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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Numerical Analysis of Fuel Effects on Advanced Compression Ignition Using a Cooperative Fuel Research Engine Computational Fluid Dynamics Model

Growing environmental concerns and demand for a better fuel economy are driving forces that motivate the research for more advanced engines. Multi-mode combustion strategies have gained attention for their potential to provide high thermal efficiency and low emissions for light-duty applications. These strategies target optimizing the engine performance by correlating different combustion modes to load operating conditions. The extension from boosted spark ignition (SI) mode at high loads to advanced compression ignition (ACI) mode at low loads can be achieved by increasing the compression ratio and utilizing intake air heating. Further, in order to enable an accurate control of intake charge condition for ACI mode and rapid mode-switches, it is essential to gain fundamental insights into the autoignition process. Within the scope of ACI, homogeneous charge compression ignition (HCCI) mode is of significant interest. It is known for its potential benefits, operation at low fuel consumption, low NOx, and particulate matter (PM) emissions. In the present work, a virtual Cooperative Fuel Research (CFR) engine model is used to analyze fuel effects on ACI combustion. In particular, the effect of fuel octane sensitivity (S) (at constant Research Octane Number (RON)) on autoignition propensity is assessed under beyond-RON (BRON) and beyond-MON (BMON) ACI conditions. The three-dimensional CFR engine computational fluid dynamics (CFD) model employs a finite-rate chemistry approach with a multi-zone binning strategy to capture autoignition. Two binary blends with Research Octane Number (RON) of 90 are chosen for this study: primary reference fuel (PRF) with S = 0 and toluene–heptane (TH) blend with S = 10.8, representing paraffinic and aromatic gasoline surrogates. Reduced mechanisms for these blends are generated from a detailed gasoline surrogate kinetic mechanism. Simulation results with the reduced mechanisms are validated against experimental data from an in-house CFR engine, with respect to in-cylinder pressure, heat release rate, and combustion phasing. Thereafter, the sensitivity of combustion behavior to ACI operating condition (BRON versus BMON), air-fuel ratio (λ = 2 and 3), and engine speed (600 and 900 rpm) is analyzed for both fuels. It is shown that the sensitivity of a fuel’s autoignition characteristics to λ and engine speed significantly differs at BRON and BMON conditions. Moreover, this sensitivity is found to vary among fuels, despite the same RON. It is also observed that the presence of low-temperature heat release (LTHR) under BRON condition leads to more sequential autoignition and longer combustion duration than BMON condition. Finally, the study indicates that the octane index (OI) fails to capture the trend in the variation of autoignition propensity with S under the BMON condition.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

Initial conceptual demonstration of control co-design for WEC optimization

Abstract While some engineering fields have benefited from systematic design optimization studies, wave energy converters have yet to successfully incorporate such analyses into practical engineering workflows. The current iterative approach to wave energy converter design leads to sub-optimal solutions. This short paper presents an open-source MATLAB toolbox for performing design optimization studies on wave energy converters where power take-off behavior and realistic constraints can be easily included. This tool incorporates an adaptable control co-design approach, in that a constrained optimal controller is used to simulate device dynamics and populate an arbitrary objective function of the user’s choosing. A brief explanation of the tool’s structure and underlying theory is presented. To demonstrate the capabilities of the tool, verify its functionality, and begin to explore some basic wave energy converter design relationships, three conceptual case studies are presented. In particular, the importance of considering (and constraining) the magnitudes of device motion and forces in design optimization is shown.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. Here, in this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 hours in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production at 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols.

1-decanol↗
DOE OSTI2020

Sooting tendencies of 20 bio-derived fuels for advanced spark-ignition engines

The sooting tendencies of 20 bio-derived fuels indicated as potential blendstocks for spark-ignition engines by the Co-Optimization of Fuels & Engines (Co-Optima) Initiative are studied. The Yield Sooting Index (YSI) is used to quantify the sooting tendencies. The Co-Optima Chemical Model is used to predict the numerical YSIs for all test fuels, and these results are compared with measurements. Experimental YSIs are newly measured for 2 furans and are taken from our previous work for the other compounds. Overall, the predicted YSIs agree well with measurements, within the experimental uncertainties, except for 2,5-dimethylfuran (2,5-DMF). It is found that Polycyclic Aromatic Hydrocarbons (PAH) growth reactions have little influence on the relative soot production from each fuel and therefore on YSI predictions. A modified sensitivity coefficient formulation is proposed to evaluate reaction sensitivities specifically for YSI. This formulation is applied to the 2,5-DMF-doped flame, and six 2,5-DMF initial decomposition reactions, which lead to different major soot precursors, are identified as the most sensitive reactions. The impact of the chemical kinetic uncertainties embedded in these reactions is quantified by randomly perturbing their reaction rates within a factor of two. The resulting prediction uncertainty in the 2,5-DMF-doped flame is found to be ± 8 YSI units (±11%), which demonstrates that the test-fuel-specific decomposition reactions indeed have considerable influence on its YSI prediction. Our research suggests that more accurate kinetic parameters for fuel initial decomposition reactions can potentially improve YSI predictions effectively, without altering the YSI predictions of other fuels with significantly different molecular structures.

09 BIOMASS FUELS↗
DOE OSTI2021

Rapid Construction of Validated Chemistry Models for Advanced Biofuels (Co-Optima Final Report)

Computer methods were developed and demonstrated that make it possible to predict the combustion and pyrolysis chemistry of proposed biofuels, even before the biofuels are ever manufactured or experimentally tested. The methods are based on first-principles calculations of reaction rates and equilibria. A large number of complicated calculations are required, so we developed a computer workflow that automates many of the steps. With the chemical structure of the biofuel and the system conditions (temperature, pressure, compositions, etc.) as the input, the computer methods can construct a detailed kinetic model with refined parameters without intense human intervention. The automation of model construction makes it practical for a single engineer to make the predictions in a reasonable time period. The accuracy of the computer predictions was tested by measuring the time-profiles of various reaction intermediates (carbon monoxide, carbon dioxide, water, formaldehyde, methane, and ethylene) formed as the biofuels pyrolyze or ignite using sophisticated laser shock tube methods. Several biofuels, including methyl propyl ether, cyclopentanone, butyl acetate isomers, etc., were carefully studied to demonstrate the validity of the proposed computational and experimental methodology. This research project opens up the possibility for assessing some proposed biofuels on the computer without expensive experimental campaigns. The new computer methods are open source and well-documented, allowing a knowledgeable modeler to easily access the developed methods and implement them in their work routine. Moreover, they are also convenient and powerful, promising for developing the fuel chemistry models needed for use in engine simulators, facilitating co-optimization of new engine designs with new fuels.

09 BIOMASS FUELS↗
DOE OSTI2022

Data-centric machine learning in quantum information science

Abstract We propose a series of data-centric heuristics for improving the performance of machine learning systems when applied to problems in quantum information science. In particular, we consider how systematic engineering of training sets can significantly enhance the accuracy of pre-trained neural networks used for quantum state reconstruction without altering the underlying architecture. We find that it is not always optimal to engineer training sets to exactly match the expected distribution of a target scenario, and instead, performance can be further improved by biasing the training set to be slightly more mixed than the target. This is due to the heterogeneity in the number of free variables required to describe states of different purity, and as a result, overall accuracy of the network improves when training sets of a fixed size focus on states with the least constrained free variables. For further clarity, we also include a ‘toy model’ demonstration of how spurious correlations can inadvertently enter synthetic data sets used for training, how the performance of systems trained with these correlations can degrade dramatically, and how the inclusion of even relatively few counterexamples can effectively remedy such problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Economically Viable Intermediate to Long Duration Hydrogen Energy Storage Solutions for Fossil Fueled Assets

This report was prepared as an account of work sponsored by the Office of Fossil Energy and Carbon Management of U.S. Department of Energy under Funding Opportunity Announcement Number DE-FOA-0002332 “Energy Storage for Fossil Power Generation”. The work aimed to explore and advance an innovative hydrogen energy storage system – the synergistically integrated hydrogen energy storage system (SIHES) – that has the following characteristics: • Compatible with existing or new coal and gas fuel electricity generation units, • best suited for intermediate to long duration energy storage, from 12 hours to weeks even months, and • capable of storing energy at the utility scale – hundreds of MWh to GWh energy storage with power output level in tens to hundreds of MW. Preliminary front-end engineering design (Pre-FEED) studies was carried out to develop and refine a site-specific SIHES as peaking power generation units (so named as HyPeaker) as the first market entry point, to demonstrate both the technical feasibility and the economic viability to integrate the HyPeaker “within the fence” of a fossil power plant. This specific site was TVA’s Johnsonville Combustion Turbine Plant. The HyPeaker was designed and engineered to integrate with a 60MW aeroderivative gas turbine unit already available at TVA’s Johnsonville site. This site-specific HyPeaker consists of an alkaline electrolyzer to produce hydrogen from CO 2 free electricity sources, an innovative low-cost high-pressure hydrogen storage system (Big-Ton) and the aero gas turbine to generate electricity using blend of hydrogen and natural gas. A holistic system level technoeconomic analysis tool specific to HyPeaker was developed to optimize the engineering design of the Johnsonville site-specific HyPeaker for cost and performance. The optimal design and specification of the Johnsonville site-specific HyPeaker are the following: • Alkaline electrolyzer: 3MW • Big-Ton storage vessel: 11,000kg H 2 at 3000psi. • 4-stage diaphragm hydrogen compressor: 55kg-H 2 /hr from 150psi to 3000psi. The HyPeaker is designed to provide sufficient hydrogen for 90% continuous operation of the HyPeaker. All major components have design life of 30 years. The capex of HyPeaker is estimated at $\$$7.1M. This included $\$$1.5M for the electrolyzer, $\$$5.6M for the storage vessel and compressor. The cost of aero gas turbine was included as it is already available at the site. Key findings are: • HyPeaker can be designed, manufactured, installed and integrated with the fossil power plants, with sub-systems and components commercially available on the market today, even when it is scaled up to an order of magnitude larger than the one at the Johnsonville site. HyPeaker is a technologically viable solution to cover a wide range of energy storage duration needs, from daily peaking operation to seasonal shifting for fossil fueled assets. • The cost advantage of SCCV based Big-Ton H 2 storage vessel made it possible to “oversize” the H 2 storage subsystem to achieve overall system level cost optimization. The benefits are two-fold. First, it allows to significantly reduce the capacity and cost of electrolyzer by spreading H 2 production over a much longer period of time when the fuel cost for electricity production is low. Second, it allows to balance the hydrogen production and usage shift over weeks to months to meet the peak demands. As such, the capital cost of HyPeaker system using the Big-Ton was less than half of the cost of a system with today’s steel tube based H 2 storage system. The HyPeaker has even better cost advantage Li-ion battery based energy storage system. The estimated capital cost of Li-Ion battery system would be at $\$$38M, under the same projected 20-year electricity generation profile of the Johnsonville site. This is over 5 times more expensive than the HyPeaker system. • Since industry scale energy storage systems do not have 100% energy conversion and storage efficiency, energy storage systems using fossil fuel generated electricity would increase the CO 2 emission. This is particularly the case for HyPeaker due to its low round trip efficiency. Therefore, a more sensible solution would be to the excessive or curtailed electricity from CO 2 emission free sources such as solar farms, wind farms or nuclear power plants, to produce hydrogen, and integrate them with the HyPeaker. Electricity from TVA’s nuclear power plants was used for the Johnsonville HyPeaker. • The economic viability of HyPeaker is expected to be further improved when global supply chains are taken into consideration. For the same Johnsonville site specific HyPeaker, the capex would be reduced to ~$\$$3.6M from ~$\$$7.1M, and the added LCOE is reduced to ~$\$$85/MWh. With the bipartisan Infrastructure Investment and Jobs Act, the cost of domestically produced HyPeaker sub-systems would be at the level of today’s global suppliers. Since the peaking units generally operate at peak usage period, thereby demanding higher price, the projected $\$$85/MWh LCOE would be within the realm of financial viability for utility operators.

08 HYDROGEN↗
DOE OSTI2022

Dispatch optimization of a concentrating solar power system under uncertain solar irradiance and energy prices

The integration of thermal energy storage into a concentrating solar power system allows for mitigating some of the risk associated with uncertain solar irradiance and uncertain energy prices. We solve a 48 h dispatch optimization model with continually updated conditional point forecasts of both direct normal irradiance (DNI) and electricity prices with a rolling-horizon scheme at hourly resolution over the course of a year. Joint, conditional forecasts for DNI and prices are formed using an autoregressive moving-average time series model with exogenous weather predictors. We guide dispatch using a mixed-integer programming model, but in order to evaluate performance we use the System Advisor Model (SAM) of the National Renewable Energy Laboratory. SAM is a techno-economic simulation model that accounts for plant thermodynamics with higher fidelity. Our conditional DNI forecasts improve annual revenue by 4%–12% over using historical forecasts based on data from previous years. Conditional price forecasts improve annual revenue by 6%–19% in the real-time market over analogous historical forecasts. Updating these forecasts every six hours, rather than every 24 h, further improves annual revenue by 5%–6%. Here, we also investigate a method that values terminal inventory in our dispatch optimization model, again when used in a rolling-horizon scheme.

14 SOLAR ENERGY↗
DOE OSTI2020

Novel geometries for air-cooled condensation of ammonia-water mixtures

An analytical and experimental investigation of air-cooled condensers for small-scale ammonia-water absorption heat pumps is presented. Conventional round-tube corrugated fin design and a novel multi-pass tube array design are considered for a condenser operating at severe ambient conditions within a compact footprint. Segmental heat and mass transfer models are developed to gain a deeper understanding of the characteristics of each design. Predicted heat duties are within 5% of the measured values. The limitations of correlations to predict air-side pressure drop in corrugated fins are identified. The performance of the novel multi-pass tube array condenser was comparable to that of conventional condensers, but is determined to be air-side limited throughout length of the heat exchanger. An improved multi-pass condenser design with fins for increased air-side area is proposed using the insights gained from the modeling and experiments. In closing this design meets the heat duty requirements at severe ambient conditions, while decreasing the size of the heat exchanger by 33%.

42 ENGINEERING↗
DOE OSTI2024

A holistic platform for accelerating sorbent-based carbon capture

Abstract Reducing carbon dioxide (CO 2 ) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO 2 from various sources and deliver it to different sinks 1,2 . The quest for optimal solutions for specific source–sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design 3 and engineers on optimizing processes 4,5 , which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant’s lifetime, is typically one of the final steps 6 . Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO 2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.

Science & Technology - Other Topics↗
DOE OSTI2022

Control of second-harmonic generation in all-dielectric intersubband metasurfaces by controlling the polarity of χ (2)

All-dielectric metasurfaces have recently led to a paradigm shift in nonlinear optics as they allow for circumventing the phase matching constraints of bulk crystals and offer high nonlinear conversion efficiencies when normalized by the light-matter interaction volume. Unlike bulk crystals, in all-dielectric metasurfaces nonlinear conversion efficiencies primarily rely on the material nonlinearity, field enhancements, and the modal overlaps, therefore most efforts to date have only focused on utilizing these degrees of freedom. In this work, we demonstrate that for second-harmonic generation in all-dielectric metasurfaces, an additional degree of freedom is the control of the polarity of the nonlinear susceptibility. We demonstrate that semiconductor heterostructures that support resonant nonlinearities based on quantum-engineered intersubband transitions provide this new degree of freedom. We can flip and control the polarity of the nonlinear susceptibility of the dielectric medium along the growth direction and couple it to the Mie-type photonic modes. Here we demonstrate that engineering the χ (2) polarity in the meta-atom enables the control of the second-harmonic radiation pattern and conversion efficiency. Our results therefore open a new direction for engineering and optimizing second-harmonic generation using all-dielectric intersubband nonlinear metasurfaces.

42 ENGINEERING↗
DOE OSTI2020

Supercritical Reforming of Wet Ethanol for High Efficiency Direct-injection Heavy-duty Compression-ignition Engines

The purpose of the research was to investigate the potential of using a mature bio-fuel in heavy-duty compression ignition engines. By co-optimizing both the fuel characteristics and engine system the potential for a superior outcome was demonstrated. The use of wet bio-ethanol eliminates the majority of the energy intensive distilling and dehydrating fuel production processes, which moves the fuel towards carbon neutral and also lowers the fuel costs. The relatively high water content of the resulting fuel is leveraged in the proposed novel combustion system by incorporating an integrated high efficiency exhaust waste heat recovery system. This results in significantly higher thermal efficiency. In addition the combustion system features low criteria pollutant emissions and the potential to reduce the initial cost of the engine system hardware. Substantial societal benefits are demonstrated through the co-optimization of the fuel and engine system. A computational proof-of-concept study has been performed to demonstrate the potential benefits of a novel wet ethanol heavy-duty compression ignition combustion system featuring integrated exhaust waste heat recovery. A combined in-cylinder closed cycle 3D computational fluid dynamics (CFD) - 1D engine system simulation approach was used. The models were validated to baseline engine data using diesel fuel and then applied to the wet ethanol study. The original concept was to maximize exhaust waste heat recovery through supercritical reforming of the wet ethanol fuel. Phase I simulation results indicated that the optimal solution for maximum engine efficiency gains were realized through maximizing thermo-mechanical recuperation with negligible fuel reformation. The results show the potential to achieve impressive gains in brake thermal efficiency (BTE) over the base diesel engine. The potential to increase BTE up to 20.9% over the base diesel engine was demonstrated, with even larger gains possible through reduced in-cylinder heat transfer losses. The majority of the efficiency gains were realized through integrated high efficiency exhaust waste heat recovery. The concept also has the potential to achieve future ultra-low NO x emissions standards and negligible engine-out soot emissions. The mixing controlled combustion of high temperature wet ethanol features relatively low engine-out NO x emissions without the need for exhaust gas recirculation (EGR). The soot free combustion enabled by the relatively high oxygen content of ethanol also allows for the use of stoichiometric mixing controlled combustion, which is not practical with diesel fuel. When stoichiometric combustion is used a simple passive 3-way catalyst can be used for exhaust emissions after-treatment and near zero tailpipe emissions. The Phase I simulations results have defined the system layout and requirements in preparation for the Phase II experimental proof-of-concept study. The potential applications of the research include most current applications of diesel engines. The Phase I study focused on heavy-duty on-highway class 8 trucks. However, virtually any application that requires highly efficient clean power generation would benefit from the novel engine system proposed. The results indicate substantial fuel cost savings and reduced greenhouse gas emissions with similar or reduced initial system hardware costs compared to modern diesel engine systems.

09 BIOMASS FUELS↗
DOE OSTI2020

Power System Resilience Enhancement in Typhoons Using a Three-Stage Day-Ahead Unit Commitment

In this work, we propose a three-stage resilient unit commitment model which considers uncertain typhoon paths and line outages to improve the power system resilience against typhoon events. The proposed solution coordinates resources in response to the worst-case scenario for each possible typhoon path. The optimal decision is based on the characterization of the power system schedule into three stages of preventive control, emergency control, and restoration. Preventive control is performed before the typhoon occurs by quickly adjusting the three-stage resilient unit commitment schedule; emergency control is conducted during the typhoon by shedding local loads to meet the power balance, while other control strategies are assumed to be unavailable due to possible interruptions in the communication system; restoration is realized after the typhoon, when resources are optimally dispatched to repair the outages of critical devices and recover the normal operation state of the power system quickly. Considering the typhoon path uncertainty, we have introduced a stochastic model for possible typhoon paths where all possible affected lines along each typhoon path are assumed to be on outage during the typhoon. Accordingly, we explore the strategy for co-optimizing the three stages in unit commitment. The proposed model is tested on the IEEE 118-bus system and the real-world provincial system to verify its effectiveness.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Expanding the synthetic biology toolbox of Cupriavidus necator for establishing fatty acid production

Abstract The Gram-negative betaproteobacterium Cupriavidus necator is a chemolithotroph that can convert carbon dioxide into biomass. Cupriavidus necator has been engineered to produce a variety of high-value chemicals in the past. However, there is still a lack of a well-characterized toolbox for gene expression and genome engineering. Development and optimization of biosynthetic pathways in metabolically engineered microorganisms necessitates control of gene expression via functional genetic elements such as promoters, ribosome binding sites (RBSs), and codon optimization. In this work, a set of inducible and constitutive promoters were validated and characterized in C. necator, and a library of RBSs was designed and tested to show a 50-fold range of expression for green fluorescent protein (gfp). The effect of codon optimization on gene expression in C. necator was studied by expressing gfp and mCherry genes with varied codon-adaptation indices and was validated by expressing codon-optimized variants of a C12-specific fatty acid thioesterase to produce dodecanoic acid. We discuss further hurdles that will need to be overcome for C. necator to be widely used for biosynthetic processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Predicting Dynamic-to-Static Correction Factor from Petrophysical Data and Chemostratigraphy using Unsupervised Machine Learning

Estimating static mechanical properties of stratigraphic layers is critical for optimizing subsurface engineering applications. To estimate dynamic-to-static correction factor F ds (static-to-dynamic Young’s modulus ratio) across the Caney shale interval in Oklahoma, USA, we integrated triaxial test measurements and petrophysical data, including well logs and X-ray fluorescence (XRF) using unsupervised machine learning (ML). We used a novel workflow that includes principal component analysis (PCA) to reduce data set dimensionality of well logs and XRF data sets—both separately and combined—creating three scenarios, and later applied inverse distance weighting (IDW) to derive F ds profiles for these scenarios. Furthermore, we applied K-means clustering on each scenario to predict depositional facies, and built a stiffness zonation profile through chemostratigraphic analysis of the terrigenous elements to validate the predicted F ds . The predicted F ds profile from each scenario using the PCA-IDW method was compared with the constant F ds approach from our previous study by calculating the root mean square error (RMSE). The combined data sets scenario yielded the lowest RMSE value of 0.113, while the RMSE values for the well logs and XRF scenarios were 0.131 and 0.129, respectively. In addition, the predicted F ds from the XRF scenario well-matched the stiffness zonation from the chemostratigraphic analysis that was built using the optimized K-means clustering of nine clusters for that scenario. These methods and findings offer a valuable tool for refining lithological classification and improving the F ds profile, potentially enhancing drilling and stimulation strategies for subsurface energy engineering applications.

clastic rock↗
DOE OSTI2020

Quantum Dynamics at Scale: Ultrafast Control of Emergent Functional Materials

Confluence of extreme-scale quantum dynamics simulations (i.e. quantum@scale) and cutting-edge x-ray free-electron laser experiments are revolutionizing materials science. An archetypal example is the exciting concept of using picosecond light pulses to control emergent material properties on demand in atomically-thin layered materials. This paper describes efforts to scale our quantum molecular dynamics engine toward the United States' first exaflop/s computer, under an Aurora Early Science Program project named "Metascalable layered material genome". Key algorithmic and computing techniques incorporated are: (1) globally-scalable and locally-fast solvers within a linear-scaling divide-conquer-recombine algorithmic framework; (2) algebraic `BLASification' of computational kernels; and (3) data alignment and loop restructuring, along with register and cache blocking, for enhanced vectorization and efficient memory access. The resulting weak-scaling parallel efficiency was 0.93 on 131,072 Intel Xeon Phi cores for a 56.6 million atom (or 169 million valence-electron) system, whereas the various code transformations achieved 5-fold speedup. The optimized simulation engine allowed us for the first time to establish a significant effect of substrate on the dynamics of layered material upon electronic excitation.

Algebraic BLASification↗
DOE OSTI2021

Finding the order in complexity: The electronic structure of 14-1-11 zintl compounds

Yb 14 MnSb 11 and Yb 14 MgSb 11 have rapidly risen to prominence as high-performing p-type thermoelectric materials. However, the fairly complex crystal structure of A 14 MX 11 Zintl compounds renders the interpretation of the electronic band structure obscure, making it difficult to chemically guide band engineering and optimization efforts. In this work, we delineate the valence-balanced Zintl chemistry of A 14 MX 11 compounds using the molecular orbital theory. By analyzing the electronic band structures of Yb 14 MgSb 11 and Yb 14 AlSb 11 , we show that the conduction band minimum is composed of either an antibonding molecular orbital originating from the (Sb 3 ) 7– trimer or a mix of atomic orbitals of A, M, and X. The singly degenerate valence band is comprised of non-bonding Sb pz orbitals primarily from the Sb atoms in the (MSb 4 ) m– tetrahedra and of isolated Sb atoms distributed throughout the unit cell. Such a chemical understanding of the electronic structure enables strategies to engineer electronic properties (e.g., the bandgap) of A 14 MX 11 compounds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗