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Use of biofuels, especially in automotive applications, is a growing trend due to their potential to lower greenhouse gas emissions from combustion. Ketones are a class of biofuel candidates which are produced from cellulose. However, ketones received rather scarce attention from the combustion community compared to other classes such as, alcohols, esters, and ethers. There is little knowledge on their combustion performance and pollutant generation. Hence their combustion chemistry needs to be investigated in detail. Diisopropyl ketone (DIPK) is a promising biofuel candidate, which is produced using endophytic fungal conversion. A detailed understanding of the combustion kinetics of the oxidation of DIPK in advanced engines such as, the homogeneous charge compression ignition (HCCI) engine is warranted. This dissertation concentrates on the combustion kinetics of DIPK over a wide range of temperature and pressure with a focus on HCCI engine application. An existing DIPK kinetic mechanism has been reviewed and a single zone HCCI engine model has been modeled and validated against recent experimental data from Sandia National Lab. Therefore different HCCI modeling assumptions were tested and the DIPK reaction mechanism was modified with missing reactions and the required thermochemical data. As a result, the HCCI pressure trace, heat release rate and reactivity have been improved. In order to improve the ignition delay time simulation results, the low temperature oxidation of DIPK was studied as the fuel chemistry effects on the autoignition behavior becomes important in low temperature. Therefore DIPK low temperature oxidation experimental data was obtained from the synchrotron photoionization experiments conducted at the Advanced Light Source (ALS) so that the primary products as well as the dominant oxidation pathways are identified. Furthermore, the aldehydes oxidation, as a result of partial or incomplete combustion and as the primary stable intermediate products in oxidation and pyrolysis of biofuel were studied at low temperature in ALS. A high temperature reaction mechanism was created using the reaction class approach. The reaction mechanism for DIPK was improved using the experimental data along with quantum chemical calculation of activation energies and barriers as well as vibrational modes for the important reactions identified in ALS experiment. The rate constants for important reactions were calculated based on modified Arrhenius equation. DIPK oxidation and pyrolysis were studied at high temperature and pressure using UCF shock tube. The ignition delay times as well as the product (methane) time histories were investigated and used as validation targets for the new model.

Lignocellulosic ethanol offers a promising alternative to conventional fossil fuels. One among the major limitations in the lignocellulosic biomass hydrolysis is unavailability of efficient and environmentally biomass degrading technologies. Plantbased production of these enzymes on large scale offers a cost effective solution. Cellulases, hemicellulases including mannanases and other accessory enzymes are required for conversion of lignocellulosic biomass into fermentable sugars. β- mannanase catalyzes endo-hydrolysis of the mannan backbone, a major constituent of woody biomass. In this study, man1 gene encoding β-mannanase was isolated from Trichoderma reesei and expressed via the chloroplast genome. PCR and Southern hybridization analysis confirmed the site-specific transgene integration into the tobacco chloroplast genomes and homoplasmy. Transplastomic plants were fertile and set viable seeds. Germination of seeds showed inheritance of transgenes into the progeny without Mendelian segregation. Expression of the endo-β-mannanase gene for the first time in plants facilitated its characterization for use in enhanced lignocellulosic biomass hydrolysis. Gel diffusion assay for endo-β-mannanase showed the zone of clearance confirming functionality of chloroplast-derived mannanase. Endo-β-mannanase expression levels reached up to 25 units per gram of leaf (fresh weight). Chloroplastderived mannanase had higher temperature stability (40 °C to 70 °C) and wider pH optima (pH 3.0 to 7.0) than E.coli enzyme extracts. Plant crude extracts showed 6-7 fold iv higher enzyme activity than E.coli extracts due to the formation of disulfide bonds in chloroplasts, thereby facilitating their direct utilization in enzyme cocktails without any purification. Chloroplast-derived mannanase when added to the enzyme cocktail containing a combination of different enzymes yielded 20% more glucose equivalents from pinewood than the cocktail without mannanase. Our results demonstrate that chloroplast-derived mannanase is an important component of enzymatic cocktail for woody biomass hydrolysis and should provide a cost-effective solution for its diverse applications in the paper, oil, pharmaceutical, coffee and detergent industries.

The recent spikes in oil prices have spurred an already bullish demand on biofuels as a source of alternative energy. However, the unprecedented price records set simultaneously by staple food have raised high concerns about potential impacts of biofuels on the global agricultural landscape as fuel and food markets are being inextricably coupled. The revival of interest in the Fischer-Tropsch (FT) process comes into full force since it offers a promising way to produce carbon-neutral liquid fuels which are readily usable with today's existing infrastructure. The FT synthesis offers the possibility of using crop waste as feedstock instead of the crop itself thus avoiding the risk of further straining water and land resources while helping to alleviate the national energy bill and to achieve independence from foreign oil. As the airline industry is the hardest-hit sector with fuel jumping ahead of labor as the primary cost item, this thesis investigates the prospects of the FT process to transform sugar cane waste (namely bagasse, tops and green leaves) and landfill gas in order to produce kerosene (C12H26) as jet fuel for civil aviation. Established chemical correlations and thermodynamics of chemical reactions are used to assess the water footprint inherent to kerosene production using the above feedstocks at optimal conditions of temperature, pressure, catalyst and reactor type. It has been estimated that 9 to 19 gallons of water are needed for every gallon of kerosene produced. In addition, for the case of sugar cane, less land area per unit energy is required compared to ethanol production since all non-food waste of the plant can be used to produce FT fuel as opposed to ethanol which would utilize only the sugar (food) portion of the plant. This translates into a much lower water footprint for irrigation and consequently a lower water footprint overall.

The use of biofuels as an alternative to gasoline in the transportation sector is seen by policy makers as an important strategy to reduce global greenhouse gas emissions. Biobutanol is one such biofuel that is gathering increasing attention in the biofuel community, because of its preferable fuel qualities over bioethanol. However, despite increasing research into biobutanol production, the thermochemical route for biobutanol production has not been adequately studied in the peer-reviewed literature. In light of this motivation, this thesis considers the design, and economic and environmental assessment of thermochemical plants for producing second and third generation biobutanol. In addition, the potential for using process intensification technology such as dividing wall columns (DWC) in place of conventional distillation columns is also investigated as a way to improve thermochemical biobutanol plants. As a first step, a novel thermochemical plant for producing second generation biobutanol is developed. Detailed economic analysis of this plant show that it is competitive with gasoline under certain process, and market conditions. The designed plant is then extended, with some modifications, to evaluate the economic and environmental potential of a thermochemical plant for producing third generation biobutanol from macroalgae. It was concluded from the results that the thermochemical route is preferable for producing second generation biobutanol over third generation biobutanol. The novel thermochemical plant design is then updated by using a kinetic model of a pilot-scale demonstrated catalyst to represent the critical mixed alcohol synthesis reaction step. This change allows optimal unreacted syngas recycle configurations for maximizing butanol yield to be established. Furthermore, integrating a DWC, designed using a methodology developed in the thesis, into the updated thermochemical plant leads to additional plant improvements. Overall, the work carried out in this thesis demonstrates that the thermochemical route is a viable option for producing second generation biobutanol. / Thesis / Doctor of Philosophy (PhD)

To reduce reliance on fossil fuels, sustainable biofuels are being pursued, especially advanced biofuels like 1-butanol that have higher energy content and greater compatibility with existing infrastructure than ethanol. A persistent challenge is the yield-limiting toxicity of biofuels and process solvents, such as tetrahydrofuran, to the microbes that ferment biomass into biofuel. The cell membrane is a focal point of toxicity, and understanding how it interacts with fuels and solvents is key to improving yield. Phospholipid bilayers are the core of biomembranes, and model biomembranes of defined composition provide the ideal platform for biophysical studies. To this end, glycerophospholipids characteristic of Bacillus subtilis, a model producer organism, were synthesized. Two fatty acids (iso- and anteisopentadecanoic acids) characteristic of Bacilli were synthesized and incorporated into representative phosphatidic acid, phosphatidylethanolamine and phosphatidylglycerol lipids. The validated synthetic approach opens the door to future studies on the interaction of biofuels and solvents with biomembranes.

In the current pursuit of sustainable energy, biofuel cells are attracting considerable attention. Within biomedical engineering, the concept of harnessing energy from biological fluids, such as blood, holds significant promise, enabling both full autonomy and miniaturization. In this context, this study aims to identify the most efficient biofuel cells for miniaturised implantable biosensors and design a prototype based on the obtained results. To achieve this goal, a systematic literature review was conducted, comparing biofuel cells based on relevant parameters for powering devices, including power density and operative voltages. This categorization guided material selection, considering a cost-performance trade-off. Carbon nanotubes and Laccase were chosen to facilitate oxygen reduction at the cathode, while carbon nanotubes with Glucose Oxidase (with and without ferrocenemethanol) played a similar role at the anode—where glucose proved to be the most advantageous fuel. Electrode functionalization and assessment involved electrochemical and morphological analyses, culminating in the recording of initial results for the biofuel cell prototype. The analysis of scientific literature revealed that under physiological conditions, including pH, glucose concentration, and single-chamber biofuel cells, the maximum power density obtained was 1 mW/cm$^2$ at 0.65 V. The use of nanomaterials, such as carbon nanotubes, and enzymes proved crucial for achieving this performance by enhancing electron transfer, increasing the effective area, and introducing specificity to each electrode, enabling the biofuel cell to operate without the need for a membrane. During the design phase, the functionalisation of the cathode highlighted the critical role of oxygen, which has a limited concentration in the solution. At the anode, the attempt to achieve mediated electron transfer proved successful, in contrast to the method of direct electron transfer. Finally, the characterisation of the biofuel cell demonstrated a preliminary power generation of 0.38 $\micro$W/cm$^2$ at 0.2 V in 500 mM glucose. The preliminary development of the prototype confirms the feasibility of generating energy with the selected materials and highlights its limitations, laying the foundation for its optimization—such as through a more robust stabilization method. Furthermore, the project proves valuable in the context of active medical device development, enabling a comparison between the requirements of a hypothetical implantable sensors and cutting-edge technology.

The increase of petroleum cost as well as global warming and climate change result in investigation to discover new renewable energy resources. Bioenergy is one of the most important sources that is concerning the scientists and industrial sector. Although bioethanol had to be known as one of the most important renewable energy sources in order to reduce greenhouse gases and global warming, there is a limited number of publications reporting on them. In this review, a brief overview is offered about bioethanol production from algae. It can be given a deeper insight in dificulties and promising potential of bioethanol from algae. / Sự gia tăng giá nhiên liệu hóa thạch cùng với cảnh báo toàn cầu về biến đổi khí hậu hướng đến việc nghiên cứu tìm ra những nguồn năng lượng có thể tái tạo. Năng lượng sinh học là một trong những nguồn quan trọng được các nhà khoa học và doanh nghiệp quan tâm. Mặc dù ethanol sinh học đã được biết đến như là một trong những dạng năng lượng tái tạo quan trọng nhất để giảm thiểu các khí nhà kính và cảnh báo toàn cầu, nhưng chỉ có một số ít bài báo về nó. Trong bài tổng quan này, chúng tôi giới thiệu vắn tắt việc sản xuất ethanol sinh học từ tảo. Nó đưa ra cái nhìn sâu hơn về những khó khăn và tiềm năng hứa hẹn của sản xuất ethanol sinh học từ tảo.

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