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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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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Physics-Based Real-time Analysis and Control to Achieve Transient-Free Operations for the ITER Era (Final Report)

This is the final report for the early career award for Prof. Egemen Kolemen that aimed to develop the physics and technical basis of real-time transient – i.e. disruptions and Edge Localized Modes (ELMs) – avoidance and feedback control at the DIII-D nuclear fusion facility for the ITER era. During this project, we reconstructed high quality real-time DIII-D equilibria using kinetic information from the motional Stark effect (MSE), Thomson Scattering (TS), and Charge Exchange Recombination (CER) spectroscopy. These equilibria were analyzed in real-time to determine the low-n ideal MHD stability and the pedestal stability thresholds, and to obtain plasma response models. These calculations were used to understand which physical process evolves to lead to the onset of disruption in ITER-relevant scenarios at DIII-D, and how disruption can be predicted using stability analysis as opposed to the current methods of correlation of various signals, which are descriptive but lack predictive power. In the disruption studies, we focused on tearing modes, since these constitute the vast majority of disruptions in this regime. With this knowledge, real-time disruption avoidance algorithms were developed and tested. The enhanced situation awareness and physics insight were used in advanced real-time feedback control of pedestal and core profiles, which allowed the pursuit and sustainment of transient-free high-confinement regimes that cannot be achieved via feed-forward design based on in-between shot analysis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Development of a framework for sequential Bayesian design of experiments: Application to a pilot-scale solvent-based CO 2 capture process

In this paper, a methodology is developed for sequential design of experiments (SDoE) for process systems and applied to a solvent-based CO 2 capture system. In this approach, the prior knowledge of the system is used to prioritize process data collection at specific operating conditions. These data are then incorporated into a Bayesian inference methodology for updating a stochastic model by refining estimations of its underlying parameters, and the updated model is then used to generate the next set of test runs. Thus, the new knowledge obtained from the data is used to guide subsequent iterations of the experimental runs, ensuring that the overall data collection is maximally informative given that most experimental campaigns, especially at pilot or higher-scale plants, are costly, time-consuming, and resource-limited. The test run objective for this work was to minimize the maximum model prediction uncertainty for key output variables, but the methodology is generic and can be readily applied to other test run objectives. This methodology is applied to an aqueous monoethanolamine (MEA) pilot plant campaign at the National Carbon Capture Center (NCCC) in Wilsonville, Alabama, USA. The SDoE framework was utilized for two iterations, while collecting 18 sets of data representing different process conditions, and this resulted in an overall average reduction in uncertainty of approximately 50% in the prediction of CO 2 capture percentage. Moreover, 11 additional data sets were obtained with variation of absorber packing height for further model validation. This work shows the capability of the SDoE framework to maximize learning given limited resources, allowing for the reduction of model uncertainty, which is of great importance for many applications including reduction of technical risk associated with scale-up and economic analysis.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2020

Confronting Dark Matter with the Multiwavelength Sky (Final Technical Report)

The existence of dark matter is a key clue to new fundamental physics, yet its nature and non-gravitational interactions remain mysterious. In the course of this five-year project (spanning July 2015 - July 2020), we have developed novel analysis techniques to separate dark matter signals from astrophysical backgrounds in the inner Galaxy, and measured hitherto-unknown properties of the Fermi Bubbles and the Galactic Center excess in gamma-rays from the inner Milky Way. We have improved predictions for the spatial distribution and energy spectra of photon signals from dark matter, and set new limits from astrophysical and cosmological datasets on dark matter inhabiting complex dark sectors, multi-particle dark matter annihilation, and tiny primordial black holes. We have successfully adapted effective field theory techniques from collider physics to make high-precision predictions for signals from heavy weakly-interacting DM, allowing us to essentially exclude the possibility that DM is a thermal wino, and have discovered novel theoretical and observational implications for dark matter bound states and self-interactions. We have developed a comprehensive public code package for modeling the effects of exotic energy injections, such as from dark matter annihilation and decay, on the ionization and temperature history of the early cosmos, and have used these tools to set robust, powerful and broadly-applicable constraints on models of light dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Analysis of short‐ and long‐term system response during gas production from a gas hydrate deposit at the UBGH2‐6 site of the Ulleung Basin in the Korean East Sea

Abstract This study is a continuation of an investigation into the feasibility of long‐term production from a marine hydrate accumulation that has the properties and conditions of the UBGH2‐6 (UBGH2, Ulleung Basin Gas Hydrates 2; 2 is the number of the scientific expedition) site at the Ulleung Basin in the Korean East Sea. The 12.7 m‐thick system is in deep water (2157 m), but at 140 m below the seafloor. It is characterized by alternating hydrate‐free clays and muds and hydrate‐rich sand layers. The layered stratigraphy and the presence of mud layers favours the use of vertical wells rather than horizontal wells for production. The analysis indicates that production from such a hydrate accumulation is technically feasible, but the gas production rates are generally low. Water production accompanying gas production from this deposit appears manageable under all the scenarios investigated in this study, however, the water‐to‐gas ratio is high. Subsidence at the ocean floor at the end of a 14 day test is quite limited. However, there is significant uncertainty in the predictions of the geomechanical system's behaviour because they are not based on measured system properties but only on estimates/assumptions from analogues. The long‐term production potential of the reservoir at the site investigated here appears challenging because of the limited effectiveness of dissociation and large water production, in addition to substantial subsidence.

Moridis, George J.↗
DOE OSTI2023

Power Electronics Materials and Bonded Interfaces - Reliability and Lifetime

High temperature operation of wide bandgap devices continue to be a challenge for the power electronics packages. Thermal performance and reliability are important factors that determine the viability of a bonded interface for operation at high temperatures. In this presentation, we present the technical approach and key results from the research on sintered silver, transient liquid phase alloy, and polymeric materials. A lifetime prediction model that incorporates the thermomechanical behavior of sintered silver at 200C was developed. The copper-aluminum transient alloy completed 350 thermal cycles from -40C to 200C and little increase in the defect level was observed. In addition to material research, we initiated a time-series analysis on the scanning acoustic microscope images of eutectic solder to explore statistical forecasting methods and machine learning techniques. Initial results that report the accuracy of a few different statistical models are presented.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Risk Analysis of Various Design Architectures for High Safety-significant Safety-related Digital Instrumentation and Control Systems of Nuclear Power Plants during Accident Scenarios

This report documents the plus-up activities performed by Idaho National Laboratory (INL) during Fiscal Year (FY) 2022 for the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program, Risk Informed Systems Analysis (RISA) Pathway, digital instrumentation and control (DI&C) risk assessment project. In FY 2019, the RISA Pathway initiated a project to develop a risk assessment strategy for delivering a strong technical basis to support effective, licensable, and secure DI&C technologies for digital upgrades/designs. An integrated risk assessment technology for the DI&C systems was proposed for this strategy, which aims to (1) provide a best-estimate, risk-informed capability to quantitatively and accurately estimate the safety margin obtained from plant modernization, especially for the high safety-significant safety-related (HSSSR) DI&C systems, (2) support and supplement existing advanced risk-informed DI&C design guides by providing quantitative risk information and evidence, (3) offer a capability of design architecture evaluation of various DI&C systems to support system design decisions and diversity and redundancy applications, (4) assure the long-term safety and reliability of HSSSR DI&C systems, and (5) reduce uncertainty in costs and support integration of DI&C systems in the plant. To achieve these technical goals and deal with the expensive licensing justifications from regulatory insights, the LWRS-developed framework instructs nuclear vendors and utilities on how to effectively lower the costs associated with digital compliance and speed industry advances by: (1) defining an integrated risk-informed analysis process for DI&C upgrade, including hazard analysis, reliability analysis, and consequence analysis, (2) applying systematic and risk-informed tools to address common cause failures (CCFs) and quantify corresponding failure probabilities for DI&C technologies, particularly software CCFs, (3) evaluating the impact of digital failures at the component level, system level, and plant level, and (4) providing insights and suggestions on designs to manage the risks, thus to support the development, licensing, and deployment of advanced DI&C technologies on nuclear power plant (NPPs). Adding diversity within system or components is the main means to eliminate and mitigate CCFs, but diversity also increases plant complexity and errors and may not address all sources of systematic failures. How to optimize the diversity and redundancy applications for the safety-critical DI&C systems remains a challenge. To deal with the technical issues in addressing potential software CCFs in HSSSR DI&C systems of NPPs and supporting relevant design optimization, the framework provides: ? An integrated best-estimate, risk-informed capability to address new technical digital issues quantitatively, accurately, and efficiently in plan modernization progress, such as software CCFs in HSSSR DI&C systems of NPPs ? A common and a modularized platform for DI&C designers, software developers, cybersecurity analysts, and plant engineers to efficiently predict and prevent risk in the early design stage of DI&C systems ? Technical bases and risk-informed insights to assist U.S. Nuclear Regulatory Commission (NRC) and industry to address and fulfill the risk-informed alternatives for evaluation of CCFs in HSSSR DI&C systems of NPPs ? An integrated risk-informed tool that offers a capability of design architecture evaluation of various DI&C systems to support system design decisions in diversity and redundancy applications. The plus-up research and development efforts of this project in FY 2022 are focused on methodology improvement of software CCF modeling and estimation, prevention analysis, importance analysis and risk analysis of various design architectures of HSSSR DI&C systems. This work greatly enhances the capability of the LWRS-developed framework for the risk assessment and design optimization of safety-critical DI&C systems. It should be noted that all the analyses are performed for the demonstration of the LWRS-developed framework, not for the evaluation of relevant systems. Results are obtained based on very limited design information and testing data.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

On the Need to Align Intent and Implementation in Uncertainty Quantification for Machine Learning

Quantifying uncertainties for machine learning (ML) models is a foundational challenge in modern data analysis. This challenge is compounded by at least two key aspects of the field: (a) inconsistent terminology surrounding uncertainty and estimation across disciplines, and (b) the varying technical requirements for establishing trustworthy uncertainties in diverse problem contexts. In this position paper, we aim to clarify the depth of these challenges by identifying these inconsistencies and articulating how different contexts impose distinct epistemic demands. We examine the current landscape of estimation targets (e.g., prediction, inference, simulation-based inference), uncertainty constructs (e.g., frequentist, Bayesian, fiducial), and the approaches used to map between them. Drawing on the literature, we highlight and explain examples of problematic mappings. To help address these issues, we advocate for standards that promote alignment between the \textit{intent} and \textit{implementation} of uncertainty quantification (UQ) approaches. We discuss several axes of trustworthiness that are necessary (if not sufficient) for reliable UQ in ML models, and show how these axes can inform the design and evaluation of uncertainty-aware ML systems. Our practical recommendations focus on scientific ML, offering illustrative cases and use scenarios, particularly in the context of simulation-based inference (SBI).

Trivedi, Shubhendu [MIT] (ORCID:0000000312374301)↗
DOE OSTI2023

Thermodynamic analysis of a two-stage binary-fluid ejector heat pump water heater

Ejector heat pump water heaters (EHPWHs) could significantly increase the thermal efficiency of domestic water heating and reduce greenhouse gas emissions. This study addresses two major technical barriers to using EHPWHs in domestic water heating—low heating cycle coefficient of performance (COP) and low condensation temperatures—using binary fluid pairs as a working fluid in a two-stage ejector system. A comprehensive, geometry-free model of binary-fluid ejectors was built and validated to predict the entrainment ratios of binary-fluid ejectors. A thermodynamic model of a two-stage binary-fluid ejector EHPWH was built to predict the heating cycle COP of EHPWHs. The performance of the EHPWH was theoretically evaluated using HFE7000 and Novec649 as primary fluids and R600 and R1234ze(Z) as secondary fluids. HFE7000/R600 gave the highest heating cycle COP (i.e., 1.356) in producing domestic hot water at 60.0 °C. An optimum evaporation temperature of the primary fluid was identified for the maximum effective entrainment ratio and effective pressure lift ratio of two-stage ejectors. Here, the effective entrainment ratio of the two-stage ejector dominated the heating cycle COP of the EHPWH. Primary fluids with lower latent heats of evaporation and/or secondary fluids with higher latent heats of evaporation yielded higher heating cycle COPs of EHPWHs.

42 ENGINEERING↗
DOE OSTI2025

Contextualizing Non-Powered Dam Site Selection for Archimedes Screw Turbines: A Methodology for Responsible Archimedes Screw Turbine Conversion at Existing Dams

Non-powered dams represent 97% of dams in the United States and their energy generation potential has not been fully realized. The use of an Archimedes screw turbine to generate power at non-powered dams offers a dual benefit; producing electricity, and acting as downstream fish passage, helping to reconnect previously separated ecosystems. In this study, we assess the technical, environmental, social, and economic feasibility of generating power at non-powered U.S. dam sites using Archimedes screw turbines by integrating mechanical constraints, social impact metrics, proximity to infrastructure, and environmental sensitivity data. Results account for future precipitation predictions and show, between 2024 and 2050, the number of sites where Archimedes screw turbines are viable decreases by one site, but overall generation capacity increases due to increased flow rates across persisting locations. Our analysis identified 82 non-powered dam sites with a mean generation capacity of 49 kW that meet the mechanical requirements for Archimedes screw turbine technology in 2024. Our analysis presents a framework for considering social, environmental, and economic impacts of specific turbine technologies to convert non-powered dams to generate power.

Archimedes screw turbine↗
DOE OSTI2021

Artificial Intelligence for Autonomous Molecular Design: A Perspective

Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Numerical framework for integrated additive manufacturing-compression molding (AM-CM) of thermoplastic composites

Additive manufacturing-compression molding (AM-CM) has emerged as a transformative technology in advanced composite manufacturing. Additive manufacturing (AM) offers high design flexibility and the ability to produce complex geometries with precisely aligned fibers in the preferred orientation. Compression molding (CM) enhances composite materials by providing excellent dimensional stability, reduced porosity, high production rates, and a smooth surface finish. Despite these advantages, extensive integrated analysis is required to optimize processing conditions for improved fiber orientation distribution (FOD) and porosity control. Here, this study develops a comprehensive numerical model to simulate the AM-CM manufacturing process. The model isolates the effects of both the AM and CM phases while also capturing their integration. Additionally, it accounts for heat transfer, temperature-dependent viscosity, and fiber orientation in the extruded fiber-filled polymer, accurately representing material behavior during processing. This approach enables the analysis of interactions between deposited beads of complex strand shapes and their interface regions after full compression. Moreover, the model predicts key parameters such as polymer flowability, fiber orientation, and temperature evolution in AM-CM parts. By optimizing processing conditions, it facilitates a controlled and predictable microstructure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Technical and economic feasibility of molten chloride salt thermal energy storage systems

A techno-economic study is performed to assess the feasibility of molten chloride salt thermal energy storage (TES) systems for next generation concentrating solar power. Refractory liners internally insulate tanks to allow tank shells to be constructed from carbon steel. The liner must not be wetted by salt to maintain predictable thermal properties and manageable heat loss out of the tank. The commercial scale tank liner is an anchored brick and mortar design with expansion joints to accommodate thermal expansion. Furthermore, finite element analysis is performed to optimize the thermal and mechanical profile of the tank. Equalizing the shell temperature between the water-cooled foundation and the shell wall is necessary to minimize differential thermomechanical stress and lower overall stress values below industrial allowable limits. The cost of the TES system is estimated to be $60/kWhth, which is four times greater than Department of Energy targets. Solutions to reduce system cost and overall risk are proposed.

14 SOLAR ENERGY↗
DOE OSTI2023

Hybrid Natural Gas Geothermal Combined Cycle Power Plant Analysis

Low temperature geothermal resources, including those associated with oil and gas production, are an underutilized source of low carbon energy. The present work investigates coupling of low-temperature geothermal resources with concentrating solar and/or natural gas energy sources to increase the number of locations at which power generation from low temperature geothermal resources would be technically and economically viable. Stand-alone and hybrid geothermal power cycles are simulated using SimTech IPSEpro process modeling software. Design point strategies for a hybrid power cycle that may operate with either a single heat source or two simultaneous heat input sources are considered. Additionally, off-design power plant operation is investigated to consider the impacts of the heat source availability and ambient temperature variations. The off-design analysis utilizes a modeling tool that predicts power plant performance at each time step as a function of topping cycle heat input (from gas or solar), bottoming cycle heat input (from geothermal), and ambient temperature. Addition of a steam topping cycle to an organic Rankine cycle geothermal power plant provides opportunities to increase the efficiency and power output relative to a stand-alone geothermal power plant. Additionally, use of the waste heat from gas turbine power generation in a geothermal bottoming cycle provides opportunities to increase the amount of power generation associated with each unit of carbon dioxide emitted. This paper will describe the hybrid plant configuration evaluated, discuss the predicted power cycle performance, and compare with stand-alone natural gas and geothermal power generation cases. The power cycle investigated is expected to be applicable for use with conventional hydrothermal resources as well as with geologic thermal energy storage applications and/or enhanced geothermal systems. The steam topping cycle could use a concentrated solar heat source for fully renewable hybrid plant configuration. A plant initially constructed with a natural gas topping cycle heat source could be converted to a solar heat source part way though the power cycle operational life to achieve life cycle carbon emission reductions.

concentrating solar power↗
DOE OSTI2021

Renewable energy analysis in indigenous communities using bottom-up demand prediction

This paper provides a methodology for the holistic analysis of hybrid renewable energy systems in rural communities. Electric demand is an important component for modeling and analysis of renewable energy systems. Typically, electric demand data is not available due to the internal privacy policies of utility providers. Therefore, this study proposes the use of bottom-up approaches for the development of the electric demand profile, considering the general homogeneity of residential and commercial buildings in rural communities. As a test case, this study develops the electric demand profile and investigates the technical and environmental feasibility of a hybrid renewable energy system for the New Town community on the Fort Berthold Indian Reservation (FBIR) in North Dakota. This study conducts the hybrid renewable energy system’s analysis by developing scripts in the LK scripting language and integrating System Advisor Model software’s open-source modules for modeling of renewable energy systems. Here, the results for the validation testbed of this study show that hybrid renewable resources have higher ratios of energy used for self-consumption to the total energy generated compared to stand-alone wind and PV farms.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Quantifying the Effect of Economic Development Zones on Electrical Load Growth in Kentucky [Slides]

The Kentucky Energy and Environment Cabinet has recently undertaken a comprehensive effort to map and catalog potential economic development sites across the state. The purpose of this technical assistance is to quantify the potential impact of developing designated sites on Kentucky's electricity load growth, providing insights at both state and county level considering the next 10 years. This analysis should explicitly incorporate and address key project uncertainties by developing various load growth scenarios that account for development scale, site specificity, and sector variability. The need for a site-specific analysis comes from the understanding that conventional econometric (top-down) load forecasting models cannot sufficiently isolate or predict the discrete load increases resulting from the development of these unique and targeted economic sites.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Monitoring Plan for the Idaho National Laboratory Remote Handled Low Level Waste Disposal Facility

This monitoring plan for Idaho National Laboratory’s Remote-Handled Low Level Waste Disposal Facility was developed to meet the requirements for monitoring low-level waste disposal facilities according to the U.S. Department of Energy (DOE) Order 435.1, “Radioactive Waste Management,” and the guidance provided in the associated technical standard “Disposal Authorization Statement and Tank Closure Documentation” (DOE-STD-5002-2017). The purpose of this monitoring plan is to document a monitoring strategy that includes (1) compliance monitoring activities to demonstrate compliance with regulatory standards/limits and (2) performance monitoring to build confidence the facility is performing as demonstrated in the facility performance assessment (PA) (DOE-ID 2018a), composite analysis (CA) (DOE ID 2012), and CA addendum (DOE-ID 2018b). The de minimus impact to the aquifer predicted by the PA suggests that aquifer compliance monitoring should be augmented with performance monitoring of the drainage course materials and sedimentary interbeds in the vadose zone beneath the facility to provide a more effective means of identifying performance deviations. The monitoring approach delineated in this document was informed by the systems evaluation of natural and engineered facility features presented in the PA, an assessment of aquifer baseline conditions (INL 2017d), the dose analysis conducted in support of the PA and CA, and monitoring data collected during the first four years of facility operations (baseline monitoring phase) (INL 2023b). This plan provides monitoring locations, sampling frequencies, and sampling methods; recommendations for data evaluation; and a description of the monitoring plan implementation. Collected data will be used to demonstrate facility compliance and to identify conditions that are not consistent with the key assumptions made by the PA and CA.

12 - MGMT OF RADIOACTIVE AND NON-RADIOACTIVE WASTE↗
DOE OSTI2023

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗