With growing concerns over emissions, homogeneous charge compression ignition (HCCI) engines offer a promising solution through reducing NOx and particulate emissions and increasing efficiency. However, this technology is not without its challenges and numerical modeling of these engines can offer some insight into addressing these challenges. This study uses domain decomposition with FORTRAN MPI to subdivide computationally intensive sections of a 10 zone simulation model. Using an Intel i7 quadcore workstation the parallelized model reduced runtimes by half compared to serial computations. From here, two sets of biofuel experimental data were used to improve the validation base of the model. The fuels used were a simulated biomass derived gas (consisting of H2, CH4, CO, CO2, and N2) and a butanol/n-heptane blend. Once calibrated, the model showed good pressure, heat release, and products of incomplete combustion prediction for biogas. NOx emissions were high, however the overall trend was captured. Similarly, once calibrated to the butanol/n-heptane data to account for some of the effects of negative valve overlap (NVO), excellent pressure and heat release predictions were obtained. However, products of incomplete combustion and NOx were low and this was attributed to the inability of the model to properly account for inhomogeneity and all the effects of NVO. Once again though, the overall trend in NOx levels was captured by the model. It was also found that the model does not operate very well near the misfire limit of the engine as it cannot capture the cyclic variability that can occur here. Based on the two new validation cases, it is concluded that once calibrated, the model can be used as a predictive tool for pressure, heat release, and combustion phasing of biofuelled HCCI engines. Furthermore, to improve its predictive capabilities, it is recommended that the model be restructured to incorporate mass transfer between zones, a fixed crevice volume and variable thermal boundary layer, and a CFD solver to improve emissions predictions and reduce reliance on calibration. Finally, changing the zone distribution from ring like zones to lumped stirred reactors is recommended to allow for more realistic modeling of actual experimental HCCI conditions.

A growing world population drives an ever-increasing need for food and energy. These challenges, along with depletion of water and fossil fuel resources, call for improvements in crop production systems and the cultivars used within them. Perennial cropping systems present an attractive solution to many of these problems. A greater understanding of the genetic control of over-wintering ability within crop species is one way to begin the process of making perennial cropping systems a possibility. In this study an F3:F4 family derived from a cross between Sorghum bicolor (L.) Moench and S. propinquum (Kunth) Hitchc. segregating for rhizome production was phenotyped in both field and greenhouse environments for traits relating to rhizomatousness and over-wintering. Several statistical models were created to correlate rhizome growth and over-wintering. A known rhizome quantitative trait locus (QTL) region was saturated with SSR markers and the QTL interval was reduced from previous estimates of about 16 Mb or 7 cM to 12 Mb or 2 cM, a 25% or 71% reduction in physical or linkage distance respectively. Two previously unidentified QTL regions associated with over-wintering were also identified. Our results also support the hypothesis that rhizome growth is important and possibly necessary for over-wintering in Sorghum.

Pollution and environmental concerns require further improvements in engine technologyas well as research of alternative fuels. Users of handheld products are directlyexposed to the exhaust gas and thus to the occurring emissions, which cancause significant damage. Pursuing to reduce emissions is therefore a vital task.The European commission proposed a renewable energy directive, that claims abiofuel share of at least 6,8% by 2030 and a reduction of first generation fuel butan increasing of second generation fuels. Ethanol is up to now the most commonsource of renewable alternatives in gasoline blends. Isobutanol has several advantagesover ethanol and can be produced as a second generation biofuel.This thesis aims to get a better understanding on how isobutanol influences theemission and combustion in small two-stroke engines and furthermore what effectdifferent isobutanol blends with neat gasoline and alkylate have on the engine performance.Different isobutanol blends with neat gasoline as well as alkylate fuel have beenused and analyzed.This thesis has via an experimental study shown, that hydrocarbon as well as carbonmonoxide emission increased with increasing isobutanol percentage. Hence, nitrogenoxides emission decreased with isobutanol. Lower cylinder and exhaust temperatureswere measured with isobutanol blends. Through cylinder pressure measurements,the mass fraction burned, mass fraction burned 50% and rapid burningangle could be analyzed. It has shown that isobutanol blends reach a mass fractionburned of 50% slightly later and have a greater rapid burning angle.

Doctor of Philosophy / Department of Industrial & Manufacturing Systems Engineering / Jessica L. Heier Stamm / This dissertation focuses on logistics challenges arising in the biofuels industry. Studies have found that logistics costs in the biomass-to-biofuel supply chain (BBSC) account for 35%-65% of total biofuel production cost. This is mainly due to the low density of biomass that results in high costs associated with biomass transportation, storage, and handling in the biomass-to-biofuel supply chain. Densification provides an as-yet-unexplored opportunity to reduce logistic costs associated with biomass-to-biofuel supply chains. This research advances understanding about biomass-to-biofuel supply chain management through new optimization models. As a first step, the author presents an extensive overview of densification techniques and BBSC optimization models that account for biomass densification. This literature review helps the author to recognize the gaps and future research areas in BBSC studies. These gaps direct the author toward the remaining components of the dissertation. In particular, the literature review highlights two research gaps. First, the review indicates that mobile pelleting holds promise for improved BBSC management, but that there is no mathematical optimization model that addresses this opportunity. Second, currently, there does not exist a model that explicitly accounts for farmers’ objectives and their probability to sell biomass to the bioenergy plant in BBSC optimization. To fill the first gap, the author focuses on managing the BBSC considering mobile densification units to account for chances to minimize logistics costs. A mixed integer linear programming model is proposed to manage the BBSC with different types and forms of biomass feedstock and mobile densification units. Sensitivity analysis and scenario analysis are presented to quantify conditions that make mobile densification an attractive choice. The author conducts a case study to demonstrate model applicability and type of analysis that can be drawn from this type of models. The result indicates that mobile pelleting is not an attractive choice under the current economic status. However, modest changes in pelleting cost, satellite storage location fixed cost, and/or travel distances are enough to make mobile pelleting an attractive choice. To fill the second gap, the author introduces a model that explicitly accounts for mobile densification and farmers’ probability to supply a bioenergy plant with biomass feedstock. Farmers’ probability to provide biomass to the bioenergy plant depends on contract attributes, including expected net return and services provided by the bioenergy plant. The proposed model helps the bioenergy plant to meet biofuel demand while considering farmers’ choices that satisfy their own objectives and preferences. The model makes it possible to determine most important factors that influence type of contract offered to each supplier and optimal BBSC design. A case study based on the state of Kansas is conducted to demonstrate how bioenergy plant can benefit from this type of model.

AN ABSTRACT OF THE THESIS OF Thara G. Siddaramu, for the Master of Science degree in Civil and Environmental Engineering, presented on February 5, 2011, at Southern Illinois University Carbondale. TITLE: EVALUATION OF DIFFERENT PRETREATMENT APPROACHES FOR DISRUPTING LIGNOCELLULOSIC STRUCTURES MAJOR PROFESSOR: Dr. Yanna Liang There are two major steps in biofuel production- pretreatment of lignocellulosic materials and enzymatic hydrolysis. The present study investigated the ability of two pretreatment methods, namely traditional oven and microwave oven treatments for disrupting lignocellulosic structures. The substrates tested were Jatropha seed cake and sweet sorghum bagasse. In recent years, Jatropha curcas also known as physic nut or purging nut has attracted extensive attention due to its several unique characteristics. Similarly, sweet sorghum has the potential to provide great value to energy sectors and food industries being that the entire plant is rich in various sugars and nutrients. Both crops can adapt to various climates, and can withstand extended drought conditions compared to other crops. Additionally, both Jatropha seed cakes and sweet sorghum bagasse are good sources of lignin and carbohydrates, which could be used for production of biofuels only if the sugars can be unlocked. Several treatment methods such as mechanical, physical, chemical and biological treatments have been reported to breakdown the cellulosic structure of biomass. However, other low cost and quicker methods, such as ovenpretreatment and microwave irradiation have not been evaluated for Jatropha seed cake and Sweet Sorghum Bagasse (SSB), respectively. Composition change of Jatropha seed cake samples was evaluated upon lime pretreatment at 100 oC with different parameters. With a lime dose of 0.2 g and a water content of 10 ml per gram of cake and a treatment period of 1 h, 38.2 ± 0.6% of lignin was removed. However, 65 ± 16% of hemicellulose was also lost under this condition. For all the treatments tested, cellulose content was not affected by lime supplementation. Through further examining total reducing sugar (TRS) release by enzymatic hydrolysis after lime pretreatment, results indicated that 0.1 g of lime and 9 ml of water per gram of cake and 3 h pretreatment produced the maximal 68.9% conversion of cellulose. Without lime pretreatment, the highest cellulose conversion was 33.3%. Finally, this study shows that Jatropha seed cake samples could be hydrolyzed by enzymes. Even though the cellulose content was not high for this Jatropha cake sample, the fractionation by lime presented in this study opened the door for other applications, such as removal of lignin and toxicity for use as animal feed and fertilizer. The microwave radiation pretreatment of SSB was evaluated with or without lime (0.1 g/g bagasse) at 10 ml water/g bagasse for 4 min. TRS release over 72-h enzymatic hydrolysis was different for samples treated differently and at different solid loadings. The TRS concentration was increased by 2 and 5-fold from 0 to 24 hours in non lime-pretreated and lime-pretreated samples, respectively. Further incubation of samples for 48 and 72 h did not result in increased TRS. Comparing different solid loadings of samples treated with or without lime, 1% solid content resulted in 1.4 times higher TRS increase than that of 5% solid concentration. Therefore, lime was effective in disintegrating lignocellulosic structures and making cellulose more accessible for saccharification. Higher solid loadings which can lead to higher sugar concentrations are desired for downstream biofuel production. But, as shown in this study, higher concentration of bagasse samples decreased rate of cellulose hydrolysis due to poorer mixing efficiency and hindrance to interactions between enzymes and solid materials. Thus, an optimal solid content needs to be determined for maximal cellulose hydrolysis and for preparing the hydrolysates for downstream processes, either bioethanol or lipid production.

With recent emphasis on development of alternatives to fossil fuels, sincere attempts are being made on finding suitable lignocellulosic feedstocks for biochemical conversion to fuels and chemicals. Sweet Sorghum is among the most widely adaptable cereal grasses, with high drought resistance, and ability to grow on low quality soils with low inputs. It is a C4 crop with high photosynthetic efficiency and biomass yield. Since sweet sorghum has many desirable traits, it has been considered as an attractive feedstock. Large scale sweet sorghum juice extraction results in excessive amounts of waste sweet sorghum bagasse (SSB), which is a promising low cost lignocellusic feed stock. The ability of two pretreatment methods namely conventional oven and microwave oven pretreatment for disrupting lignocellulosic structures of sweet sorghum bagasse with lime [Ca(OH)2] and sodium hydroxide [NaOH] was evaluated. The primary goal of this study was to determine optimal alkali pretreatment conditions to obtain higher biomass conversion (TRS yield) while achieving higher lignin reduction for biofuel production. The prime objective was achieved using central composite design (CCD) and optimization of biomass conversion and lignin removal simultaneously for each alkali separately by response surface method (RSM). Quadratic models were used to define the conditions that separately and simultaneously maximize the response variables. The SSB used in this study was composed of cellulose, hemicellulose, and lignin in the percentage of 36.9 + 1.6, 17.8 + 0.6, and 19.5 + 1.1, respectively. The optimal conditions for lime pretreatment in the conventional oven at 100 °C was 1.7 (% w/v) lime concentration (=0.0024 molL-1), 6.0% (w/v) SSB loading, 2.4 hr pretreatment time with predicted yields of 85.6% total biomass conversion and 35.5% lignin reduction. For NaOH pretreatment, 2% (w/v) alkali (=0.005 molL-1), 6.8% SSB loading and 2.3 hr duration was the optimal level with predicted biomass conversion and lignin reduction of 92.9% and 50.0%, respectively. More intensive pretreatment conditions removed higher amount of hemicelluloses and cellulose. Microwave based pretreatments were carried out in a CEM laboratory microwave oven (MARS 6-Xpress Microwave Reactions System, CEM Corporation, Matthews, NC) and with varying alkali concentration(0.3 - 3.7 % w/v) at varying temperatures (106.4 - 173.6 °C), and length of time (6.6 - 23.4 min). The NaOH pretreatment was optimized at 1.8 (% w/v) NaOH, 143 °C, 14 min time with predicted yields of 85.8% total biomass conversion and 78.7% lignin reduction. For lime pretreatment, 3.1% (w/v) lime, 138 °C and 17.5 min duration was the optimal level with predicted biomass conversion and lignin reduction of 79.9% and 61.1%, respectively. Results from this study were further supported by FTIR spectral interpretation and SEM images.

Les microalgues sont souvent considérées comme de potentielles candidates pour la production d'énergie. Cependant, le lien entre l'énergie contenue dans la biomasse et l'énergie nécessaire pour cultiver les microalgues, en particulier pour agiter la culture, est complexe. Le mélange a un effet direct sur la photosynthèse car il affecte la façon dont les cellules sont successivement transportées entre la lumière et les zones sombres. En particulier, l'hydrodynamique module la fréquence à laquelle la lumière est perçue par les cellules. Dans cette thèse nous avons étudié la réponse du processus de photosynthèse à divers signaux lumineux. Tout d'abord, l'effet de cycles lumière-obscurité a été étudié à l’aide d'un modèle mécaniste de photosynthèse et de croissance. Il a été montré que l'augmentation de la fréquence lumineuse augmente l'efficacité photosynthétique. Ensuite, nous avons développé un modèle de photoacclimatation, en supposant à la fois un changement dans le nombre et la section des photosystèmes. Les concepts proposés ont ensuite été validés expérimentalement. Un dispositif à base de LED a été développé et des cycles lumière-obscurité de fréquences variables ont été appliqués à Dunaliella Salina. Les résultats confirment les prédictions des modèles, comme la dynamique de photoacclimatation. Enfin, un modèle hydrodynamique 3D a été simulé pour un raceway. Cela a permis de reconstruire numériquement les trajectoires lagrangiennes de cellules, et donc d’évaluer le signal lumineux perçu par les microalgues. Ces trajectoires réalistes ont alors alimenté un modèle de photosynthèse et ont permis de comprendre l’effet du mélange sur l'efficacité photosynthétique. / Microalgae are often seen as a promising candidate to contribute to energy generation in the future. However, the link between the energy contained in the biomass and the required energy to grow the microalgae, especially to mix the culture, is complex. Mixing has a direct effect on photosynthesis since it affects the way cells are successively transported between light and dark zones, especially the hydrodynamics modulates the frequency at which light is percept by the cells. In this thesis the question of nonlinear response of the photosynthesis process to varying light signals at different time scales has been investigated. Firstly, the effect of light-dark cycle frequency on the response of a mechanistic model for photosynthesis and growth has been studied. It is shown that increasing the light supply frequency enhances photosynthetic efficiency. A model for photoacclimation has been developed assuming both a change in the number and the cross section of the photosystems. The proposed concepts have been experimentally validated using a self-developed LED device to expose the green algae Dunaliella Salina to light-dark cycles at different frequencies. The results support model hypotheses, i.e. mid-term photoacclimation depends on the average light intensity. Finally, a 3D hydrodynamic model for a raceway type culturing device has been used to compute Lagrangian trajectories numerically. Based on the trajectories, time-dependent light signals for individual cells have been calculated. Using these light signals, a photosynthesis model was integrated in order to investigate the dependency of photosynthetic efficiency on hydrodynamic regime.

Made available in DSpace on 2014-06-11T19:23:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-07-24Bitstream added on 2014-06-13T20:30:08Z : No. of bitstreams: 1 barbosa_alpbf_me_jabo.pdf: 711874 bytes, checksum: 2ed60bdad987609854ea431a1857f8b2 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Considerando-se o petróleo um recurso natural não-renovável, o Biodiesel apresenta-se como relevante alternativa de combustível, sendo ele renovável, biodegradável e podendo ser produzido a partir de gordura animal ou óleo vegetal transesterificado com álcool anidro, na presença de catalisador. O presente trabalho teve como objetivo avaliar o desempenho operacional e a opacidade da fumaça de um trator agrícola funcionando com Biodiesel de mamona, em operação de preparo de solo. O ensaio foi conduzido no Departamento de Engenharia Rural da UNESP-Jaboticabal, em delineamento inteiramente casualizado, em esquema fatorial 6x2, com quatro repetições. O primeiro fator representa seis proporções percentuais de Biodiesel + diesel de B0 (0+100), B5 (5+95), B15 (15+85), B25 (25+75), B50 (50+50) e B75 (75+25) e o segundo representa duas operações de preparo do solo (gradagem e escarificação). Ressalta-se que B75 foi a máxima proporção de mistura, devido ao alto índice de viscosidade do biocombustível, sendo tal característica limitadora para o funcionamento do motor diesel. Os resultados evidenciaram aumento no consumo específico de 19% quando se utilizou B75 em relação a B0. A operação de gradagem teve consumo específico 16% maior em relação à operação de escarificação. Para a opacidade da fumaça, houve redução de 35% de B75 comparado com B0. / Considering petroleum as a non-renewable natural resource, Biodiesel presents itself as a relevant fuel alternative, being renewable, biodegradable and can be produced from vegetal oil transesterification with anhydride alcohol in the presence of a catalisator. This work has the goal of analyzing the operational performance and smoke opacity of a agricultural tractor running with mamona Biodiesel in soil tillage operations. The test was done in the Department of Rural Engineering of UNESP-Jaboticabal in design completely randomized, in factorial scheme 6x2, with four repetitions. The first factor represents six percentual proportions of Biodiesel plus diesel B0 (0+100), B5 (5+95), B15 (15+85), B25 (25+75), B50 (50+50) e B75 (75+25) and the second represents two soil tillage operations (harrowing and chiseling). It is important to note that B75 was the maximum mixture proportion due to the high level of biofuel viscosity, this characteristic being not recommended for diesel engines. The results showed that the specific consumption raised by 19% when B75 was used instead of B0. The harrowing operation had specific consumption 16% higher than the chiseling operation. For smoke opacity, it was noted a reduction of 35% of B75 compared to B0.

abstract: Overall, biofuels play a significant role in future energy sourcing and deserve thorough researching and examining for their best use in achieving sustainable goals. National and state policies are supporting biofuel production as a sustainable option without a holistic view of total impacts. The analysis from this research connects to policies based on life cycle sustainability to identify other environmental impacts beyond those specified in the policy as well as ethical issues that are a concern. A Life cycle assessment (LCA) of switchgrass agriculture indicates it will be challenging to meet U.S. Renewable Fuel Standards with only switchgrass cellulosic ethanol, yet may be used for California's Low Carbon Fuel Standard. Ethical dilemmas in food supply, land conservation, and water use can be connected to biofuel production and will require evaluation as policies are created. The discussions around these ethical dilemmas should be had throughout the process of biofuel production and policy making. Earth system engineering management principles can help start the discussions and allow anthropocentric and biocentric viewpoints to be heard. / Dissertation/Thesis / Masters Thesis Civil and Environmental Engineering 2014

A degradação enzimática rápida, eficiente e robusta de polissacarídeos derivados de biomassa lignocelulósica é atualmente um grande desafio na produção de biocombustíveis e considerada uma alternativa viável e promissora para se enfrentar a crise energética mundial e diminuir a dependência das fontes fósseis de energia. O bagaço de cana-de-açúcar no Brasil é a principal matéria lignocelulósica sustentável de grande potencial para a produção do etanol de 2ª geração. O principal requisito para a consolidação dessa abordagem é a disponibilidade de enzimas que hidrolisam a celulose, hemicelulose e outros polissacarídeos em açúcares fermentescíveis e em condições adequadas para a utilização industrial. O presente estudo visou à caracterização molecular, estrutural e funcional da endoglucanase GH12 do fungo Aspergillus terreus (AtGH12) por diferentes técnicas. O gene que codifica para essa enzima foi clonado e expressado no fungo filamentoso A. nidulans linhagem A773. A cepa com maior secreção foi selecionada e a sequência da enzima confirmada por espectrometria de massas MALDI TOF MS. Posteriormente, através de estudos funcionais de parametrização enzimática como pH e temperatura ótimos, estabilidade térmica, efeitos supressores e potencializadores de aditivos, a enzima AtGH12 foi caracterizada bioquímica e fisicamente. A espectrometria de massas do substrato hidrolisado pela catálise enzimática foi tomada como uma forma de investigar o padrão de clivagem da hidrólise e estudo do reconhecimento enzima/substrato para a AtGH12. As caracterizações estruturais das enzimas recombinantes obtidas utilizando as técnicas de espalhamento dinâmico de luz, dicroísmo circular, espalhamento de raios X a baixo ângulo e gel nativo serviram para determinação do enovelamento e estado oligomérico em solução da AtGH12. Com o intuito de fornecer subsídios para o desenvolvimento de coquetéis enzimáticos mais eficazes para hidrólise da biomassa lignocelulósica, a atividade da AtGH12 foi avaliada frente ao bagaço de cana-de-açúcar pré-tratados pelos processos hidrotérmicos e organossolve. Posteriormente, o seu grau de sinergismo nesse tipo de substrato foi determinado com o coquetel enzimático comercial Acellerase&reg. / Fast, more efficient and robust enzymatic degradation of lignocellulosic biomassderived polysaccharides is currently a major challenge in the production of biofuels and considered a feasible and promising alternative to confront the global energy crisis and reduce the dependence on fossil energy resources. The sugarcane bagasse in Brazil is the most abundant and sustainable lignocellulosic material for the production of 2nd generation ethanol. The main requirement for the consolidation of this approach is the availability of enzymes that hydrolyze cellulose, hemicelluloses and other polysaccharides into fermentable sugars suitable for industrial use. The present study was aimed at molecular, structural and functional characterization of an endoglucanase from the fungus Aspergillus terreus (AtGH12) using different techniques. The gene encoding this enzyme has been cloned and expressed in the filamentous fungus Aspergillus nidulans strain A773. The strain with increased secretion was selected and the enzyme sequence was confirmed by mass spectroscopy MALDI TOF MS. Later, functional studies such as analysis of optimal pH and temperature, thermal stability, suppression and enhance effects of additives were applied to the AtGH12 characterization. The mass spectrometry of hydrolyzed substrate from the enzyme catalysis was acquired as a way to investigate the cleavage pattern of hydrolysis and the study of the enzyme/substrate interaction. Structural characterization of the recombinant enzymes was obtained using techniques such as dynamic light scattering, circular dichroism as well as small angle X-ray scattering and native gel, aided to determine the folding and oligomeric state of AtGH12 in solution. In order to provide support for the development of more effective enzyme cocktails for hydrolysis of lignocellulosic biomass, the activity of AtGH12 was evaluated using sugarcane bagasse pretreated by hydrothermal and organosolv processes. Subsequently, the degree of synergism in this type of substrate was measured using a commercial enzyme cocktail Acellerase&reg.