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DOE OSTI2020

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ~40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Streamlining heterologous expression of top carbonic anhydrases in Escherichia coli : bioinformatic and experimental approaches

Carbonic anhydrase (CA) enzymes facilitate the reversible hydration of CO 2 to bicarbonate ions and protons. Identifying efficient and robust CAs and expressing them in model host cells, such as Escherichia coli, enables more efficient engineering of these enzymes for industrial CO 2 capture. However, expression of CAs in E. coli is challenging due to the possible formation of insoluble protein aggregates, or inclusion bodies. This makes the production of soluble and active CA protein a prerequisite for downstream applications. In this study, we streamlined the process of CA expression by selecting seven top CA candidates and used two bioinformatic tools to predict their solubility for expression in E. coli. The prediction results place these enzymes in two categories: low and high solubility. Our expression of high solubility score CAs (namely CA5-SspCA, CA6-SazCAtrunc, CA7-PabCA and CA8-PhoCA) led to significantly higher protein yields (5 to 75 mg purified protein per liter) in flask cultures, indicating a strong correlation between the solubility prediction score and protein expression yields. Furthermore, phylogenetic tree analysis demonstrated CA class-specific clustering patterns for protein solubility and production yields. Unexpectedly, we also found that the unique N-terminal, 11-amino acid segment found after the signal sequence (not present in its homologs), was essential for CA6-SazCA activity. Overall, this work demonstrated that protein solubility prediction, phylogenetic tree analysis, and experimental validation are potent tools for identifying top CA candidates and then producing soluble, active forms of these enzymes in E. coli. The comprehensive approaches we report here should be extendable to the expression of other heterogeneous proteins in E. coli.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1988

Particle-laden weakly swirling free jets: Measurements and predictions

A theoretical and experimental investigation of particle-laden, weakly swirling, turbulent free jets was conducted. Glass particles, having a Sauter mean diameter of 39 microns, with a standard deviation of 15 microns, were used. A single loading ratio (the mass flow rate of particles per unit mass flow rate of air) of 0.2 was used in the experiments. Measurements are reported for three swirl numbers, ranging from 0 to 0.33. The measurements included mean and fluctuating velocities of both phases, and particle mass flux distributions. Measurements were also completed for single-phase non-swirling and swirling jets, as baselines. Measurements were compared with predictions from three types of multiphase flow analysis, as follows: (1) locally homogeneous flow (LHF) where slip between the phases was neglected; (2) deterministic separated flow (DSF), where slip was considered but effects of turbulence/particle interactions were neglected; and (3) stochastic separated flow (SSF), where effects of both interphase slip and turbulence/particle interactions were considered using random sampling for turbulence properties in conjunction with random-walk computations for particle motion. Single-phase weakly swirling jets were considered first. Predictions using a standard k-epsilon turbulence model, as well as two versions modified to account for effects of streamline curvature, were compared with measurements. Predictions using a streamline curvature modification based on the flux Richardson number gave better agreement with measurements for the single-phase swirling jets than the standard k-epsilon model. For the particle-laden jets, the LHF and DSF models did not provide very satisfactory predictions. The LHF model generally overestimated the rate of decay of particle mean axial and angular velocities with streamwise distance, and predicted particle mass fluxes also showed poor agreement with measurements, due to the assumption of no-slip between phases. The DSF model also performed quite poorly for predictions of particle mass flux because turbulent dispersion of the particles was neglected. The SSF model, which accounts for both particle inertia and turbulent dispersion of the particles, yielded reasonably good predictions throughout the flow field for the particle-laden jets.

Bulzan, Daniel L.↗

DOE OSTI2020

Microkinetic Modeling: A Tool for Rational Catalyst Design

The design of heterogeneous catalysts relies on understanding the fundamental surface kinetics that controls catalyst performance, and microkinetic modeling is a tool that can help the researcher in streamlining the process of catalyst design. Microkinetic modeling is used to identify critical reaction intermediates and rate-determining elementary reactions, thereby providing vital information for designing an improved catalyst. In this review, we summarize general procedures for developing microkinetic models using reaction kinetics parameters obtained from experimental data, theoretical correlations, and quantum chemical calculations. We examine the methods required to ensure the thermodynamic consistency of the microkinetic model. We describe procedures required for parameter adjustments to account for the heterogeneity of the catalyst and the inherent errors in parameter estimation. We discuss the analysis of microkinetic models to determine the rate determining reactions using the degree of rate control and reversibility of each elementary reaction. We introduce incorporation of Brønsted–Evans–Polanyi relations and scaling relations in microkinetic models and the effects of these relations on catalytic performance and formation of volcano curves. We review the analysis of reaction schemes in terms of the maximum rate of elementary reactions, and we outline a procedure to identify kinetically significant transition states and adsorbed intermediates. Here, we explore the application of generalized rate expressions for the prediction of optimal binding energies of important surface intermediates and to estimate the extent of potential rate improvement. We also explore the application of microkinetic modeling in homogeneous catalysis, electro-catalysis, and transient reaction kinetics. We conclude by highlighting the challenges and opportunities in the application of microkinetic modeling for catalyst design.

42 ENGINEERING↗

DOE OSTI2016

SU-F-J-53: A 3D Printed Phantom for the Use of Daily Quality Assurance Alignment Tests

Purpose: To discuss experiences and results for a 3D printed QA phantom used for daily alignment purposes for a six degrees-of-freedom (6DoF) table Methods: A 3D model was created using a fused deposition modeling (FDM) printer using free online computer-aided design (CAD) software. The model has been under use for daily QA alignment tests for a 6DoF couch. An aligned and angled baseplate were also printed in order to introduce known angles for 6DoF corrections during image-guidance. Unique registration contours were created on the faces of the phantom in order to achieve a better cone-beam computed tomography (CBCT) match using an auto-registration algorithm. A BB was also introduced at the center of the phantom in order to deliver an integrated daily Winston-Lutz (WL) test. Translational, rotational, and WL results were tabulated over one month. Results: The ’honeycomb’ structure of the print was apparent in the EPID images for the WL test, which affected the results of the analysis software. This was fixed by inserting a cube made of polyoxymethylene within the 3D phantom that encompass the BB. Auto-registration results for the three translational and three rotational from a known offset to the BB isocenter consistently fell within 1 mm and 0.2°, respectively. WL tests resulted in an average of 0.71 ± 0.14 mm. Conclusion: 3D printed models allow for accurate builds that can be customized to a variety of clinical needs. Results from translational, rotational, and WL show consistent results over a month’s time. Given its relatively cheap and streamlined workflow, 3D printing could be implemented into any clinic looking to create customized phantoms.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1973

Base pressure in laminar supersonic flow.

An asymptotic description is proposed for supersonic laminar flow over a wedge or a backward-facing step, for large Reynolds number and for a base or step height which is small compared with the boundary-layer length. The analysis is carried out for adiabatic wall conditions and a viscosity coefficient proportional to temperature. In a particular limit corresponding to a very thick boundary layer, a similarity law is obtained for the base pressure. For a thinner boundary layer an asymptotic form for the base pressure is obtained which shows the dependence on the parameters explicitly and which permits good agreement with experiment. This latter result is based on an inviscid-flow approximation for the corner expansion and for reattachment with viscous forces important primarily in a thin sublayer about the dividing streamline. A prediction of the pressure distribution at reattachment is given and the result is compared with experimental pressure distributions.

Messiter, A. F.↗

NASA NTRS2019

Discovery and Vetting of Exoplanets. I. Benchmarking K2 Vetting Tools

We have adapted the algorithmic tools developed during the Kepler mission to vet the quality of transit-like signals for use on the K2 mission data. Using the four sets of publicly available light curves at MAST, we produced a uniformly vetted catalog of 772 transiting planet candidates from K2 as listed at the NASA Exoplanet Archive in the K2 Table of Candidates. Our analysis marks 676 of these as planet candidates and 96 as false positives. All confirmed planets pass our vetting tests. Sixty of our false positives are new identifications, effectively doubling the overall number of astrophysical signals mimicking planetary transits in K2 data. Most of the targets listed as false positives in our catalog show either prominent secondary eclipses, transit depths suggesting a stellar companion instead of a planet, or significant photocenter shifts during transit. We packaged our tools into the open-source, automated vetting pipeline Discovery and Vetting of Exoplanets (DAVE), designed to streamline follow-up efforts by reducing the time and resources wasted observing targets that are likely false positives. DAVE will also be a valuable tool for analyzing planet candidates from NASA's TESS mission, where several guest-investigator programs will provide independent light-curve sets—and likely many more from the community. We are currently testing DAVE on recently released TESS planet candidates and will present our results in a follow-up paper.

Kostov, Veselin B.↗

NASA NTRS1975

Evaluation of some control-volume techniques for analysis of shock-boundary layer interactions in supersonic inlets

Various control-volume models used to analyze the shock boundary layer bleed interaction were investigated. The bleed assumptions of the models and their influence on the analytical solutions are discussed. The results of the analysis using these models are compared with experimental boundary-layer data taken in a supersonic inlet. The experimental Mach number upstream of the interaction was 1.66, and the oblique-shock pressure ratio was 1.33. The boundary layer data included bleed flow rates up to approximately 0.6 of the upstream boundary layer mass flow rate. The first model assumed the bleed was removed from the control volume with a momentum that was characterized by a pressure intermediate between the upstream and downstream pressures. The second model assumed the control volume was bounded by a streamline dividing the bleed and residual flows and eliminated the need to specify the momentum of the bleed flow. Comparison of the results using the models showed that specifying the bleed pressure in one model was equivalent to specifying the pressure along the dividing streamline in the other.

Hingst, W. R.↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

Abstract Nanoporous materials are of great interest in many applications, such as catalysis, separation, and energy storage. The performance of these materials is closely related to their pore sizes, which are inefficient to determine through the conventional measurement of gas adsorption isotherms. Nuclear magnetic resonance (NMR) relaxometry has emerged as a technique highly sensitive to porosity in such materials. Nonetheless, streamlined methods to estimate pore size from NMR relaxometry remain elusive. Previous attempts have been hindered by inverting a time domain signal to relaxation rate distribution, and dealing with resulting parameters that vary in number, location, and magnitude. Here we invoke well‐established machine learning techniques to directly correlate time domain signals to BET surface areas for a set of metal‐organic frameworks (MOFs) imbibed with solvent at varied concentrations. We employ this series of MOFs to establish a correlation between NMR signal and surface area via partial least squares (PLS), following screening with principal component analysis, and apply the PLS model to predict surface area of various nanoporous materials. This approach offers a high‐throughput, non‐destructive way to assess porosity in c.a. one minute. We anticipate this work will contribute to the development of new materials with optimized pore sizes for various applications.

Fricke, Sophia N.↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Optimization models for integrated biorefinery operations

Variations of physical and chemical characteristics of biomass lead to an uneven flow of biomass in a biorefinery, which reduces equipment utilization and increases operational costs. Uncertainty of biomass supply and high processing costs increase the risk of investing in the US’s cellulosic biofuel industry. We propose a stochastic programming model to streamline processes within a biorefinery. A chance constraint models system’s reliability requirement that the reactor is operating at a high utilization rate given uncertain biomass moisture content, particle size distribution, and equipment failure. The model identifies operating conditions of equipment and inventory level to maintain a continuous flow of biomass to the reactor. Furthermore, the sample average approximation method approximates the chance constraint and a bisection search-based heuristic solves this approximation. A case study is developed using real-life data collected at Idaho National Laboratory’s biomass processing facility. An extensive computational analysis indicates that sequencing of biomass bales based on moisture level, increasing storage capacity, and managing particle size distribution, increases utilization of the reactor and reduces operational costs.

09 BIOMASS FUELS↗

DOE OSTI2024

Aerial Data and Processed Models of Port Arthur Coastal Neighborhood and Pleasure Island Golf Course, June 2024

Our Co-design team is from the University of Texas, working on a Department of Energy-funded project focused on the Beaumont-Port Arthur area. As part of this project, we will be developing climate-resilient design solutions for areas of the region. More on www.caee.utexas.edu.We captured aerial photos in the Port Arthur Coastal Neighborhood Community and the Golf Course on Pleasure Island, Texas, in June 2024.Aerial photos taken were through DroneDeploy autonomous flight, and models were processed through the DroneDeploy engine as well. All aerial photos are in .JPG format and contained in zipped files for each area.The processed data package includes 3D models, geospatial data, mappings, and point clouds. Please be aware that DTM, Elevation toolbox, Point cloud, and Orthomosaic use EPSG: 6588. And 3D Model uses EPSG: 3857.For using these data:- The Adobe Suite gives you great software to open .Tif files.- You can use LASUtility (Windows), ESRI ArcGIS Pro (Windows), or Blaze3D (Windows, Linux) to open a LAS file and view the data it contains.- Open an .OBJ file with a large number of free and commercial applications. Some examples include Microsoft 3D Builder, Apple Preview, Blender, and Autodesk.- You may use ArcGIS, Merkaartor, Blender (with the Google Earth Importer plug-in), Global Mapper, and Marble to open .KML files.- The .tfw world file is a text file used to georeference the GeoTIFF raster images, like the orthomosaic and the DSM. You need suitable software like ArcView to open a .TFW file.This dataset provides researchers with sufficient geometric data and the status quo of the land surface at the locations mentioned above. This dataset could streamline researchers' decision-making processes and enhance the design as well.

2D mapping↗

NASA NTRS2010

Analysis of Dependencies and Impacts of Metroplex Operations

This report documents research performed by Purdue University under subcontract to the George Mason University (GMU) for the Metroplex Operations effort sponsored by NASA's Airportal Project. Purdue University conducted two tasks in support of the larger efforts led by GMU: a) a literature review on metroplex operations followed by identification and analysis of metroplex dependencies, and b) the analysis of impacts of metroplex operations on the larger U.S. domestic airline service network. The tasks are linked in that the ultimate goal is an understanding of the role of dependencies among airports in a metroplex in causing delays both locally and network-wide. The Purdue team has formulated a system-of-systems framework to analyze metroplex dependencies (including simple metrics to quantify them) and develop compact models to predict delays based on network structure. These metrics and models were developed to provide insights for planners to formulate tailored policies and operational strategies that streamline metroplex operations and mitigate delays and congestion.

DeLaurentis, Daniel A.↗

DOE OSTI2025

Developing an Automated Microscopic Traffic Simulation Scenario Generation Tool

Traffic simulation is an effective tool for urban planners, traffic engineers, and researchers to study traffic. In particular, microscopic traffic simulation, which simulates individual vehicles’ movements within a transportation network, has demonstrated its importance in analyzing and managing transportation systems. However, integrating data from various sources, generating traffic scenarios, and importing information into traffic simulators to conduct microscopic simulations have always been a challenge. This paper presents a solution to overcome this challenge: RealTwin, a comprehensive tool for automated scenario generation for microscopic traffic simulation. Following a streamlined scenario generation and calibration workflow, RealTwin effectively bridges gaps between traffic data from various sources and traffic simulators, making microscopic traffic simulation more accessible for researchers and engineers across various levels of expertise. Using RealTwin to generate a real-world traffic scenario in Simulation of Urban Mobility (SUMO), VISSIM, and AIMSUN, RealTwin’s ability is demonstrated in the construction of realistic and consistent traffic scenarios in different simulators. Furthermore, this paper introduces and illustrates RealTwin’s capability for technology (e.g., autonomous vehicle) scenario generation. This feature can contribute to more comprehensive microscopic simulations, facilitating the analysis of potential effects of various technological innovations on mobility, energy efficiency, and safety. Finally, RealTwin is used to calibrate a simulation in SUMO. In conclusion, the calibration module enhances RealTwin’s ability to generate consistent simulations across different platforms and more realistic simulations that reflect real-world traffic operations.

autonomous vehicle↗

NASA NTRS1996

CFD Study of Turbo-Ramjet Interactions in Hypersonic Airbreathing Propulsion System

Advanced airbreathing propulsion systems used in Mach 4-6 mission scenarios, usually involve turbo-ramjet configurations. As the engines transition from turbojet to ramjet, there is an operational envelope where both engines operate simultaneously. In the first phase of our study, an over/under nozzle configuration was analyzed. The two plumes from the turbojet and ramjet interact at the end of a common 2-D cowl, where they both reach an approximate Mach 3.0 condition and then jointly expand to Mach 3.6 at the common nozzle exit plane. For the problem analyzed, the turbojet engine operates at a higher nozzle pressure ratio than the ramjet, causes the turbojet plume overpowers the ramjet plume, deflecting it approximately 12 degrees downward and in turn the turbojet plume is deflected 6 degrees upward. In the process, shocks were formed at the deflections and a shear layer formed at the confluence of the two jets. This particular case was experimentally tested and the data were used to compare with a computational fluid dynamics (CFD) study using the PARC2D code. The CFD results were in good agreement with both static pressure distributions on the cowl separator and on nozzle walls. The thrust coefficients were also in reasonable agreement. In addition, inviscid relationships were developed around the confluence point, where the two exhaust jets meet, and these results compared favorably with the CFD results. In the second phase of our study, a 3-D CFD solution was generated to compare with the 2-D solution. The major difference between the 2-D and 3-D solutions was the interaction of the shock waves, generated by the plume interactions, on the sidewall. When a shock wave interacts with a sidewall and sidewall boundary layer, it is called a glancing shock sidewall interaction. These interactions entrain boundary layer flow down the shockline into a vortical flow pattern. The 3-D plots show the streamlines being entrained down the shockline. The pressure of the flow also decreases slightly as the sidewall is approached. Other difference between the 2-D and 3-D solutions were a lowering of the nozzle thrust coefficient value from 0.9850 (2-D) to 0.9807 (3-D), where the experimental value was 0.9790. In the third phase of our study, a different turbo-ramjet configuration was analyzed. The confluence of a supersonic turbojet and a subsonic ramjet in the turbine based combined-cycle (TBCC) propulsion system was studied by a 2-D CFD code. In the analysis, Mach 1.4 primary turbojet was mixed with the subsonic ramjet secondary flow in an ejector mode operation. Reasonable agreements were obtained with the supplied I-D TBCC solutions. For low downstream backpressure, the Fabri choke condition (Break-Point condition) was observed in the secondary flow within mixing zone. For sufficient high downstream backpressure, the Fabri choke no longer exist, the ramjet flow was reduced and the ejector flow became backpressure dependent. Highly non-uniform flow at ejector exit were observed, indicated that for smooth downstream combustion, the mixing of the two streams probably required some physical devices.

Chang, Ing↗

NASA NTRS2010

Aeroheating Mapping to Thermal Model for Autonomous Aerobraking Capability

Thermal modeling has been performed to evaluate the potential for autonomous aerobraking of a spacecraft in the atmosphere of a planet. As part of this modeling, the aeroheating flux during aerobraking must be applied to the spacecraft solar arrays to evaluate their thermal response. On the Mars Reconnaissance Orbiter (MRO) mission, this was done via two separate thermal models and an extensive suite of mapping scripts. That method has been revised, and the thermal analysis of an aerobraking pass can now be accomplished via a single thermal model, using a new capability in the Thermal Desktop software. This capability, Boundary Condition Mapper, has the ability to input heating flux files that vary with time, position on the solar array, and with the skin temperature. A recently added feature to the Boundary Condition Mapper is that this module can also utilize files that describe the variation of aeroheating over the surface with atmospheric density (rather than time); this is the format of the MRO aeroheating files. This capability has allowed a huge streamlining of the MRO thermal process, simplifying the procedure for importing new aeroheating files and trajectory information. The new process, as well as the quantified time savings, is described.

Amundsen, Ruth M.↗

NASA NTRS1999

X-33 (Rev-F) Aeroheating Results of Test 6770 in NASA Langley 20-Inch Mach 6 Air Tunnel

Aeroheating characteristics of the X-33 Rev-F configuration have been experimentally examined in the Langley 20-Inch Mach 6 Air Tunnel (Test 6770). Global surface heat transfer distributions, surface streamline patterns, and shock shapes were measured on a 0.013-scale model at Mach 6 in air. Parametric variations include angles-of-attack of 20-deg, 30-deg, and 40-deg; Reynolds numbers based on model length of 0.9 to 4.9 million; and body-flap deflections of 10-deg and 20-deg. The effects of discrete roughness elements on boundary layer transition, which included trip height, size, and location, both on and off the windward centerline, were investigated. This document is intended to serve as a quick release of preliminary data to the X-33 program; analysis is limited to observations of the experimental trends in order to expedite dissemination.

Berry, Scott A.↗

DOE OSTI2013

The use of computed radiography plates to determine light and radiation field coincidence

Purpose: Photo-stimulable phosphor computed radiography (CR) has characteristics that allow the output to be manipulated by both radiation and optical light. The authors have developed a method that uses these characteristics to carry out radiation field and light field coincidence quality assurance on linear accelerators.Methods: CR detectors from Kodak were used outside their cassettes to measure both radiation and light field edges from a Varian linear accelerator. The CR detector was first exposed to a radiation field and then to a slightly smaller light field. The light impinged on the detector's latent image, removing to an extent the portion exposed to the light field. The detector was then digitally scanned. A MATLAB-based algorithm was developed to automatically analyze the images and determine the edges of the light and radiation fields, the vector between the field centers, and the crosshair center. Radiographic film was also used as a control to confirm the radiation field size.Results: Analysis showed a high degree of repeatability with the proposed method. Results between the proposed method and radiographic film showed excellent agreement of the radiation field. The effect of varying monitor units and light exposure time was tested and found to be very small. Radiation and light field sizes were determined with an uncertainty of less than 1 mm, and light and crosshair centers were determined within 0.1 mm.Conclusions: A new method was developed to digitally determine the radiation and light field size using CR photo-stimulable phosphor plates. The method is quick and reproducible, allowing for the streamlined and robust assessment of light and radiation field coincidence, with no observer interpretation needed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗