, long-range communication in a wireless-hostile environment. Sampling times of sensor nodes within a local sensor network were synchronized at the gateway station. Error detection algorithms were developed to detect errors caused by interference and other impairments of the transmission path. GSM and CDMA cellular modems were used at different locations based on cellular coverage. Data were analyzed to verify the effectiveness and reliability of the three-tier WSN.

Master of Science / Department of Biological and Agricultural Engineering / Naiqian Zhang / In order to meet food, fiber, and bio-fuel needs of a growing world population, crop-breeding methods must be improved and new technologies must be developed. One area under focus is the decoding of the genetic basis of complex traits, such as yield and drought stress tolerance, and predicting these traits from genetic composition of lines or cultivars. In the last three decades, significant advances in genotyping methods have resulted in a wealth of genomic information; however, little improvement has occurred for methods of collecting corresponding plant trait data, especially for agronomic crops. This study developed a mobile, field-based, high-throughput sensor platform for rapid and repeated measurement of plant characteristics. The platform consisted of three sets of sensors mounted on a high-clearance vehicle. Each set of sensors contained two infrared thermometers (IRT), one ultrasonic sensor, one Crop Circle, and one GreenSeeker. Each sensor set measured canopy temperature, crop height, and spectral reflectance. In addition to the sensors, the platform was equipped with an RTK-GPS system that provided precise, accurate position data for georeferencing sensor measurements. Software for collecting, georeferencing, and logging sensor data was developed using National Instruments LabVIEW and deployed on a laptop computer. Two verification tests were conducted to evaluate the phenotyping system. In the first test, data timestamps were analyzed to determine if the system could collect data at the required rate of 10 Hz and 5 Hz for sensor data and position data, respectively. The determination was made that, on average, IRT, ultrasonic, and Crop Circle data are received in intervals of 100 ms (SD = 10 ms), GreenSeeker data are received in intervals of 122 ms(SD=10 ms), and position data are received in intervals of 200 ms (SD = 32 ms). The second test determined that a statistically significant relationship exists between sensor readings and ambient light intensity and ambient temperatures. Whether the relationship is significant from a practical stand point should be determined based on specific application of the sensors.

Doctor of Philosophy / Department of Biological & Agricultural Engineering / Naiqian Zhang / A three-tier wireless sensor network (WSN) was developed and deployed to remotely monitor suspended sediment concentration and stream velocity in real-time. Two years of field experiments have demonstrated the achievement of such capabilities. But several weak points emerged and required essential performance improvement and additional research on the radio propagation mechanism within the original three-tier WSN. In the original three-tier WSN, long time delay, potential data loss, and limited network throughput all restricted the network transmission performance. Upon the above issues, the transmission delay was reduced through shortening the raw data storage buffer and the data packet length; the data loss rate was decreased by adopting a mechanism using semaphores and adding feedback after data transmission; the network throughput was enlarged through the event- and time-driven scheduling method. In order to find a long-range wireless transmission method as an alternative to the commercial cellular service used in the original WSN, a central station using meteor burst communication (MBC) technology was developed and deployed. During an 8-month field test, it was capable of performing long distance communication with a low data loss rate and transmission error rate. But due to unstable availability of the meteor trails, the MBC network throughput was constrained. To reduce in-situ maintenance, over-the-air programming was implemented. Thus, programs running in the central station and the gateway station can be updated remotely. To investigate the radio propagation in densely vegetative areas, a 2.4 GHz radio propagation path loss model was derived to predict the short-range path loss from the path loss in the open area and the path loss due to dense vegetation. In addition, field experiments demonstrated that ambient air temperature, relative humidity, and heavy rainfall could also affect wireless signal strength.

Master of Science / Department of Biological & Agricultural Engineering / Wenqiao Yuan / Biomass gasification is a promising route utilizing biomass materials to produce fuels and chemicals. Gas product from the gasification process is so called synthesis gas (or syngas) which can be further treated or converted to liquid fuels or certain chemicals. Since gasification is a complex thermochemical conversion process, it is difficult to distinguish the physical conditions during the gasification stages. And, gasification with different materials can result in different product yields. The main purpose of this research was to develop a downdraft gasifier system with a fully-equipped instrumentation system and a well-functioned tar measurement system, to evaluate temperature, pressure drop, and gas flow rate, and to investigate gasification performance using different biomass feedstock. Chromel-Alumel type K thermocouples with a signal-conditioning device were chosen and installed to monitor the temperature profile inside the gasifier. Protel 99SE was applied to design the signal conditioning device comprised of several integrated chips, which included AD 595, TS 921, and LM 7812. A National Instruments (NI) USB-6008 data acquisition board was used as the data-collecting device. As for the pressure, a differential pressure transducer was applied to complete the measurement. An ISA1932 flow nozzle was installed to measure the gas flow rate. Apart from the gaseous products yield in the gasification process, a certain amount of impurities are also produced, of which tar is one of the main components. Since tar is a critical issue to be resolved for syngas downstream applications, it is important to determine tar concentration in syngas. A modified International Energy Agency (IEA) tar measurement protocol was applied to collect and analyze the tars produced in the downdraft gasifier. Solvent for tar condensation was acetone, and Soxhlet apparatus was used for tar extraction. The gasifier along with the instrumentation system and tar measurement method were tested. Woodchips, Corncobs, and Distiller’s Dried Grains with Solubles (DDGS) were employed for the experimental study. The gasifier system was capable of utilizing these three biomass feedstock to produce high percentages of combustible gases. Tar concentrations were found to be located within a typical range for that of a general downdraft gasifer. Finally, an energy efficiency analysis of this downdraft gasifer was carried out.

Master of Science / Department of Biological & Agricultural Engineering / Danny H. Rogers / Center pivot irrigation systems are used in crop production across the state of Kansas. The American Society of Agricultural and Biological Engineers (ASABE) standard on uniformity testing of a center pivot system calls for collectors to be used to measure the water depth emitted by the irrigation system. The standard was designed without specially considering the low pressure sprinklers now commonly used on center pivot systems; the recommended collectors may not accurately measure the applied depth from these sprinklers. The collector size effect on measured water depth and measured depth variability was studied for spinning plate, fixed plate, and wobbling plate sprinkler systems. Five different collector sizes (C2 (5.5 cm), C4 (10.0 cm), C6 (14.8 cm), C8 (20.0 cm), and C10 (27.4 cm)) were studied using four 5x5 Latin squares. Each collector’s water depth was measured and statistically analyzed. Two analysis of variance (ANOVA) tests of the collector size effect were reported. Past experimental results were compared to this experiment’s results. The ANOVA for the measured water depth reported no collector size effect for the spinning plate and wobbling plate systems. The ANOVA of the variability of measured depths showed significant differences between collector sizes for the spinning plate system but not for the wobbling plate system. Previous studies of spinning plate and wobbling plate systems reported acceptable variability for all collector sizes. Although some collector sizes measured significantly different mean depths, the numerical difference in mean depths was small. Any studied collector size could be used to measure the water depth of wobbling plate systems, but the C4 collector is ideal. C4 and C6 collectors are ideal for measuring spinning plate systems. Significant differences between measured depths were reported for the fixed plate system. The C10 measured significantly lower water depths than all other collectors, and the C4 collector measured lower depths than the C2 and C8 collectors. The variability of mean depths was similar and high for all collector sizes. Previous experiments also indicated that different collector sizes measured different depths and had high variability of depth measurements for the fixed plate sprinkler systems. The distinct stream pattern provides a challenge for accurately measuring the water depth with these collector sizes; other methods of measuring uniformity should be considered for fixed plate sprinklers.

Master of Science / Department of Biological and Agricultural Engineering / Wenqiao Yuan / Many of the current industrial fermentation processes cannot use pentose as the carbon source. However, complete substrate utilization of sugars in lignocellulose is one of the prerequisites to render economic development of biofuels or bioproducts from biomass. In this study we proposed a new process for DHA production from renewable carbon sources by first using anaerobic bacteria, Clostridium tyrobutyricum to convert pentose into organic acids with butyric acid as the main product, and then using the organic acids to feed microalgae, Crypthecodinium cohnii to produce DHA. The effect of glucose and xylose on the yield of butyric acid produced by C. tyrobutyricum was investigated, separately. Cell growth of C. tyrobutyricum increased with increasing initial glucose or xylose concentration, but was not affected significantly when the concentration was above 55g/l for glucose or 35g/l for xylose. Butyric acid yield increased as the initial sugar concentration increased in both xylose and glucose, but the conversion rate from xylose or glucose to butyric acid decreased as the sugar concentration increased. The xylose to glucose ratio in their mixture did not significantly affect cell growth or butyric acid yield. The effect of arabinose on the yield of butyric acid produced by C. tyrobutyricum was also studied. As for butyric acid production, compared with glucose or xylose, the arabinose was in a low efficiency, with butyric acid output of 2.25g/l in 10g/l arabinose and a long lag period of about 3-4 d. However, a low concentration of arabinose could be used as a nutritional supplement to improve the fermentability of a mixture of xylose and glucose. The conversion rate of sugar to butyric acid increased as the supplement arabinose increased. In order to obtain low cost xylose, corncobs were hydrolyzed and this xylose-rich product was used to culture C. tyrobutyricum. The results showed that at end of the 9 d fermentation, the concentration of butyric acid from corncob hydrolysate reached 10.56 g/l, and the mimic medium reached 11.3 g/l. This suggests that corncob hydrolysate can be used as a carbon source for butyric acid production by C. tyrobutyricum, although some inhibitory effects were found on cell growth with corncob hydrolysate. The effect of butyric acid, lactic acid and acetic acid on the yield of DHA produced by C. cohnii was also investigated, separately. The DHA yield was highly related to both biomass and DHA content in the cell, whereas lower growth rate could bring higher DHA content. The best concentration for DHA yield seemed to be 1.2g/l in three single organic acid media. In two organic acids mixture media, acetic acid tended to be beneficial for biomass accumulation, regardless whether butyric acid or lactic acid was mixed with acetic acid, the OD could reach 1.3 or above. When butyric acid was mixed with lactic acid, the highest DHA yield was achieved, due to increased DHA content from mutual influence between butyric acid and lactic acid.

Master of Science / Department of Biological and Agricultural Engineering / Mei He / Thermobifida fusca, an aerobic moderately thermophilic, filamentous soil bacterium is capable of producing butyric acid. Butyric acid is a 4-carbon short chain fatty acid that is widely used in the chemical, food, and pharmaceutical industries. Currently, butyric acid is primarily produced through petroleum-based chemical synthesis, but could be a candidate to be produced by fermentation. By producing through a fermentation platform, production of butyric acid can be shifted from a non-renewable to a renewable source. In an effort to make T. fusca produce a high yield of butyric acid, multiple fermentation parameters were explored and optimized. The effect of different carbon sources (mannose, xylose, lactose, cellobiose, glucose, sucrose, and acetates) on butyric acid production was studied, where cellobiose produced the highest yield of 0.67 g/g C (g-butyric acid/g-carbon input). The best stir speed and aeration rate for butyric acid production were found to be 400 rpm and 2 vvm in a 5-L fermentor. The maximum titer of 2.1 g/L butyric acid was achieved on 9.66 g/L cellulose. Fermentation was performed on ground corn stover as a substrate to evaluate the production of butyric acid on lignocellulosic biomass, and the optimized conditions resulted in a titer of 2.37 g/L butyric acid. The butyric acid synthesis pathway was identified involving five genes that catalyzed reactions from acetyl-CoA to butanyol-CoA in T. fusca. A study into the transcriptomics of T. fusca was begun by growing T. fusca under a variety of fermentation conditions, isolating the messenger RNA, and performing a sequence of the mRNA using whole transcriptome shotgun sequencing. The results of sequencing of various samples were plotted to determine correlation across numerous fermentation parameters. This correlation based analysis determined that the carbon to nitrogen ratio has the largest overall impact on gene transcription of T. fusca among all of the fermentation parameters studied. Overall, the work from this study proves that production of butyric acid is possible from a renewable cellulosic feedstock.

Doctor of Philosophy / Department of Biological & Agricultural Engineering / Ronaldo G. Maghirang / This research was conducted to investigate the potential of charged-water spray in controlling dust in livestock buildings. Specific objectives were to: (1) develop a method to measure the electrostatic charge of airborne particles; (2) characterize the size distribution and charge of airborne particles in a livestock building; (3) evaluate the effectiveness of charged-water spray in controlling dust concentration in enclosed spaces under laboratory conditions; (4) model the effectiveness of charged-water spray in controlling dust in an enclosed building; and (5) develop and evaluate an electrostatically-assisted particulate wet scrubber (EAPWS). A dynamic Faraday-cage sampler was developed for measuring the net charge-to-mass ratio of particles. The device involves collecting particles on a filter and measuring the charge induced. The sampler was calibrated and then used to measure the charge of dispersed particles (i.e., corn starch, NaHCO3, positively charged water spray, negatively charged water spray, and uncharged water spray). The corresponding net charge-to-mass ratios were -0.11 (SD=0.07), +0.20 (0.001), +7.24 (1.6), -6.47 (0.9), and -0.30 (0.12) mC/kg. Characterization of dust in a swine building showed mean dust concentration of 0.89 (SD=0.45) mg/m3, geometric mean diameter of particles of 9.34 μm, and geometric standard deviation of 2.11. The Faraday-cage sampler was also used in the swine building; the net charge-to-mass ratio of particles was +0.68 mC/kg (SD=0.31 mC/kg). The effectiveness of charged-water spray in reducing dust concentration was investigated in an experimental chamber. Test particles (i.e., corn starch, NaHCO3) were dispersed into the chamber and then charged water was sprayed into the chamber. The charged-water spray was significantly more effective than either the uncharged-water spray or no water spray. The removal efficiency of the charged water spray (4 min spray duration, 120 mL/min), based on mass, ranged from 88% to 92% for particles ≤ 10 µm equivalent aerodynamic diameter (EAD) and from 34% to 70% for particles ≤ 2.5 µm EAD. A model based on coagulation was used to predict the particle concentration after spraying of charged water. Predicted values of concentration and removal efficiency agreed well with measured values. A prototype EAPWS was also developed. Laboratory and field evaluations of the EAPWS indicated that it had significantly higher particle removal efficiency than either the control (i.e., no water spray) or the uncharged wet scrubber.

Master of Science / Department of Biological & Agricultural Engineering / James K. Koelliker / In 2003, the EPA changed Confined Animal Feedlot Operation (CAFO) regulations to allow an alternative treatment system for feedlot runoff if a 25-year simulation can show better performance for the alternative treatment system when compared to a traditional lagoon system. A continuous computer simulation model written in C was developed to compare the release of water, nitrogen (N), phosphorous (P) and chemical oxygen demand (COD) from a Vegetated Treatment Area (VTA) system and a conventional lagoon system in Kansas. The model simulates the transport of water and constituents in a feedlot, settling basin, lagoon, and VTA. The feedlot runoff is based on NRCS unit hydrograph method for the water balance and AnnAgNPS for the constituent runoff concentrations. The settling basin is a simple water balance with sediment, organic-N, P, and COD removed with settling of the solids. The VTA is designed to calculate infiltration with Green-Ampt Equation and overland flow with Manning's Law. The VTA removes organic-N and P with the Kentucky Filtration Model. The lagoon is derived from Koelliker et al. model water balance and pumping schedule with constituent balance from Miner et al. model. VTA portion of the model was analyzed for sensitivity and calibrated with three storms. The sensitivity analysis showed that the size of the VTA and conductivity of the soil in the VTA causes the greatest variability in the release of N, P, and COD. The calibration of the release of organic-N and P for mean particle diameter showed that a diameter of 1.5 µm produced the best agreement. The model was used for a lagoon and VTA system at two sites in Kansas with 35 years of weather data. The sites were located in Ottawa and Greenwood Counties, KS. The simulated results showed that the lagoon system performed better for both sites when comparing the mean values of total-N, total-P, and COD released over the 35 years. The VTA system performance was better when median values of total-P and COD were compared at Greenwood County. This model was designed for use in Kansas, but with modifications may be useful in other areas.