Experiences with enhancing data sharing in a large disciplinary engineering journal,
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96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
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Results for “knowledge engineering”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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How technoscientific knowledge advances: A Bell-Labs-inspired architecture
Understanding how science and technology advance has long been of interest to diverse scholarly communities. Thus far, however, such understanding has not been easy to map to, and thus to improve, the operational practice of research and development. Indeed, one might argue that the operational practice of research and development, particularly its exploratory research half, has become less effective in recent decades. In this paper, we describe a rethinking of how science and technology advance, one that is consistent with many (though not all) of the perspectives of the scholarly communities just mentioned, and one that helps bridge the divide between theory and practice. In conclusion, the result is an architecture we call “Bell's Dodecants,” to reflect its six mechanisms and two flavors, and their balanced nurturing at Bell Labs, the iconic 20th century industrial research and development laboratory.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Probing single-chain conformation and its impact on the optoelectronic properties of donor–accepter conjugated polymers
The chain conformation of donor–acceptor conjugated polymers (D–A CPs) is critical to their optical and electronic properties. However, probing the conformation of D–A CPs (e.g., persistence length and contour length) at a single-chain level is challenging due to the formation of aggregates in dilute solution, even in a good solvent. In this work, we studied the chain conformation and corresponding optical spectra for high-performance D–A CPs in the single-chain state by multimodal variable-temperature scattering and spectroscopy techniques, as well as by molecular dynamics simulations. Here we found a critical role of the side-chain length and branch point in the persistence length and optical absorption due to steric effects. Hence, it is important to consider both the chain rigidity and coplanarity of the polymer backbone to achieve desirable optoelectronic properties. Our findings bridge the fundamental knowledge gaps to design new CPs with desired optoelectronic properties via molecular engineering for next-generation electronic devices.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris
ABSTRACT While lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogeneous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a by-product of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions via the benzoyl coenzyme A (CoA) degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to metabolize meta -methoxylated phenolics, such as syringic acid. We isolated a strain of R. palustris (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of the vanARB operon ( rpa3619 , rpa3620 , rpa3621 ), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with a vanARB deletion mutant demonstrated the involvement of the vanARB operon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation of meta -methoxylated and other aromatics by R. palustris . IMPORTANCE Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris . This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources.
59 BASIC BIOLOGICAL SCIENCES↗
A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”
Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection. While the majority of viruses and their associated impacts remain poorly characterized, a number of mechanisms by which viruses alter microbial cells and ecosystems have already been revealed. Here I outline how a comprehensive host-resolved mapping of viral sequence space will enable a thorough characterization of virus-encoded mechanisms for microbial manipulation. With soon-to-be millions of virus genomes obtained from metagenomes, one of the major challenges resides in the development of methods for high-throughput and high-resolution virus-host pairing, before multi-omics approaches can be leveraged to fully decipher virus-host dynamics in nature. Beyond novel fundamental biological knowledge, these studies will likely provide new molecular tools enabling a precise engineering of microbial cells and communities.
59 BASIC BIOLOGICAL SCIENCES↗
Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters
Efforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the Z. mobilis genome presented in this work, we provide crucial knowledge for the development of synthetic genetic parts tailored to Z. mobilis . This information is vital as researchers continue to develop Z. mobilis for synthetic biology applications. Our methods and statistical analyses also provide ways to rapidly advance the understanding of poorly characterized bacteria via empirical data that enable the experimental validation of sequence-based prediction for genome characterization and annotation.
59 BASIC BIOLOGICAL SCIENCES↗
Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas
Abstract Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii , to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.
09 BIOMASS FUELS↗
Thermochemical Conversion of Woody Biomass to Fuels and Chemicals Final Report
Maine and its industries identified more efficient utilization of biomass as a critical economic development issue. In Phase I of this implementation project, a research team was assembled, research equipment was implemented and expertise was demonstrated in pyrolysis, hydrodeoxygenation of pyrolysis oils, catalyst synthesis and characterization, and reaction engineering. Phase II built upon the infrastructure to innovate reaction pathways and process engineering, and integrate new approaches for fuels and chemical production within pulp and paper and other industries within the state. This research cluster brought together chemists, engineers, physicists and students from the University of Maine, Bates College, and Bowdoin College. The project developed collaborations with Oak Ridge National Laboratory and Brookhaven National Laboratory. The specific research projects within this proposal were of critical interest to the DoE - in particular the biomass program within EERE and the catalysis/chemical transformations program within BES. Scientific and Technical Merit highlights of this project included: (1) synthesis and physical characterization of novel size-selective catalyst/supports using engineered mesoporous (1-10 nm diameter pores) materials, (2) advances in fundamental knowledge of novel support/ metal catalyst systems tailored for pyrolysis oil upgrading, (3) a microcalorimetric sensing technique, (4) improved methods for pyrolysis oil characterization, (5) production and characterization of woody biomass-derived pyrolysis oils, (6) development of two new patented bio oil pathways: thermal deoxygenation (TDO) and formate assisted pyrolysis (FASP), and (7) technoeconomics of pyrolysis of Maine forest biomass. This research cluster has provided fundamental knowledge to enable and assess pathways to thermally convert biomass to hydrocarbon fuels and chemicals.
09 BIOMASS FUELS↗
FY2017 Advanced Combustion Systems and Fuels Annual Progress Report
The Advanced Combustion Systems and Fuels Program supports VTO’s goal and focuses early-stage research and development (R&D) to improve understanding of the combustion processes, fuel properties, and emission control technologies while generating knowledge and insight necessary for industry to develop the next generation of engines.
33 ADVANCED PROPULSION SYSTEMS↗
2019 Vehicle Technologies Office Annual Merit Review Report
The 2019 U.S. Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy’s (EERE) Vehicle Technologies Office (VTO) Annual Merit Review (AMR) was held June 10-13, 2019, in Arlington, Virginia. The review encompassed work done by VTO: 287 individual activities were reviewed by 272 reviewers. Exactly 1,162 individual review responses were received for the VTO technical reviews. The objective of the meeting was to review the accomplishments and plans for VTO over the previous 12 months, and provide an opportunity for industry, government, and academia to give inputs to DOE on the Office with a structured and formal methodology. The meeting also provided attendees with a forum for interaction and technology information transfer.
03 NATURAL GAS↗
Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product (Final Report)
The goal is to achieve a comprehensive understanding of the nature, mechanism of function and biogenesis of c-type cytochromes and their oligomeric complexes. These cytochrome are ubiquitous heme proteins that are required for cellular bioenergetics, including photosynthesis (Ps) and respiration (Res), which are central to chemical energy (ATP) production by oxidative- and photophosphorylation. We contribute to the molecular characterization of individual and membrane-integral cytochromes as parts of Ps and Res electron transport (ET) pathways, using the facultative phototrophic bacteria of as excellent models for multidisciplinary investigations. Supported by this grant we discovered novel membrane-bound cytochromes and cyts c complexes that are important for Ps- and Res-ET. We worked out their biogenesis including maturation (covalent heme addition) and assembly of mature subunits into complexes. These involve fundamental process found virtually in all organisms and are fundamental processes with major significance to the “Photosynthetic Systems” program of DOE-BES, because the cytochromes are integral components of natural energy production systems. Elucidation of basic principles, and the knowledge gained by their study greatly impact on our ability to design, engineer, and create new natural, bio-hybrid, bio-inspired and artificial systems to better capture light, transduce and store its energy with improved efficacy and are of broad significance.
14 SOLAR ENERGY↗
A Comparative Evaluation and Selection of High-Temperature Heat Exchangers for Application to Integrated Energy Systems
The following report aims to create a refined and well-structured method for comparatively evaluating heat exchanger technologies for integrated energy systems that caters customers’ specific needs while meeting engineering requirements. For the evaluation, this study elevates previous evaluation metrics, enhances the knowledge base via literature and market surveys, and identifies the figures of merit with robust rationales to enhance the quality of decisions made throughout the proposed heat exchanger evaluation process. The heat exchanger designs evaluated as part of the case study are shell and tube heat exchangers, printed circuit heat exchangers, plate heat exchangers, spiral heat exchangers, and heat pipe heat exchangers. The information presented in this report is meant for industries interested in making a preliminary screening process to identify the most suitable heat exchanger design for their application of interest.
42 ENGINEERING↗
A Comparative Evaluation and Selection of High-Temperature Heat Exchangers for Application to Integrated Energy Systems
The following report aims to create a refined and well-structured method for comparatively evaluating heat exchanger technologies for integrated energy systems that caters customers’ specific needs while meeting engineering requirements. For the evaluation, this study elevates previous evaluation metrics, enhances the knowledge base via literature and market surveys, and identifies the figures of merit with robust rationales to enhance the quality of decisions made throughout the proposed heat exchanger evaluation process. The heat exchanger designs evaluated as part of the case study are shell and tube heat exchangers, printed circuit heat exchangers, plate heat exchangers, spiral heat exchangers, and heat pipe heat exchangers. The information presented in this report is meant for industries interested in making a preliminary screening process to identify the most suitable heat exchanger design for their application of interest.
42 - ENGINEERING↗
Transforming ENERGY through Computational Excellence
Computational methods underpin advancing the science and engineering of energy efficiency, sustainable transportation, renewable power technologies, and developing a knowledge base to optimize energy systems. Researchers with access to enough computing, and the right type, can focus their ingenuity and creativity on addressing the energy challenges. NREL’s advanced computing influence spans several common themes across the Office of Energy Efficiency and Renewable Energy (EERE), including materials discovery, process modeling, fluid dynamics, resource mapping, and analysis of large-scale systems with real-time optimization.
advanced computing↗
Transforming Energy Through Computational Excellence: NREL's Computational Science Center
Computational methods underpin advancing the science and engineering of energy efficiency, sustainable transportation, renewable power technologies, and developing a knowledge base to optimize energy systems. NREL's Computational Science Center (CSC) proudly focuses on providing the service of computing, advancing the science of computing, and enabling NREL's clean energy mission.
applied mathematics↗
Estimation of process steady state with autoregressive models and Bayesian inference
To improve efficiency, separations engineers will typically design process circuits containing recirculating streams, which mix one or more of the process outputs with the feed material. Doing so can improve efficiency, but will cause a delay in the system reaching steady state conditions until the recirculating load mass flows stabilize. In testing separation circuits, engineers will often test a variety of factors and complete an analysis from sample results. Knowledge of if a process is at steady state, as well as the steady state conditions of a process, is essential for a valid techno-economic analysis. However, the definition of process steady state is often poorly defined, or does not include uncertainty quantification. If the performance of a process operating under two different sets of conditions are compared, an engineer who does not test for steady state or quantify steady state conditions risks producing a faulty analysis. In this work, a Bayesian statistical method for testing if all streams are at steady state is further motivated and then derived. Then after testing for steady state, the same model is used with a prior distribution that enforces a steady state assumption to estimate steady state conditions. Further, these methods were validated in a solvent extraction pilot plant where steady state conditions for all outflows were inferred with uncertainty quantification. Analysis is completed with functions available to the reader as part of the BayesMassBal (V 1.1.0) software package written in R.
01 COAL, LIGNITE, AND PEAT↗
Verazine biosynthesis from simple sugars in engineered Saccharomyces cerevisiae
Steroidal alkaloids are FDA-approved drugs (e.g., Zytiga) and promising drug candidates/leads (e.g., cyclopamine); yet many of the ≥697 known steroidal alkaloid natural products remain underutilized as drugs because it can be challenging to scale their biosynthesis in their producing organisms. Cyclopamine is a steroidal alkaloid produced by corn lily (Veratrum spp.) plants, and it is an inhibitor of the Hedgehog (Hh) signaling pathway. Therefore, cyclopamine is an important drug candidate/lead to treat human diseases that are associated with dysregulated Hh signaling, such as basal cell carcinoma and acute myeloid leukemia. Cyclopamine and its semi-synthetic derivatives have been studied in (pre)clinical trials as Hh inhibitor-based drugs. However, challenges in scaling the production of cyclopamine have slowed efforts to improve its efficacy and safety profile through (bio)synthetic derivatization, often limiting drug development to synthetic analogs of cyclopamine such as the FDA-approved drugs Odomzo, Daurismo, and Erivedge. If a platform for the scalable and sustainable production of cyclopamine were established, then its (bio)synthetic derivatization, clinical development, and, ultimately, widespread distribution could be accelerated. Ongoing efforts to achieve this goal include the biosynthesis of cyclopamine in Veratrum plant cell culture and the semi-/total chemical synthesis of cyclopamine. Herein, this work advances efforts towards a promising future approach: the biosynthesis of cyclopamine in engineered microorganisms. We completed the heterologous microbial production of verazine (biosynthetic precursor to cyclopamine) from simple sugars (i.e., glucose and galactose) in engineered Saccharomyces cerevisiae (S. cerevisiae) through the inducible upregulation of the native yeast mevalonate and lanosterol biosynthetic pathways, diversion of biosynthetic flux from ergosterol (i.e., native sterol in S. cerevisiae) to cholesterol (i.e., biosynthetic precursor to verazine), and expression of a refactored five-step verazine biosynthetic pathway. The engineered S. cerevisiae strain that produced verazine contains eight heterologous enzymes sourced from seven different species. Importantly, S. cerevisiae-produced verazine was indistinguishable via liquid chromatography-mass spectrometry from both a commercial standard (Veratrum spp. plant-produced) and Nicotiana benthamiana-produced verazine. To the best of our knowledge, this is the first report describing the heterologous production of a steroidal alkaloid in an engineered yeast. Verazine production was ultimately increased through design-build-test-learn cycles to a final titer of 83 ± 3 μg/L (4.1 ± 0.1 μg/g DCW). Finally, this research lays the groundwork for future microbial biosynthesis of cyclopamine, (bio)synthetic derivatives of cyclopamine, and other steroidal alkaloid natural products.
59 BASIC BIOLOGICAL SCIENCES↗
Unravelling the hidden power of esterases for biomanufacturing of short-chain esters
Abstract Microbial production of esters has recently garnered wide attention, but the current production metrics are low. Evidently, the ester precursors (organic acids and alcohols) can be accumulated at higher titers by microbes like Escherichia coli . Hence, we hypothesized that their ‘direct esterification’ using esterases will be efficient. We engineered esterases from various microorganisms into E. coli , along with overexpression of ethanol and lactate pathway genes. High cell density fermentation exhibited the strains possessing esterase-A (SSL76) and carbohydrate esterase (SSL74) as the potent candidates. Fed-batch fermentation at pH 7 resulted in 80 mg/L of ethyl acetate and 10 mg/L of ethyl lactate accumulation by SSL76. At pH 6, the total ester titer improved by 2.5-fold, with SSL76 producing 225 mg/L of ethyl acetate, and 18.2 mg/L of ethyl lactate, the highest reported titer in E. coli . To our knowledge, this is the first successful demonstration of short-chain ester production by engineering ‘esterases’ in E. coli .
59 BASIC BIOLOGICAL SCIENCES↗