The objective was to create a feasibility framework for assessing the feasibility of a cellulosic ethanol refinery. In addition, the research aimed to create a base case scenario based on data from literature and conduct sensitivity analysis to determine significant parameters of a cellulosic ethanol refinery. The base case was found to be not feasible in the financial and economic analysis given the assumptions used.

No description available.

This thesis studied the catalytic upgrading of pyrolysis oil derived from both ethanol organosolv (EOL) lignin and whole biomass. There are four major components of this thesis. In the first part, several lignin model compounds and the commonly used noble metal catalysts were evaluated. During the reaction, coke formation deactivated several catalysts. The reaction pathway of the coke formation was proposed. Ruthenium/activated carbon can hydrogenate the aromatic ring and remove the methoxyl group as well due to its unique catalytic behavior. The reaction mechanism was deduced based on the products distribution of the model compounds. The second part of this study focuses on the catalytic HDO reaction with real EOL pyrolysis oil. The results indicate the reaction mechanism with EOL pyrolysis oil is similar to the results of the model compound study. Due to the deactivation of the Ru/C catalyst by tar produced during the upgrading, two-step hydrodeoxygenation at different temperature was adopted in this study. The second part mainly discussed the first-step HDO reaction. The upgraded pyrolysis oil was analyzed using GC-MS, ¹H, ¹³C, and HSQC ²D NMR. The chemical structure change after the first-step upgrading and the cleavage of the inter-linkages were included. The third part focuses on the product analysis after the second-step HDO. All the products were completely hydrogenated. The molecular weight of the upgraded oil is in the monomer range and the GC-MS study provided detailed compound structures. However, some of them still contain oxygen atoms. To produce completely deoxygenated products, alkali treated ZSM-5 was used as a supporting material and it was effective in catalyzing the dehydration reaction and producing deoxygenated compounds. In the fourth part, light oil derived from whole biomass also underwent treatment under the same HDO reaction conditions as those used in upgrading EOL pyrolysis oil. In this reaction, the biomass were separated into three components: stem, residue and bark. The compound structures of the three different types of light oil were analyzed by GC, ¹H and ¹H-¹³C HSQC-NMR. Then the light oil was processed under the same condition as the heavy oil upgrading. The reaction mechanisms with cellulose and hemicellulose were also studied. These results will be of value in developing of complete hydrogenation of whole biomass pyrolysis oils.

Iowa finds itself positioned at the epicenter of agricultural pollution due to the intensity of crop and livestock production, fertilizer inputs, altered hydrological landscapes, and other factors. To address such issues, the overarching objective of this research work was to understand the implications of an expansion in bioenergy crops as mandated by the Environmental Protection Agency's Renewable Fuel Standard 2 (through 2022) on hydrology and water quality in an agricultural watershed. In this research, the Soil Water Assessment Tool (SWAT) model was calibrated and validated using field data obtained through water quality sensors and grab samples, and then model parameters were estimated for sensitivity and uncertainty analysis. Scenarios were generated based on Renewable Fuel Standards and evaluated for understanding the impacts of expanding bioenergy production on hydrology and water quality. Also output from an agent-based model was incorporated into SWAT for simulating watershed responses to different crop market scenarios. Finally SWAT model output under eighteen scenarios, was generated for six different climate models and analyzed to see changes in various water quantity outputs e.g. surface flow, base flow, and ET. The SWAT Model was calibrated and validated within statistically acceptable limits e.g. R2 > 0.85 of observed monthly hydrologic mass and R2 > 0.7 for nutrients loads. Sediment load was reduced by 15% due to conversion of corn acreage into switch grass on high elevation land with a slope of>5% (roughly 12% of the watershed). Model simulations also showed that linear climatic inputs (i.e. linear temporal trends increase in precipitation and max/min air temperature) can generate non-linear responses amongst different components of the water cycle (i.e. surface flow, base flow, ET, and deep percolation rates) in the watershed model. This research effort will help to produce a prototype Intelligent Digital Watershed (IDW) to understand the interactions between water and human systems, with the goal of a sustainable agricultural economy. The IDW should enable discovery of scenarios that result in water quality that meets water quality standards.

No description available.

There has been an increased global interest in biofuels which provide a renewable and sustainable alternative to fossil fuels. Isobutanol is an attractive and superior alternative to the currently produced bioethanol possessing several key advantages. Previous work focuses on strategies for metabolic optimisation of carbon utilisation. However, existing solutions reach a stage where the amount of alcohol produced reaches toxic thresholds for bacteria. This inhibits growth and reduces carbohydrate consumption resulting in lower product yields rendering the biofuel production process uneconomical. In this project, a novel strategy has been adopted which uses a whole system integrated genomics approach consisting of expression profiling, selection to create isobutanol-adapted lineages, next generation sequencing, and comparative behavioural genomics to interrogate the system thoroughly and identify critical determinants of resistance to isobutanol. These were used in the highly-defined model species, E. coli K12 to deliver results of the adaptive mechanisms which take place across the entire genome. 41 gene candidates (4 previously identified in literature) were identified to play a role in isobutanol tolerance. These candidates belong to a range of functional groups such as carbohydrate metabolism, oxidative stress response, osmotic stress response; but also identified novel membrane-associated functions such as the Tol-Pal system, BAM complex and colanic acid production. The results also identify critical genes with unknown functions. The results support previous notions that central carbon metabolism shifts from aerobic to anaerobic metabolism in the presence of isobutanol, but also shows there is a transitionary phase where mixed acid fermentation pathways are utilised. This shift was previously thought to be mediated by the ArcA-ArcB two-component system. However, these results suggest the inactive 2Fe-2S core of the anaerobic-regulator Fnr is re-activated by Fe2+ to form the 4Fe-4S core transported by the FeoAB ferrous iron transport system. The strategy also identified the Tol-Pal system and show it is essential to grow in the presence of isobutanol, which is responsible for the maintaining the integrity of the cell envelope structure and increasing the rate of cell division. The BAM complex is responsible for folding and assembly of outer membrane proteins (OMP) and OMP membrane permeability- this system was found to be important for growth in isobutanol, and SurA, which is the primary OMP assembly pathway provided tolerance which was specific to isobutanol. Colanic acid, an extracellular polysaccharide is produced when the cell experiences stress, and provides protection by forming a physical barrier around the cell. The results show that the presence of colanic acid plays a large role in allowing E. coli to grow in presence of isobutanol, and its role becomes essential at critical concentrations. The results also show deletion of the negative regulator of the colanic acid gene cluster improves growth at critical and growth-inhibiting concentrations. When consolidated, these results facilitated knowledge-led based design and subsequently led to the identification of components for a synthetic design schedule, which lists the genetic manipulations proposed to exploit E. coli to enhance isobutanol tolerance.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Biofuels are being promoted as a global necessity to meet climate change targets through the replacement of fossil fuels. Many countries have identified biofuels as a potential mechanism to meet these challenges, with policy directives driving biofuel production. The South African government has proposed that biofuels form part of the country’s future renewable energy and has proposed a draft biofuel strategy. This study aims to investigate appropriate approaches to determine potential biodiversity impacts from biofuel production. Since biofuels are not currently grown to any large extent in South Africa, impact was modelled using future scenarios of converting available land within the Eastern Cape Province of South Africa. Suitable species were identified using the species distribution modelling programme MaxEnt. Some of the proposed biofuel crops were considered as invasive (i.e. they spread from sites where they are cultivated) or are very likely to be invasive in South Africa. This study also highlighted the considerable overlap between suitable growing areas and areas considered important for future biodiversity conservation. The biodiversity intactness index (BII), a broad based biodiversity indicator, was used to assess the biodiversity implications of transforming available land to biofuels. The BII indicates losses of biodiversity between 17.6% and 42.1% for the land use scenarios identified. An important finding was that excluding important biodiversity areas that occur outside of protected areas can reduce biodiversity losses by as much as 13% and maintain an overall intactness of ~70%. Currently the BII does not account for fragmentation or landscape configuration. This was addressed by developing a revised biodiversity intactness index (R-BII) which included the effect of patch-size and habitat fragmentation on biodiversity intactness. This study found that although the original BII reported on the biodiversity trends of large-scale shifts in land-use across multiple scales it could not detect changes in landscape configuration which was reflected by the R-BII. Land-use change can impact on ecosystem processes that underpin the provisioning of ecosystem services by changing the combinations of species and the plant functional traits within communities. The impacts of cultivating potential biofuel species (Acacia mearnsii, Sorghum halepense and Eucalyptus species) were investigated using a plant functional traits approach. These species were shown to affect the leaf nitrogen content, leaf phosphorous content and leaf dry matter content associated with important ecosystem functions within an ecosystem service hotspot in the Eastern Cape. A decline in functional diversity was reported for all transformed land-uses by as much as ~40%. These shifts may be used to identify potential changes to ecosystem services associated with natural vegetation. The methods used in this thesis highlight the overall relevance of this work and its importance to minimising biodiversity resulting from biofuel production. Some of the key findings address resolving spatial conflict, using biodiversity indicators, assessing impacts of potential invasive species and planning for ecosystem services. New drivers of change to land-use, such as biofuel production, are a major challenge to conservation biologists and planners and the insights derived in from this study can be successfully applied to guide biofuel production. / AFRIKAANSE OPSOMMING: Biobrandstof word internasionaal beskou as 'n noodsaaklike komponent in die bereiking van klimaatsverandering doelwitte deur fossielbrandstowwe daarmee te vervang. Daarom word biobrandstof deur verskeie lande geïmplementeer as 'n potensiële meganisme om aan hierdie uitdaging te voldoen. Die Suid-Afrikaanse regering het voorgestel dat biobrandstof deel vorm van die land se hernubare energie toekoms en het daarom 'n konsep biobrandstofstrategie voorgestel. Die aanvaarding van so 'n strategie sal waarskynlik ‘n aantal verreikende gevolge inhou. Hierdie studie gebruik verskeie benaderings ten einde die impak van biobrandstof produksie op biodiversiteit te bepaal. Aangesien biobrandstof nie tans ‘n beduidende bydra maak tot tradisionele brandstofproduksie in Suid-Afrika nie, word die impak daarvan geskoei op die omskakeling van beskikbare grond. Die Oos-Kaap provinsie van Suid-Afrika speel a sleutelrol in hierdie opsig en vorm daarom die fokus van hierdie analise. Geskikte spesies is geïdentifiseer deur die sagtewareprogram, MaxEnt, waardeur spesiesverspreiding gemodelleer word. Hierdie studie beklemtoon die aansienlike oorvleueling wat daar bestaan tussen geskikte aanplantingsgebiede en belangrike biodiversiteitsareas wat nie tans formeel bewaar word nie. Sommige van die voorgestelde biobrandstofgewasse is tans indringers, of het die potensiaal om indringerplante te word en daarom is daar toenemende kommer oor die kweek van biobrandstof gewasse in Suid-Afrika. Die “Biodiversity Intactness Index” (BII), 'n algemene biodiversiteitsaanwyser, is gebruik om die implikasies van grondomskakeling na biobrandstof op biodiversiteit te evalueer. Die BII dui op verliese van tussen 17,6% en 42,1% vir die grondgebruikscenario's wat geïdentifiseer is. 'n Belangrike bevinding was dat die uitsluiting van belangrike biodiversiteitsareas buite beskermde gebiede die verlies van biodiversiteit met soveel as 13% kan verminder en biodiversiteit eenheid van ~ 70% kan behou. Die BII maak egter nie tans voorsiening vir landskap fragmentasie nie. ‘n “Revised-Biodiversity Intactness Index” (R-BII) is ontwikkel wat die effek van kol-grootte en habitat op biodiversiteit eenheid insluit. Hierdie studie het bevind dat alhoewel die oorspronklike BII grootskaalse verandering in die grondgebruik op verskeie skale aandui, dit egter nie verandering in landskapsamestelling kon opspoor soos die R-BII nie. Ten slotte, die impak van die aanplanting van potensiële biobrandstofspesies (Acacia mearnsii, Sorghum halepense en Eucalyptus spesies) op biodiversiteit is ondersoek deur ‘n plant funksionele eienskappe benadering te gebruik. Daar is bevind dat hierdie spesies die stikstof, fosfor en droë materiaal inhoud van blare verander wat geassosieer word met belangrike ekosisteem funksies binne 'n biodiversiteit brandpunt in die Oos- Kaap. ‘n Vermindering van funksionele diversiteit van soveel as ~ 40% is binne alle omgeskakelde grondgebruike gevind. Hierdie skuiwe kan gebruik word om potensiële veranderinge van ekosisteemdienste te identifiseer en benadruk ook die potensiële impak van uitheemse spesies. Die metodes wat gebruik word in hierdie studie beklemtoon die relevansie van die werk asook die belangrikheid daarvan om die nadelige uitwerking van biobrandstofproduksie op biodiversiteit te minimaliseer. Verskeie benaderings tot die oplossing van ruimtelike konflik, die gebruik van biodiversiteitaanwysers, die beoordeling van die impak van die potensiële indringerspesies en die beplanning vir ekosisteemdienste. Nuwe dryfvere van grondgebruikverandering soos biobrandstof is 'n groot uitdaging en die insigte wat uit hierdie studie verkry is dra by tot die vermindering van die potensiële impak van biobrandstofproduksie op biodiversiteit.

This dissertation examines the influence that economic and technological factors have on the penetration of biodiesel and ethanol into the transportation fuels market. This dissertation focuses on four aspects. The first involves the influence of fossil fuel prices, because biofuels are substitutes and have to compete in price. The second involves biofuel manufacturing technology, principally the feedstock-to-biofuel conversion rates, and the biofuel manufacturing costs. The third involves prices for greenhouse gas offsets. The fourth involves the agricultural commodity markets for feedstocks, and biofuel byproducts. This dissertation uses the Forest and Agricultural Sector Optimization Model-Greenhouse Gas (FASOM-GHG) to quantitatively examine these issues and calculates equilibrium prices and quantities, given market interactions, fossil fuel prices, carbon dioxide equivalent prices, government biofuel subsidies, technological improvement, and crop yield gains. The results indicate that for the ranges studied, gasoline prices have a major impact on aggregate ethanol production but only at low prices. At higher prices, one runs into a capacity constraint that limits expansion on the capacity of ethanol production. Aggregate biodiesel production is highly responsive to gasoline prices and increases over time. (Diesel fuel price is proportional to the gasoline price). Carbon dioxide equivalent prices expand the biodiesel industry, but have no impact on ethanol aggregate production when gasoline prices are high again because of refinery capacity expansion. Improvement of crop yields shows a similar pattern, expanding ethanol production when the gasoline price is low and expanding biodiesel. Technological improvement, where biorefinery production costs decrease over time, had minimal impact on aggregate ethanol and biodiesel production. Finally, U.S. government subsidies have a large expansionary impact on aggregate biodiesel production, but only expand the ethanol industry at low gasoline prices. All of these factors increase agricultural welfare with most expanding producer surplus and mixed effects on consumers.

With increasing global populations and demand for energy, greater strain is placed on the limited supply of fossil derived fuels, which in turn drives the need for development of alternative energy sources. The discovery of biophotolysis in Chlamydomonas reinhardtii and the development of a spectral-selective photosystem I activating/photosystem II deactivating light (PSI-light) method provides a promising platform for commercial hydrogen production systems. The PSI-light method allows electrons to pass through the photosynthetic electron transport chain while reducing radiation available for photosynthetic oxygen evolution that inactivates hydrogenase. Exploring the physiology of photohydrogen production using the PSI-light method can provide insight on how to optimize conditions for maximum hydrogen production. Through the use of photosynthetic mutant strains of C. reinhardtii, it was possible to suppress photosynthetic oxygen evolution further than using photosystem I light alone to extend photohydrogen production longevity and total yield. A preliminary investigation of an iterating light treatment revealed that longevity and yield could be increased further by providing a period of darkness to allow cells to consume evolved oxygen and resynthesize hydrogenase. Work with these mutants provided understanding that a balance of radiation was required to provide electrons to hydrogenase while limiting oxygen evolution, and that when no light was provided, fermentation of stored starch was the major contributor of electrons to hydrogen production. To determine the role of starch during hydrogen production, wild type cells were exposed to different media and light treatments and monitored for starch consumption and hydrogen production. The results indicated that starch was required for hydrogen production in the dark, but for photohydrogen production, starch likely played a minor role in contributing electrons to hydrogenase. The experiments also showed the importance of acetate in the medium during the hydrogen production phase to allow any significant photohydrogen production. The role of acetate was further investigated as a growth medium constituent that stimulates metabolic activity while reducing photosynthetic oxygen evolution when added to cells grown auto- or mixotrophically. By exposing cells to CO₂ during growth, photohydrogen production was significantly increased over cells grown only in the presence of acetate.

With additional research on species characteristics and continued work towards cost effective production methods, algae are viewed as a possible alternative biofuel crop to current feedstocks such as corn. Current open pond production methods involve bubbling carbon dioxide (CO_(2)) gas into the media to provide a carbon source for photosynthesis, but this can be very inefficient releasing most CO_(2) back into the atmosphere. This research began by investigating the effect of sodium bicarbonate (NaHCO_(3)) in the growth media as an alternative carbon source to bubbling CO_(2) into the cultures. The second part examined if NaHCO_(3) could act as a lipid trigger in higher (10.0 g/L) concentrations. The microalgae species Dunaliella tertiolecta (Chlorophyta), Mayamaea spp. (Baciallariophyta) and Synechoccocus sp. (Cyanophyta) were grown with 0.0 g/L, 0.5g/L, 1.0 g/L, 2.0 g/L and 5.0 g/L dissolved NaHCO_(3) in modified seawater (f/2) media. To investigate effects of NaHCO_(3) on lipid accumulation, growth media cultures were divided into two ―lipid phase‖ medias containing either 0.0g/L (non-boosted) or 10.0 g/L (boosted) NaHCO_(3) treatments. Culture densities were determined using spectrophotometry, which showed both all three species are able to successfully grow in media ameliorated with these high NaHCO_(3) concentrations. Highest growth phase culture densities occurred in NaHCO_(3) concentrations of 2.0 g/L for D. tertiolecta and Mayamaea spp., and the 5.0 g/L treatment for Synechoccocus sp. Highest growth rates occurred in the 5.0 g/L NaHCO_(3) concentration treatments for D. tertiolecta, Mayamaea spp., and Synechoccocus sp. (0.205 d-1 ±0.010, 0.119 d-1 ±0.004, and 0.372 d-1 ±0.003 respectively). As a lipid accumulation trigger two of the three species (D. tertiolecta and Mayamaea spp) had their highest end day oil indices in a 10.0 g/L treatment. Highest oil indices occurred in boosted 5.0 g/L Dunaliella tertiolecta and 2.0 g/L Mayamaea spp. (13136 ± 895 and 62844 ± 8080 respectively (relative units)). The results obtained indicate NaHCO3 could be used as a photosynthetic carbon source for growth in all three species and a lipid trigger for D. tertiolecta and Mayamaea spp.