Farmers will supply the raw ingredients for the emerging cellulosic ethanol industry. The long-term relationship between a farmer and a processing firm is expected to be contractual. A processing firm has an incentive to sign long-term contracts to ensure a cost-efficient level of raw ingredient supply. However, farmers generally prefer to operate with either no contract or a short-term contract in order to maintain options for adjustments in future acreage allocations due to changes in relative prices. Of interest in this research is to understand the incentives of farmers and calculating the efficient level of the “inflexibility premium”, which a processing firm must provide to a farmer when a long term contract is signed. A stochastic dynamic programming model is solved and with the help of Microsoft Excel numerically evaluated to illustrate the marginal inflexibility premium is increasing with contract length and the level of price variability, and is decreasing with the size of acreage adjustment costs. / Land and Food Systems, Faculty of / Graduate

Doctor of Philosophy / Department of Industrial & Manufacturing Systems Engineering / Zhijian Pei and Donghai Wang / Currently, transportation is almost entirely dependent on petroleum-based fuels (e.g. gasoline, diesel fuel, and jet fuel). Increasing demands for sustainable sources of liquid transportation fuels make it imperative to develop alternatives to petroleum-based fuels. Biofuels derived from cellulosic biomass (forest and agricultural residues and dedicated energy crops) have been recognized as promising alternatives to petroleum-based liquid fuels. Cellulosic biofuels not only reduce the nation’s dependence on foreign petroleum but also improve the environment through reduction of greenhouse gas emissions. In order to convert cellulosic biomass into biofuels, cellulosic biomass must go through a size reduction step first, because large size cellulosic biomass (whole stems of herbaceous biomass or chunks of woody biomass) cannot be converted to biofuels efficiently with the current conversion technologies. Native cellulosic biomass has limited accessibility to enzyme due to its structural complexity. Size reduction can reduce particle size and disrupt cellulose crystallinity, rendering the substrate more amenable to enzymatic hydrolysis. The purpose of this research is to provide knowledge of how size reduction alters biomass structural features, and understand the relationships between these biomass structural features and enzymatic hydrolysis sugar yield. This research is also aimed to investigate the impacts of process parameters in biomass size reduction on the conversion of cellulosic biomass to biofuels to help realize cost-effective manufacturing of cellulosic biofuels. This dissertation consists of eleven chapters. Firstly, an introduction of this research is given in Chapter 1. Secondly, Chapters 2 presents a literature review on cellulosic biomass size reduction. Thirdly, a preliminary experimental study is included in Chapter 3. Chapters 4 to 6 present a three-phase study on confounding effects of two important biomass structural features: particle size and biomass crystallinity. Chapters 7 and 8 investigate effects of sieve size used in size reduction of woody and herbaceous biomass, respectively. Chapters 9 and 10 focus on the relationship between particle size and sugar yield. Chapter 11 studies effects of cutting orientation in size reduction of woody biomass. Finally, conclusions and contributions are given in Chapter 12.

O mundo está passando por uma transformação profunda no setor energético. Ao que tudo indica estamos rumando para uma economia baseada em energias renováveis e de baixa emissão de carbono. O programa de bionenergia do Estado de São Paulo é o maior programa de bioenergia do mundo. Dentro desse programa produz-se etanol a partir da cana-de-açúcar, precisamente dos açúcares simples da cana-de-açúcar. O etanol produzido a partir dos açúcares simples da planta é denominado etanol de primeira geração. Entretanto, existe uma nova tecnologia para se produzir etanol a partir da celulose da cana-de-açúcar o etanol de segunda geração que possibilitará aumentar a eficiência energética do processo e fortalecer a competitividade do setor bioenergético nacional. O objetivo desse trabalho é prospectar cenários para o futuro do setor produtivo de etanol em São Paulo tendo em vista o etanol de segunda geração como elemento produtivo adjacente à produção atual de primeira geração. Para isso utilizou-se um modelo de construção de cenários que pressupõe uma detalhada consulta a especialistas, qualificação de variáveis quanto à sua importância e incerteza e identificação de variáveis-chaves. Por fim, foram criadas matrizes e roteiros para os cenários a partir das variáveis-chaves identificadas. Concluiu-se que dos quatro cenários construídos dois são favoráveis, um é desfavorável e um é pouco plausível. A metodologia de geração de variáveis-chaves foi aplicada com sucesso no setor produtivo de etanol. Os cenários criados podem lançar alguma luz possíveis futuros do setor estudado em relação ao etanol de segunda geração. / Nowadays the worlds energy sector is in a process of deep transformation. Apparently the world is going to a renewable energy based matrix, with low carbon emissions. The Sao Paulos bioenergetical program is the biggest renewable energy program in the world. In addition to that, it is also produced in that program ethanol from sugar cane. The ethanol that is produced in that program is made from the simple sugars of sugar cane. This ethanol is named first generation ethanol. However, there is a new technology to produce ethanol from sugar canes cellulose, named second generation ethanol. This important new technology could increase the energetic efficiency of process and make the Brazilians energetic production competitiveness stronger. The objective of this work was to prospect scenarios for the ethanols future in Sao Paulo looking at the second generation ethanol. For that it was used a model of scenario construction that presupposed an exhaustive inquire applied to specialists, qualifying trends related to their importance and uncertainty, and identifying the key parameters. At last, extracting the key parameters, matrices were made, and scripts too, both related to these scenarios. The conclusion was that the methodology for scenarios generation was applied with success on the ethanol industry, and those scenarios were able to illuminate with some light under plausible futures about the second generation ethanol.

Biofuels have been widely recognized as a potential renewable energy source that can lessen the United States’ dependence on imported petroleum and enhance the domestic economy. Particularly, biofuels derived from lignocellulosic biomass (LCB) have been the focus in the development of a sustainable biofuels industry. However, technical barriers in the LCB feedstock supply chain have been one of the major challenges impeding the economic viability of this industry. To expedite the commercialization process of LCB-based biofuels production, this paper employed a spatial mixed-integer mathematical model to explore the optimal biomass logistic system for a switchgrass-based biofuels biorefinery in East Tennessee. The evaluated logistic systems in this study included five conventional systems (one round bale system, one square bale system, and three mixed bale systems) in the baseline scenario and one stretch-wrap bale system in the preprocessing scenario. Results showed that the stretch-wrap bale system could potentially reduce total logistic cost of switchgrass by 12 to 21% compared that of the conventional systems. Also, the result of the optimal case in the conventional systems suggested that the mixed bale system without storage protection is most economical after taking into account the dry matter loss during storage. This study also provided information regarding the optimal location of a biorefinery, a switchgrass production plan, monthly harvested and delivered tonnage, and the draw area of switchgrass under each logistic system. The optimal location of a commercial-scale biorefinery was identified to be located in the northwest of Monroe County, a location close to the demonstration plant in Venore, Tennessee. Additionally, this study showed that the percentage of available hay land used for switchgrass production, the switchgrass-ethanol conversion rate, the energy prices, and the storage dry matter loss of compact switchgrass bale produce significant impacts on the total logistic cost of switchgrass for the biorefinery.

In this study, novel bio-inks formulated with horseradish peroxidase, HRP, and some additives were successfully developed for piezoelectric inkjet application. The optimized bio-ink formulation had a reliable jetting performance and maintained the biofunctionality before and after printing. The bio-ink also demonstrated a good storage life for up to 40 days at 4 oC with a negligible loss of biofunctionality. However, it was observed that some additives used in the bio-ink for obtaining necessary operational characteristics had detrimental effects on the enzyme activity. Especially, it was found that various viscosity modifiers typically used in commercial inkjet inks significantly impaired HRP activity prior to printing. Sodium Carboxymethyl Cellulose was shown to be an effective viscosity modifier that had no adverse effect on the biological activity of the HRP enzyme. Using a confocal scanning fluorescent microscope, a method for characterizing the spatial distribution of the active enzyme within the cellulosic paper substrates after inkjet printing was developed. Interestingly, it was found that the active printed HRP enzyme was mostly located in the cell walls of the cellulosic fibers instead of near the pigments or fillers. In an effort to better understand the fundamental interactions between the enzyme and the immobilization substrates, HRP adsorption isotherms on various substrate surfaces were obtained using the depletion method. The substrates included not only pulp fibers with varying degree of hydrophobicity and pigment and latex (the key materials used in papermaking), but also other types of cellulosic fibers of different morphologies, crystallinities, porosities, or surface charge densities. The influence on enzyme adsorption and inactivation behaviour of these substrates was compared with that of polystyrene beads (dialysed), which has been well studied in the literature. Results from this thesis indicated that hydrophobic interactions between the enzyme and the substrate surfaces had a major impact on the HRP adsorption behavior, while electrostatic interactions played a minor role. However, strong hydrophobic interactions could lead to enzyme inactivation. Research findings from this study suggested that cellulosic pulp fibers could be tailor-made into excellent enzyme immobilization supports by using existing fiber surface modification techniques.

In this study, novel bio-inks formulated with horseradish peroxidase, HRP, and some additives were successfully developed for piezoelectric inkjet application. The optimized bio-ink formulation had a reliable jetting performance and maintained the biofunctionality before and after printing. The bio-ink also demonstrated a good storage life for up to 40 days at 4 oC with a negligible loss of biofunctionality. However, it was observed that some additives used in the bio-ink for obtaining necessary operational characteristics had detrimental effects on the enzyme activity. Especially, it was found that various viscosity modifiers typically used in commercial inkjet inks significantly impaired HRP activity prior to printing. Sodium Carboxymethyl Cellulose was shown to be an effective viscosity modifier that had no adverse effect on the biological activity of the HRP enzyme. Using a confocal scanning fluorescent microscope, a method for characterizing the spatial distribution of the active enzyme within the cellulosic paper substrates after inkjet printing was developed. Interestingly, it was found that the active printed HRP enzyme was mostly located in the cell walls of the cellulosic fibers instead of near the pigments or fillers. In an effort to better understand the fundamental interactions between the enzyme and the immobilization substrates, HRP adsorption isotherms on various substrate surfaces were obtained using the depletion method. The substrates included not only pulp fibers with varying degree of hydrophobicity and pigment and latex (the key materials used in papermaking), but also other types of cellulosic fibers of different morphologies, crystallinities, porosities, or surface charge densities. The influence on enzyme adsorption and inactivation behaviour of these substrates was compared with that of polystyrene beads (dialysed), which has been well studied in the literature. Results from this thesis indicated that hydrophobic interactions between the enzyme and the substrate surfaces had a major impact on the HRP adsorption behavior, while electrostatic interactions played a minor role. However, strong hydrophobic interactions could lead to enzyme inactivation. Research findings from this study suggested that cellulosic pulp fibers could be tailor-made into excellent enzyme immobilization supports by using existing fiber surface modification techniques.

As the global demand for energy rises, there are significant efforts to find alternative energy sources. In the United States (US), these efforts are primarily motivated by a desire to increase energy security and reduce the potential impacts on climate change caused by carbon dioxide emissions from the burning of fossil fuels. Biofuels are considered a potential partial solution, which are being encouraged through public policy. Cellulosic ethanol is a biofuel that is required in increasing amounts over time as part of the Renewable Fuel Standards. Thus, researchers are exploring the environmental impacts of using this biofuel on a large scale. This dissertation research performed an environmental evaluation using the Life Cycle Assessment technique on Bioenergy Sorghum, a crop which was specifically produced as an energy crop, used in a conversion process (MixAlco version 1) that can produce cellulosic ethanol. Results indicate that the conversion process is highly optimized with minimal environmental concerns. Analysis of the crop production, however, demonstrate that further investigation is warranted regarding the depletion of natural resources and emissions from the fertilizers and pesticides/herbicides, due to large scale production of energy crops. A new policy is proposed to support the sustainable, environmentally responsible development of cellulosic ethanol in the US.

The carboxylate biofuels platform (CBP) involves the conversion of cellulosic biomass into carboxylate salts by a mixed microbial community. Chemical engineering approaches to convert these salts to a variety of fuels (diesel, gasoline, jet fuel) are well established. However, prior to initiation of this project, little was known about the influence of inoculum source on platform performance. The studies in this dissertation test the hypothesis that microbial communities from particular environments in nature (e.g. saline and/or thermal sediments) are pre-adapted to similar industrial process conditions and, therefore, exhibit superior performances. We screened an extensive collection of sediment samples from extreme environments across a wide geographic range to identify and characterize microbial communities with superior performances in the CBP. I sought to identify aspects of soil chemistry associated with superior CBP fermentation performance. We showed that CBP productivity was influenced by both fermentation conditions and inocula, thus is clearly reasonable to expect both can be optimized to target desired outcomes. Also, we learned that fermentation performance is not as simple as finding one soil parameter that leads to increases in all performance parameters. Rather, there are complex multivariate relationships that are likely indicative of trade-offs associated within the microbial communities. An analysis of targeted locus pyrosequence data for communities with superior performances in the fermentations provides clear associations between particular bacterial taxa and particular performance parameters. Further, I compared microbial community compositions across three different process screen technologies employed in research to understand and optimize CBP fermentations. Finally, we assembled and characterized an isolate library generated from a systematic culture approach. Based on partial 16S rRNA gene sequencing, I estimated operational taxonomic units (OTUs), and inferred a phylogeny of the OTUs. This isolate library will serve as a tool for future studies of assembled communities and bacterial adaptations useful within the CBP fermentations. Taken together the tools and results developed in this dissertation provide for refined hypotheses for optimizing inoculum identification, community composition, and process conditions for this important second generation biofuel platform.

O mundo está passando por uma transformação profunda no setor energético. Ao que tudo indica estamos rumando para uma economia baseada em energias renováveis e de baixa emissão de carbono. O programa de bionenergia do Estado de São Paulo é o maior programa de bioenergia do mundo. Dentro desse programa produz-se etanol a partir da cana-de-açúcar, precisamente dos açúcares simples da cana-de-açúcar. O etanol produzido a partir dos açúcares simples da planta é denominado etanol de primeira geração. Entretanto, existe uma nova tecnologia para se produzir etanol a partir da celulose da cana-de-açúcar o etanol de segunda geração que possibilitará aumentar a eficiência energética do processo e fortalecer a competitividade do setor bioenergético nacional. O objetivo desse trabalho é prospectar cenários para o futuro do setor produtivo de etanol em São Paulo tendo em vista o etanol de segunda geração como elemento produtivo adjacente à produção atual de primeira geração. Para isso utilizou-se um modelo de construção de cenários que pressupõe uma detalhada consulta a especialistas, qualificação de variáveis quanto à sua importância e incerteza e identificação de variáveis-chaves. Por fim, foram criadas matrizes e roteiros para os cenários a partir das variáveis-chaves identificadas. Concluiu-se que dos quatro cenários construídos dois são favoráveis, um é desfavorável e um é pouco plausível. A metodologia de geração de variáveis-chaves foi aplicada com sucesso no setor produtivo de etanol. Os cenários criados podem lançar alguma luz possíveis futuros do setor estudado em relação ao etanol de segunda geração. / Nowadays the worlds energy sector is in a process of deep transformation. Apparently the world is going to a renewable energy based matrix, with low carbon emissions. The Sao Paulos bioenergetical program is the biggest renewable energy program in the world. In addition to that, it is also produced in that program ethanol from sugar cane. The ethanol that is produced in that program is made from the simple sugars of sugar cane. This ethanol is named first generation ethanol. However, there is a new technology to produce ethanol from sugar canes cellulose, named second generation ethanol. This important new technology could increase the energetic efficiency of process and make the Brazilians energetic production competitiveness stronger. The objective of this work was to prospect scenarios for the ethanols future in Sao Paulo looking at the second generation ethanol. For that it was used a model of scenario construction that presupposed an exhaustive inquire applied to specialists, qualifying trends related to their importance and uncertainty, and identifying the key parameters. At last, extracting the key parameters, matrices were made, and scripts too, both related to these scenarios. The conclusion was that the methodology for scenarios generation was applied with success on the ethanol industry, and those scenarios were able to illuminate with some light under plausible futures about the second generation ethanol.

Second-generation biofuels have the potential to replace fossil fuels in the energy economy without negatively impacting the food supply. An effective biocatalyst must be able to convert all sugars found in lignocellulosic hydrolysates to biofuels. Few microbes exist in that have both a wide substrate range and high ethanol yields necessary for this process. Mixed culture biotechnology is a promising alternative to the use of single organisms in the production of fuels from lignocellulosic biomass. These systems mimic natural processes for the degradation of lignocellulose and exploit the native capabilities of each microbe. The segregation of metabolic pathways allows for the individual optimization of each step in the process. Preliminary work with a consortium capable of saccharification and fermentation showed promise, but the dynamics were poorly understood. Metabolic modeling is a powerful tool for understanding the interactions between microbes in mixed cultures. The development of accurate models of mixed culture metabolism will help drive the engineering of these systems for industrial applications. In this dissertation, dynamic flux balance analysis is applied to mixed culture systems by combining mathematical reconstructions of pure culture metabolism. By tuning the inoculum to sugar concentration, simulations of Saccharomyces cerevisiae and Escherichia coli mutants engineered to ferment a specific substrate display the potential for improved ethanol production over pure cultures. A framework for translating model predictions to experimental systems was developed for a co-culture of S. cerevisiae and xylose-specific E. coli. The consumption of sugar mixtures was optimized through this method, but the inability of the predicted gains in ethanol production to be replicated in experimental systems reveals the importance of selecting microbes with similar optimal growth conditions. The more compatible microbes S. cerevisiae and Scheffersomyces stipitis were modeled under microaerobic conditions to optimize ethanol production from a mixture of glucose and xylose. To further demonstrate the ability of these systems to ferment lignocellulosic hydrolysates, the effect of furan inhibitors on pure and co-cultures was assessed through modeling and experiment. The work presented here represents the first steps towards engineering and optimizing a microbial consortium for the production of ethanol from lignocellulosic biomass.