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DOE OSTI2023

Rapid and robust squashed spore/colony PCR of industrially important fungi

Fungi have been utilized for centuries in medical, agricultural, and industrial applications. Development of systems biology techniques has enabled the design and metabolic engineering of these fungi to produce novel fuels, chemicals, and enzymes from renewable feedstocks. Many genetic tools have been developed for manipulating the genome and creating mutants rapidly. However, screening and confirmation of transformants remain an inefficient step within the design, build, test, and learn cycle in many industrial fungi because extracting fungal genomic DNA is laborious, time-consuming, and involves toxic chemicals. In this study we developed a rapid and robust technique called “Squash-PCR” to break open the spores and release fungal genomic DNA as a template for PCR. The efficacy of Squash-PCR was investigated in eleven different filamentous fungal strains. Clean PCR products with high yields were achieved in all tested fungi. Spore age and type of DNA polymerase did not affect the efficiency of Squash-PCR. However, spore concentration was found to be the crucial factor for Squash-PCR in Aspergillus niger, with the dilution of starting material often resulting in higher PCR product yield. We then further evaluated the applicability of the squashing procedure for nine different yeast strains. We found that Squash-PCR can be used to improve the quality and yield of colony PCR in comparison to direct colony PCR in the tested yeast strains. The developed technique will enhance the efficiency of screening transformants and accelerate genetic engineering in filamentous fungi and yeast.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Progress Towards a New Model Chemolithoautotrophic Host (CRADA Final Report)

Some of the largest scale chemical processes for the production of important commodity chemicals and fuels involve an H 2 -containing gas mixture as an intermediate [e.g. ammonia, urea, methanol, Fischer-Tropsch (F-T) diesel, and hydrotreatment of crude petroleum to refined fuels]. The successful development of a model H 2 -oxidizing chemoautotrophic host could expand the range of fuels and chemicals produced from H 2 and CO 2 intermediates in the chemical, oil, and gas sectors in the near term, as well as from renewable and waste-derived sources of these gases that are expected to greatly expand in coming years. Among non-photosynthetic bacteria that can utilize H 2 and CO 2 , Cupriavidus necator (C. necator, formerly Ralstonia eutropha), is the best studied. C. necator is an excellent microbial host for the production of a variety of chemicals because it grows extremely quickly to very high cell densities autotrophically on H 2 and CO 2 , is genetically tractable, and has the ability to accumulate polymers, such as polyhydroxybutyrate, at industrial levels. Despite having great potential as a platform bioproduction host, genetic tools are limited, making metabolic engineering of this organism slow and laborious. In this CRADA project, we developed a number of genetic tools for C. necator: 1) Improvement of C. necator genetic transformation efficiency 2) Integration of heterologous genes into the C. necator chromosome and development of promoter library 3) Development of graded RBSs to control heterologous protein expression 4) Use of RBSs to demonstrate fatty alcohol production in C. necator 5) Demonstration of CRISPR-Cas9 gene editing in C. necator

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Carbon Dioxide Utilization Life Cycle Analysis Guidance for the U.S. DOE Office of Fossil Energy and Carbon Management (Version 2.0)

Capturing carbon dioxide (CO 2 ) and placing it in permanent storage in geologic formations is an option for reducing CO 2 emissions, but it may not be a viable one for all CO 2 emitters. For some, the added cost of capture may be too high to implement, or the geology near the source may not be suitable for storage. In these circumstances, other options will be needed. Carbon use and reuse, or CO 2 utilization (CO2U), is an alternative approach that seeks beneficial uses for captured CO 2 , such as using it as a feedstock in the production of fuels, chemicals, and building materials. These uses would give CO 2 value that could be used by suppliers (emitters) to offset capture costs. One of the principal features and challenges associated with CO2U is that the products derived from CO 2 must have lower carbon footprints than their conventional counterparts. Previous assessments of CO2U alternatives have focused on the carbon content of utilization products as an indicator of CO 2 equivalent (CO 2 e) emissions reduction potential. However, embodied emissions are—at best—only weakly correlated with the amount of carbon contained in any physical product. Therefore, the most attractive CO2U options will both displace the carbon in an existing product and improve the overall carbon efficiency of the manufacturing process. Research to overcome barriers will include identifying existing co-feeds and available low-carbon energy sources to enable the conversion of CO 2 to value-added products under favorable processing conditions. New discoveries in the fields of nano- and bio-technology will be applied to efficiently utilize CO 2 in new applications. Development of advanced materials and processes, integrating CO 2 capture with utilization processes (e.g., algae), exploring a diverse slate of products from CO 2 to effectively offset capture costs and developing processes based on waste energy are means to overcome these barriers. The research will lead to the development of advanced catalysts, materials, and equipment that can be used to convert CO 2 into useful products. The result will be multiple flexible and adaptable technology platforms that can be used to produce suites of products spanning multiple utilization pathways.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Extracellular Charge Transport in Microbial Redox Chains: Linking the Living and Non-Living Worlds

The fundamental process of electron transfer (ET) within and between molecules dictates all biological energy conversion strategies, including respiration and photosynthesis. This project resulted in a comprehensive physics-based understanding of the mechanisms and limits of redox networks that mediate and regulate electron transport through microbial metabolic pathways, with special emphasis on environmental microbes that can acquire energy by catalyzing anodic or cathodic reactions on solid-state electrodes (extracellular electron transfer, or EET). By performing electron transfer to/from electrodes, such microbes may be used as biocatalysts for converting the energy stored in diverse chemical fuels to electricity, or vice versa (microbial electrosynthesis), in renewable energy technologies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Integrated Process for Direct Air Capture of CO 2 and Electrochemical Conversion to Ethanol

This Cooperative Research and Development Agreement (CRADA) between UT-Battelle, LLC and Reactwell, L.L.C. aimed to facilitate the development of an energy-efficient and cost-effective technology that captures carbon dioxide (CO 2 ) from ambient air and converts it electrochemically to ethanol. Direct air capture (DAC) of CO 2 offers the prospect of permanently lowering the atmospheric CO 2 concentration, providing economic and energy-efficient technologies can be developed and deployed at a large scale. DAC has the potential for high-capacity atmospheric CO 2 capture, the flexibility of placement anywhere on earth, and the generation of high-purity CO 2 streams. The most significant technical challenge with DAC is the very low atmospheric concentration of CO 2 , thereby requiring sorbents that bind CO 2 quickly, strongly, and selectively against other components in the air. Integrating DAC with CO 2 conversion into useful chemicals, fuels, or materials can provide an economically feasible solution for mitigating climate change. As long as the carbon contained in these products is taken from the atmosphere and no additional carbon emissions result from their production, processing, and transportation, they can be considered carbon-neutral products. This CRADA facilitated the development of a new net-zero emission technology that closes the carbon cycle by combining DAC with the catalytic electrochemical conversion of CO 2 into ethanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Final Technical Report

The Department of Energy is interested in technologies that support the sustainable production of fuels, chemicals, and other bioproducts from plant biomass, to offset the nation’s reliance on fossil resources. The plant cell wall of energy crops provides the largest reservoir of raw materials for bioproducts. However, the widespread use of plant cell walls is hampered by their complexity and resistance to breakdown. To improve the productivity and cost-effectiveness of using energy crops to generate bioproducts, the fundamental problem of deconstructing plant cell walls must be addressed. This project developed and evaluated an innovative genetic modification technology to produce strategically designed enzymes that specifically accumulate in the plant cell wall. The resulting enzyme-engineered energy crops are expected to grow normally under natural conditions but break down more quickly and easily under high temperature during the production of biobased products. As such, this plant cell wall targeting enzyme engineering effort will reduce the cost of plant cell wall deconstruction and ultimately improve the economics of bioproducts. The overall objective of this project is to develop and evaluate the in-planta enzyme engineering technology to reduce lignocellulose deconstruction cost. The concept was first validated using tobacco plant, a model plant system that is typically used in lab testing for initial concept validation. Then the enzyme optimization was validated using switchgrass, the energy crop to be used to produce bioproducts. There are three specific objectives in this Phase I project: (1) validate the enzyme optimization concept using tobacco plant, a model plant system. (2) validate the enzyme optimization concept using switchgrass. (3) techno-economic analysis (TEA) for further scale-up application. By the end of this project, in-planta enzyme engineering was validated in both tobacco and switchgrass plants, with improved enzyme activity and saccharification efficiency. The in-planta enzyme engineering in Tabacco didn’t have a significant impact on plant growth and development. Transgenic tobacco plants with in-planta cellulose degrading enzymes showed higher biomass digestibility than wild type. Gene construction and transformation in switchgrass was much longer than expected, which delayed the research progress. Besides, in-planta engineering of lignin degrading enzyme is more challenging than cellulose degrading enzyme, in terms of expression detection. Expression of lignin degrading enzyme and cellulose degrading enzyme improved biomass yield and saccharification efficiency of switchgrass, respectively. It is promising to express both genes in switchgrass for optimized overall performance. According to the results of TEA, switchgrass biomass production cost is mainly attributed to by fertility and harvesting. Biomass production profit can increase up to 10-fold depending on biomass price. The PHA production profit is also sensitive to the biomass price. The proposed technology could potentially reduce the biomass deconstruction cost from 33% to 9% of PHA revenue, making the biomass-based PHA competitive to petroleum-based polymers even in case of relatively high biomass price of biomass. Therefore, cultivation of the genetically engineered self-deconstruction switchgrass for Polyhydroxyalkanoate (PHA) production could benefit switchgrass grower and PHA producer with attractive profits for both sectors. This new enzyme optimization approach will be beneficial for bioindustries that use energy crops as feedstocks. It will improve the economic viability of converting energy crops to renewable products that support a sustainable society and helps address the Nation’s long-term strategic needs for renewable products and reduction of reliance on fossil resources.

42 ENGINEERING↗

DOE OSTI2025

Engineered Colloidal Hetero-nanocrystals for Photocatalytic Hydrogen Production

This research is focused on the development of novel semiconductor hetero-structured nanocrystals which can convert solar energy into hydrogen using photocatalytic water splitting reactions. The newly developed nanomaterials could produce cost-effective chemical fuel by employing less-energy intensive technology.

08 HYDROGEN↗

DOE OSTI2025

Probing Ultrafast Charge Transfer Dynamics in Heterostructured Nanomaterials

The increasing demand for renewable and low‐cost energy has triggered a vast amount of research aimed at developing, characterizing and optimizing materials that can efficiently convert sun light into useful chemical energy in the form of electricity or chemical fuels. So‐ called quantum dot sensitized solar cell (QDSC) materials have gained much attention in recent years based on the advantageous physicochemical properties of semiconducting quantum dots (QDs) as sensitizers, as well as their promising potential to increase the conversion efficiency beyond the Shockley‐Queisser limit of ∼33% by making use of hot‐electron transfer (HET) routes and multiple exciton generation (MEG). By finely tuning the size of the QDs, the band gap can be carefully aligned to the metal oxide (MO) conduction band such that charge transfer from the photoexcited QD is thermodynamically favorable.

14 SOLAR ENERGY↗

DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening (CRADA Final Report)

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Editorial: Bioconversion and Biorefinery of C1 Compounds

The past decade has seen significant progress in the field of metabolic engineering and synthetic biology. The exponentially growing multi-omics data and technological advances in the development of efficient genetic manipulation tools and techniques have allowed scientists to explore and expand their understanding of microbial metabolisms and further develop sophisticated engineering strategies to realize the use of industrial "workhorses" and non-conventional microorganisms for sustainable bioconversion and biorefinery. There is of great interest for the research community in using C1 compounds (i.e., CO 2 , CO/syngas, methane, methanol) as the next generation feedstocks for microbial cell factories and biocatalysts to promote the sustainable development of a green economy (Figure 1). Considering lowering input costs is also a main consideration for successful business ventures, the use of inexpensive, abundant, and widely accessible C1 compounds is envisioned as a promising route for the sustainable production of fine chemicals, fuels, and other high-value products. Many C1 compounds are waste gases from industrial activities and may have detrimental effects on climate change upon emission into the atmosphere. Therefore, promoting the use of C1 compounds as renewable carbon feedstocks can greatly contribute to the reduction of anthropogenic emission of air pollutants.

09 BIOMASS FUELS↗

DOE OSTI2021

Opportunities and Challenges of Lignin Utilization

Lignin is the most abundant non-carbohydrate component of plant cell walls and the largest aromatic source on earth. It is gaining more attention due to its potentials for many industrial applications. Compared to the applications of carbohydrate components like cellulose and hemicellulose, the utilization of lignin is challenging due to its natural rigidity, heterogeneity, and complexity. On the other hand, the successful utilization of lignin can broaden the spectrum of renewable resources in producing chemicals, fuels, and materials. In addition, value-added lignin products can enhance the economic competitivity of many biofuels and biochemicals mainly produced from cellulose and hemicellulose. In the last few decades, there have been notable improvements in fundamental understandings of the plant cell wall, lignin chemistry, catalysis, and other engineering principles, as well as the development of diverse conversion and characterization technologies. Prior to the detailed discussions of recent lignin utilization strategies through decomposition approaches such as thermochemical, biological, photoelectrochemical and electrochemical depolymerization and material approaches including carbon materials, adsorbents, thermosets, thermoplastics, hydrogels and nanoparticles, this chapter briefly discusses the types of lignin and its potentials and limitations based on its characteristics and applied processes.

Geun yoo, Chang↗

DOE OSTI2021

BETO 2021 Peer Review - Catalytic Upgrading of Pyrolysis Vapors 2.3.1.314

Catalytic fast pyrolysis (CFP) is a versatile pathway for the direct liquefaction of biomass and waste carbon sources to generate a stabilized bio-oil intermediate that can be further processed into renewable fuels, chemicals, and materials. The objective of this project is advance the CFP state-of-technology through integrated catalyst and process development, expand market responsiveness by creating routes to novel co-products, and provide experimental data to inform process modelling and scale-up activities. Research advancements over the past two years include reducing analytical uncertainty by achieving 100 ± 1% carbon balances during reaction testing with woody biomass, improving process efficiency by achieving a 4x increase in catalyst cycle length, demonstrating compatibility with waste feedstocks, and confirming process durability for 100+ reaction cycles. Additionally, this project supported a comprehensive pathway review to evaluate scale-up needs. This review resulted in the early identification of technical risks and informed proactive planning for the BETO 2022 Verification. Other impacts from this project include generation of broadly enabling scientific knowledge (14 publications/18 presentations since 2019), engagement with industry partners (e.g., Johnson Matthey and ExxonMobil), and identification of a promising pathway to market that addresses emerging demands for biogenic refinery feedstocks.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗

DOE OSTI2022

Engineered yeast strains enabling anaerobic xylose fermentation decoupled from microbial growth

The present invention relates to materials and methods for the production of ethanol. More particularly, the present invention provides genetically modified strains of Saccharomyces cerevisiae exhibiting decreased level of BCY1 protein activity and capable of anaerobic fermentation of xylose into ethanol without the need for cell growth. Also provided are methods of using such genetically engineered yeast strains for improved anaerobic xylose fermentation in the yeast for industrial-scale production of various fuels, chemical feedstocks, and synthetic polymers.

Myers, Kevin S.↗

DOE OSTI2023

Recombinant yeast having increased tolerance to ionic liquids and methods of use

The present invention relates to materials and methods for the production of ethanol. More particularly, the present invention provides genetically modified strains of Saccharomyces cerevisiae having enhanced tolerance for ionic liquid (IL) toxicity. Also provided are methods of using such genetically engineered yeast strains for improved IL-mediated hydrolysis of lignocellulosic biomass for industrial-scale production of various fuels, chemical feedstocks, and synthetic polymers.

Piotrowski, Jeff Scott↗

DOE OSTI2025

In Situ Spectroscopic Monitoring of MSR Molten Salt and Off-Gas Systems

A significant challenge that must be overcome before commercialization of molten salt reactors is tracking special nuclear material (SNM) through the reactor and subsystems such as fuel chemical processing and off-gas systems. In recent years, several approaches have been explored to track SNM, fission products, and corrosion products in these different subsystems. One such approach is to employ laser and optical spectroscopy to measure the atomic and molecular signals of MSR salts. The advantages of these approaches are that they typically are non-intrusive and offer the capability of process monitoring while still providing low uncertainties. At the Idaho National Laboratory, spectroscopy approaches such as laser-induced breakdown spectroscopy (LIBS) and ultraviolet-visible (UV-Vis) spectroscopy have been utilized to investigate molten salts in an aerosol (LiCl, KCl, RbCl2, NdCl3, and PrCl3) and vapor phases (MgCl5, NdCl5, and ZrCl4) with success. Testing to date has yielded qualitative information on all the above species and quantitative data and analytical figures of merit for species in the vapor phases. These findings, including results from ongoing testing, as well as the experimental conditions and potential applications will be presented.

98 - NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL↗

DOE OSTI2021

New insights into fuel blending effects: Intermolecular chemical kinetic interactions affecting autoignition times and intermediate-temperature heat release

Fuel blending effects on chemically-dominated fuel properties, such as gasoline anti-knock quality, are influenced by fundamental chemical kinetic interactions between the blending agent and the base fuel. Historically, quantification of such interactions has focused on changes to the radical pool, including $\dot{O}$H and HO 2 , while intermolecular interactions pertaining to carbonated, non-fuel-specific intermediates are typically overlooked. In this regard, this work aims to derive new insight into intermolecular chemical kinetic interactions that are intrinsic to fuel blending effects via a case study on blends of 0–30% ethanol (by volume) into FGF-LLNL (a multi-component gasoline surrogate for FACE-F research gasoline) using a rapid compression machine at a diluted/stoichiometric fuel loading, compressed pressure of 40 bar and low- to intermediate-temperature regimes that are representative of boosted SI engine operation. Ethanol blending effects on the intermediate temperature heat release (ITHR) of FGF-LLNL are characterized using experimental measurements, where ethanol is found to promote the extent of ITHR and suppress the transition from ITHR to main ignition. Chemical kinetic modeling is undertaken using a recently updated gasoline surrogate model. Sensitivity analyses on ITHR characteristics further corroborate the ethanol blending effects, and highlight the significant dependence of ITHR on both fuel-specific and non-fuel-specific reactions. An approach allowing comprehensive characterization of the complex intermolecular chemical kinetic interactions between constitutes in a fuel blend is then proposed. Application of the approach to FGF-LLNL/E0–E30 reveals that ethanol perturbs the heat release and autoignition characteristics of FGF-LLNL not only by directly changing the $\dot{O}$H and HO 2 radical pools via fuel-specific reactions, but also through intermolecular interactions where participating intermediates can be produced and consumed by various sub-chemistries. Disabling the intermolecular interactions in carbonated species between ethanol and FGF-LLNL sub-chemistries leads to somewhat slower ITHR evolution and lower ignition reactivity. The role of the individual intermolecular interaction is also characterized using the proposed approach. Lastly, implications of intermolecular interactions for future studies that aim to improve model performance are highlighted, where it is found that further investigations on the core C0-C4 chemistry are needed for developing highly accurate chemistry models for complex fuel blends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗