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At least 721 records · Page 40

All sources NASA NTRS DOE OSTI

DOE OSTI2026

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗

DOE OSTI2023

Real-space solution to the electronic structure problem for nearly a million electrons

We report a Kohn–Sham density functional theory calculation of a system with more than 200 000 atoms and 800 000 electrons using a real-space high-order finite-difference method to investigate the electronic structure of large spherical silicon nanoclusters. Our system of choice was a 20 nm large spherical nanocluster with 202 617 silicon atoms and 13 836 hydrogen atoms used to passivate the dangling surface bonds. To speed up the convergence of the eigenspace, we utilized Chebyshev-filtered subspace iteration, and for sparse matrix–vector multiplications, we used blockwise Hilbert space-filling curves, implemented in the PARSEC code. For this calculation, we also replaced our orthonormalization + Rayleigh–Ritz step with a generalized eigenvalue problem step. We utilized all of the 8192 nodes (458 752 processors) on the Frontera machine at the Texas Advanced Computing Center. We achieved two Chebyshev-filtered subspace iterations, yielding a good approximation of the electronic density of states. Our work pushes the limits on the capabilities of the current electronic structure solvers to nearly 106 electrons and demonstrates the potential of the real-space approach to efficiently parallelize large calculations on modern high-performance computing platforms.

Chemistry↗

DOE OSTI2023

Periplasmic biomineralization for semi-artificial photosynthesis

Semiconductor-based biointerfaces are typically established either on the surface of the plasma membrane or within the cytoplasm. In Gram-negative bacteria, the periplasmic space, characterized by its confinement and the presence of numerous enzymes and peptidoglycans, offers additional opportunities for biomineralization, allowing for nongenetic modulation interfaces. We demonstrate semiconductor nanocluster precipitation containing single- and multiple-metal elements within the periplasm, as observed through various electron- and x-ray-based imaging techniques. The periplasmic semiconductors are metastable and display defect-dominant fluorescent properties. Unexpectedly, the defect-rich (i.e., the low-grade) semiconductor nanoclusters produced in situ can still increase adenosine triphosphate levels and malate production when coupled with photosensitization. We expand the sustainability levels of the biohybrid system to include reducing heavy metals at the primary level, building living bioreactors at the secondary level, and creating semi-artificial photosynthesis at the tertiary level. The biomineralization-enabled periplasmic biohybrids have the potential to serve as defect-tolerant platforms for diverse sustainable applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Enabling particle applications for exascale computing platforms

The Exascale Computing Project (ECP) is invested in co-design to assure that key applications are ready for exascale computing. Within ECP, the Co-design Center for Particle Applications (CoPA) is addressing challenges faced by particle-based applications across four “sub-motifs”: short-range particle–particle interactions (e.g., those which often dominate molecular dynamics (MD) and smoothed particle hydrodynamics (SPH) methods), long-range particle–particle interactions (e.g., electrostatic MD and gravitational N-body), particle-in-cell (PIC) methods, and linear-scaling electronic structure and quantum molecular dynamics (QMD) algorithms. Our crosscutting co-designed technologies fall into two categories: proxy applications (or “apps”) and libraries. Proxy apps are vehicles used to evaluate the viability of incorporating various types of algorithms, data structures, and architecture-specific optimizations and the associated trade-offs; examples include ExaMiniMD, CabanaMD, CabanaPIC, and ExaSP2. Libraries are modular instantiations that multiple applications can utilize or be built upon; CoPA has developed the Cabana particle library, PROGRESS/BML libraries for QMD, and the SWFFT and fftMPI parallel FFT libraries. Success is measured by identifiable “lessons learned” that are translated either directly into parent production application codes or into libraries, with demonstrated performance and/or productivity improvement. The libraries and their use in CoPA’s ECP application partner codes are also addressed.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Multiframe X-ray diffraction on the OMEGA EP laser

A method of measuring multiple temporally resolved powder x-ray diffraction measurements during a single dynamic compression laser experiment has been demonstrated on the OMEGA EP laser. Up to four time-gated snapshots of the x-ray diffraction pattern are collected on an ultrafast x-ray framing camera with a 2θ scattering angle coverage of 48°–65° and 400-ps temporal resolution with the potential for 10°–160° and 200-ps resolution. X-ray diffraction snapshots capture the transformation to a high-pressure β phase in ramp-compressed Zr, constraining the atomic structure and pressure–density equation-of-state in a single shot. Here, this platform will be used to constrain transition pressures, understand the role of kinetics, and verify the existence of hysteresis and metastability on phase transformations at the lattice level under single-shot dynamic compression.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Evaluating performance and portability of high-level programming models: Julia, Python/Numba, and Kokkos on exascale nodes

We explore the performance and portability of the high-level programming models: the LLVM-based Julia and Python/Numba, and Kokkos on high-performance computing (HPC) nodes: AMD Epyc CPUs and MI250X graphical processing units (GPUs) on Frontier’s test bed Crusher system and Ampere’s Arm-based CPUs and NVIDIA’s A100 GPUs on the Wombat system at the Oak Ridge Leadership Computing Facilities. We compare the default performance of a hand-rolled dense matrix multiplication algorithm on CPUs against vendor-compiled C/OpenMP implementations, and on each GPU against CUDA and HIP. Rather than focusing on the kernel optimization per-se, we select this naive approach to resemble exploratory work in science and as a lower-bound for performance to isolate the effect of each programming model. Julia and Kokkos perform comparably with C/OpenMP on CPUs, while Julia implementations are competitive with CUDA and HIP on GPUs. Performance gaps are identified on NVIDIA A100 GPUs for Julia’s single precision and Kokkos, and for Python/Numba in all scenarios. We also comment on half-precision support, productivity, performance portability metrics, and platform readiness. We expect to contribute to the understanding and direction for high-level, high-productivity languages in HPC as the first-generation exascale systems are deployed.

Godoy, William↗

DOE OSTI2023

Performance and Cost Potential for Direct-Fired Supercritical CO2 Natural Gas Power Plants

Direct-fired supercritical CO2 (sCO2) power cycles are being explored as an attractive alternative to natural gas combined cycle (NGCC) plants with carbon capture and storage (CCS). Therefore, understanding their performance and cost potential is important for the commercialization of the technology. This study presents the techno-economic optimization results of natural gas-fired, utility-scale power plants based on the direct sCO2 power cycle, which are lacking in public literature. To identify the optimum plant configuration, the study considered multiple cases with varying levels of thermal integration with the plant air separation unit (ASU). Several design variables for each power cycle configuration were identified and optimized to minimize the levelized cost of electricity (LCOE) for each case. The optimization design variables include the sCO2 cooler outlet temperatures, recuperator approach temperatures, and pressure drops. High fidelity models for recuperators, coolers, and turbines were developed and used to capture the impact of design variables on plant efficiency and capital costs. The optimization was conducted using a combination of manual sensitivity analyses and automated derivative-free optimization algorithms available under NETL’s Framework for Optimization and Quantification of Uncertainty and Sensitivity platform. The optimized direct sCO2 power plants offered similar or slightly higher plant efficiencies than the reference NGCC plants based on the F-class gas turbine with CCS. The LCOE of the optimized direct sCO2 plants is 13 to 17% higher than the reference NGCC plants with CCS due to high capital costs associated with the ASU and sCO2 power block, though there is significant room for improvement due to the high uncertainty in component capital costs for these new plants. Recuperators make up over 50% of the sCO2 power block costs. Consequently, any research and development efforts to reduce the recuperator capital costs will benefit the technology’s commercialization. The study also presents preliminary results showing the impact of co-firing landfill gas and natural gas on plant efficiency, LCOE, and CO2 emissions.

Pidaparti, Sandeep↗

DOE OSTI2023

Performance and Cost Potential for Direct-Fired Supercritical CO2 Natural Gas Power Plants

Pidaparti, Sandeep↗

DOE OSTI2026

Metabolic engineering strategies for producing decanoic acid and related oleochemicals: 1-decanol, 2-nonanone, and poly(3-hydroxydecanoate) in Escherichia coli

Medium-chain (mc-) oleochemicals are an important class of renewable chemicals with broad industrial applications; however, their sustainable microbial production remains challenging. In this study, we developed a versatile metabolic engineering and fed-batch strategy to produce C 10 -oleochemicals in Escherichia coli. Central to this approach is an engineered mc-acyl-ACP thioesterase Cl FatB3-tr-D10S with C 10 species accounting for around 70% of the total fatty acids produced. To expand product diversity, we established a decanoyl-CoA pool through co-expression of fadD, enabling downstream conversion into multiple product classes. Through pathway tuning, enzyme bioprospecting, strain engineering and fermentation optimization strategies, we demonstrated selective production of 1-decanol, 2-nonanone and poly(3-hydroxydecanoate) (C 10 -PHA). Production of decanoic acid and 1-decanol were achieved by optimizing expression of Cl fatB3-tr-D10S and, Mt fadD6 and Ma acr, respectively. Leveraging β-oxidation enabled the production of β-ketoacyl-CoA intermediates, which were converted to 2-nonanone via heterologous Mlu fadE, Vf fadB and Ps fadM expression. Additionally, expression of phaJ2 and phaC2 facilitated the conversion of decanoyl-CoA pool into C 10 -PHA homopolymer. Altogether, this work demonstrates a versatile and tunable platform for medium-chain oleochemical production.

1-Decanol↗

DOE OSTI2024

Virtual tower measurements during the American WAKE ExperimeNt (AWAKEN)

Dual-Doppler lidar measurements were made during the American WAKE ExperimeNt to provide height-resolved measurements of wind speed and direction at multiple locations immediately south of the leading row turbines in the King Plains wind farm in Oklahoma. These so-called virtual tower measurements were performed to characterize the inflow into the wind farm and to assess possible upwind blockage effects due to the collective action of the wind farm. The campaign was conducted from 12 November 2022 to 17 October 2023, during which time 14 unique virtual tower locations were sampled with heights ranging from 240 to 490 m AGL. The wind retrieval algorithm provided estimates of the horizontal winds and their uncertainties with a vertical resolution of about 10 m, while also accounting for the tilt of the lidar platform. The virtual tower results are compared to collocated lidar wind profiling data at the A1 site, which was located roughly 2.4 rotor diameters south of the nearest turbine. The wind speed difference between the wind profiler and the virtual tower was found to be quite sensitive to atmospheric stability and wind direction below 250 m AGL. The largest differences were observed for inflow under stable conditions, where the profiler wind speeds were observed to be about 22% lower than the virtual tower near hub height. These results suggest that there are persistent horizontal gradients in the flow upwind of the wind farm which result in biased estimates using standard ground-based lidar wind profiling methods.

17 WIND ENERGY↗

DOE OSTI2023

Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize

Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Approaches for Synthesis and Deployment of Controller Models on Automated Vehicles for Car-following in Mixed Autonomy

This paper describes the software design patterns and vehicle interfaces that were employed to transition vehicle controllers from simulation environments to open-road field experiments. The approach relies on a life cycle that utilizes model-based design and code generation, along with agile software development, and both software and hardware-in-the-loop testing, with additional safety margins. Autonomous designs should consider the dynamics of mixed autonomy in traffic to safely operate among humans. The software that provides a vehicle’s behavior intelligence is often developed through simulation, which may have a mismatch between dynamics, or as a result of a reinforcement learning workflow, which may be a black box with challenges to analyze. In each of these cases, it is important to have research interfaces that provide strongly typed data streams accessible to researchers who are not software experts while continuing to satisfy safety and liveness constraints. This paper describes how we design the hardware platform interfaces and software design process for a mixed autonomy traffic experiment with a leader-follower scenario. Controller synthesis for these vehicles requires clearly articulated vehicle interfaces and software design patterns for successful onboard deployment. Testing strategies for such controllers are also described before algorithms are transitioned to full-scale field experiments with safety operators for the vehicles. Testing strategies include software-in-the-loop simulation testing, hardware-in-the-loop simulation, ghost-car testing, and read-only testing in live traffic. With our approach, we were not only able to validate our controller synthesized in scripts and simulation, but also able to scale deployment to multiple vehicles.

Bhadani, Rahul↗

DOE OSTI2022

AI-Enabled Robots for Automated Nondestructive Evaluation and Repair of Power Plant Boilers. Final Report

Boiler failure could cause loss of life and safety issues, cost hundreds of thousands of dollars in equipment repairs, property damage and production losses, and drive up the cost of electric power. Boiler maintenance is challenging and risky for inspectors working on scaffolding in confined hazardous spaces inside of a boiler and sometimes the space is hard to access. The operation is also time-consuming due to the large area of vertical structures for inspection and the tremendous effort needed for scaffolding. Recently, the use of robotics (e.g., drones and crawlers) in power plants for maintenance is growing rapidly. However, the existing robotics solutions show two notable technological gaps: no live repair capability, and no Artificial Intelligence (AI) for smart autonomy. The objective of this project is to develop an integrated autonomous robotic platform that is equipped with compact non-destructive evaluation (NDE) sensors to perform live inspection, operates onboard repair devices to perform live repair, and uses AI for intelligent data fusion and predictive analysis for automated and smart spatiotemporal inspection, analysis and repair of the furnace walls in coal-fired boilers. The approach to achieve the objective includes developing NDE sensors with signal processing techniques, designing and evaluating repair devices for robots based on fusion and solid-state technologies, and an autonomous robotic platform that can attach to and navigate on boiler furnace walls using magnetic drive tracks. The robot is also powered by AI to automate data gathering (e.g., 3D mapping and damage localization) and predictive analysis. This project has advanced the state-of-the-art by providing technological breakthroughs including compact NDE and repair tools for robots, AI capabilities for smart autonomy, and a robotic platform for automated boiler maintenance. This project has great potential to result in significant benefits including limiting or eliminating the need to send operators to assess difficult-to-access or hazardous areas, enabling automated live inspection and repair, avoiding time consuming scaffolding (especially for partial maintenance during unplanned outage), collecting comprehensive and well-organized data smartly, and avoiding or limiting the need for onsite or remote piloting technicians. The impacts can be tremendous in terms of the time and cost savings, reducing the risk for human operators, and increasing boiler reliability, usability, and efficiency. In addition, by developing the new technologies on the autonomous inspection and repair robot, by involving multiple undergraduate and graduate students working together with the faculty members on this project, and by generating knowledge and building up collaborations with industrial partners, this effort will significantly update the education capabilities, support long-term fundamental research, and maintain the leadership of Colorado School of Mines and Michigan State University in energy fields.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2023

Avoided Level Crossing and Entangled States of Interacting Hydrogen Molecules Detected by the Quantum Superposition Microscope

Pump–probe measurements by ultrashort THz pulses can be used to excite and follow the coherence dynamics in the time domain of single hydrogen molecules (H 2 ) in the junction of a scanning tunneling microscope (STM). By tailoring the resonance frequency through the sample bias, we identified two spectral signatures of the interactions among multiple H 2 molecules. First, the avoided level crossing featured by energy gaps ranging from 20 to 80 GHz was observed because of the level repulsion between two H 2 molecules. Second, the tip can sense the signal of H 2 outside the junction through the projective measurement on the H 2 inside the junction, owing to the entangled states created through the interactions. A dipolar-type interaction was integrated into the tunneling two-level system model of H 2 , enabling accurate reproduction of the observed behaviors. Furthermore, our results obtained by the quantum superposition microscope reveal the intricate quantum mechanical interplay among H 2 molecules and additionally provide a 2D platform to investigate unresolved questions of amorphous materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Interface learning of multiphysics and multiscale systems

Complex natural or engineered systems comprise multiple characteristic scales, multiple spatiotemporal domains, and even multiple physical closure laws. To address such challenges, we introduce an interface learning paradigm and put forth a data-driven closure approach based on memory embedding to provide physically correct boundary conditions at the interface. To enable the interface learning for hyperbolic systems by considering the domain of influence and wave structures into account, we put forth the concept of upwind learning toward a physics-informed domain decomposition. The promise of the proposed approach is shown for a set of canonical illustrative problems. Here, we highlight that high-performance computing environments can benefit from this methodology to reduce communication costs among processing units in emerging machine-learning-ready heterogeneous platforms toward exascale era.

42 ENGINEERING↗

DOE OSTI2023

Tunable Van Hove Singularity without Structural Instability in Kagome Metal $CsTi_{3}Bi_{5}$

In kagome metal $CsV_{3}Sb_{5}$, multiple intertwined orders are accompanied by both electronic and structural instabilities. These exotic orders have attracted much recent attention, but their origins remain elusive. The newly discovered $CsTi_{3}Bi_{5}$ is a Ti-based kagome metal to parallel $CsV_{3}Sb_{5}$. Here, in this work, we report angle-resolved photoemission experiments and first-principles calculations on pristine and Cs-doped $CsTi_{3}Bi_{5}$ samples. Our results reveal that the van Hove singularity (vHS) in $CsTi_{3}Bi_{5}$ can be tuned in a large energy range without structural instability, different from that in $CsV_{3}Sb_{5}$. As such, $CsTi_{3}Bi_{5}$ provides a complementary platform to disentangle and investigate the electronic instability with a tunable vHS in kagome metals.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Approaching the Strain-Free Limit in Ultrathin Nanomechanical Resonators

Ultrathin mechanical structures are ideal building platforms to pursue the ultimate limit of nanomechanical resonators for applications in sensing, signal processing, and quantum physics. Unfortunately, as the thickness of the vibrating structures is reduced, the built-in strain of the structural materials plays an increased role in determining the mechanical performance of the devices. As a consequence, it is very challenging to fabricate resonators working in the modulus-dominant regime, where their dynamic behavior is exclusively determined by the device geometry. In this Letter, we report ultrathin doubly clamped nanomechanical resonators with aspect ratios as large as L/t similar to 5000 and working in the modulus-dominant regime. Here, we observed room temperature thermomechanically induced motion of multiple vibration modes with resonant frequencies closely matching the predicted values of Euler-Bernoulli beam theory under an axial strain of 6.3 x 10 -8 . The low strain of the devices enables a record frequency tuning ratio of more than 50 times. These results illustrate a new strategy for the quantitative design of nanomechanical resonators with unprecedented performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗