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DOE OSTI2026

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗

DOE OSTI2023

Multifidelity validation of digital surrogates using variable-density turbulent mixing models

In this study, ensembles of experimental data are presented and utilized to compare and validate two models used in the simulation of variable-density (Atwood = 0.22), compressible turbulent mixing. Though models of this kind (Reynolds averaged NavierStokes and large-eddy simulations) have been validated extensively with more canonical flows in previous studies, here the present approach offers novelty in the complexity of the geometry, the ensemble-based validation, and the uniformity of the computational framework on which the models are tested. Moreover, all experimental and computational tasks were completed by the authors which has led to a tightly coupled experimental configuration with its “digital twin.” The experimental divergent-shock-tube facility and its data acquisition methods are described and replicated in simulation space. A 2D Euler model which neglects the turbulent mixing at the interface is optimized to experimental data using a Gaussian process. This model then serves as the basis for both the 2D RANS and 3D LES studies that make comparisons to the mixing-layer data from the experiment. A relatively simple RANS model is shown to produce good agreement with experimental data only at late flow development times. The LES ensembles generally show good agreement with experimental data but display sensitivity to the characterization of initial conditions. Resolution-dependent behavior is also observed for certain higher-order statistics of interest. Overall, the LES model successfully captures the effects of divergent geometry, compressibility, and combined nonlinear instabilities inherent to the problem. The successful prediction of mixing width and its growth rate highlight the existence of three distinct regimes in the development of the instability, each with similarities to previously studied instabilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1978

Life test results for an ensemble of CO2 lasers

The effects of cathode material, cathode operating temperature, anode configuration, window materials, and hydrogen additives on laser lifetime are determined. Internally oxidized copper and silber-copper alloy cathodes were tested. The cathode operating temperature was raised in some tubes through the use of thermal insulation. Lasers incorporating thermally insulated silver copper oxide cathodes clearly yielded the longest lifetimes-typically in excess of 22,000 hours. The use of platinum sheet versus platinum pin anodes had no observable effect on laser lifetime. Similarly, the choice of germanium, cadmium telluride, or zinc selenide as the optical window material appears to have no impact on lifetime.

Peruso, C. J.↗

NASA NTRS2004

Starting Vortex Identified as Key to Unsteady Ejector Performance

Unsteady ejectors are currently under investigation for use in some pulse-detonation-engine-based propulsion systems. Experimental measurements made in the past, and recently at the NASA Glenn Research Center, have demonstrated that thrust augmentation can be enhanced considerably when the driver is unsteady. In ejector systems, thrust augmentation is defined as = T(sup Total)/T(sup j), where T(sup Total) is the total thrust of the combined ejector and driving jet and T(sup j) is the thrust due to the driving jet alone. There are three images in this figure, one for each of the named thrust sources. The images are color contours of measured instantaneous vorticity. Each image is an ensemble average of at least 150 phase-locked measurements. The flow is from right to left, and the shape and location of each driver is shown on the far right of each image. The emitted vortex is a clearly defined "doughnut" of highly vortical (spinning) flow. In these planar images, the vortex appears as two distorted circles, one above, and one below the axis of symmetry. Because they are spinning in the opposite direction, the two circles have vorticity of opposite sign and thus are different colors. There is also a rectangle shown in each image. Its width represents the ejector diameter that was found experimentally to yield the highest thrust augmentation. It is apparent that the optimal ejector diameter is that which just "captures" the vortex: that is, the diameter bounding the outermost edge of the vortex structure. The exact mechanism behind the enhanced performance is unclear; however, it is believed to be related to the powerful vortex emitted with each pulse of the unsteady driver. As such, particle imaging velocimetry (PIV) measurements were obtained for three unsteady drivers: a pulsejet, a resonance tube, and a speaker-driven jet. All the drivers were tested with ejectors, and all exhibited performance enhancement over similarly sized steady drivers. The characteristic starting vortices of each driver are shown in these images. The images are color contours of measured instantaneous vorticity. Each image is an ensemble average of at least 150 phase-locked measurements. The flow is from right to left. The shape and location of each driver is shown on the far right of each image. The rectangle shown in each image represents the ejector diameter that was found experimentally to yield the highest thrust augmentation. It is apparent that the optimal ejector diameter is that which just "captures" the vortex: that is, the diameter bounding the outermost edge of the vortex structure. Although not shown, it was observed that the emitted vortex spread as it traveled downstream. The spreading rate for the pulsejet is shown as the dashed lines in the top image. A tapered ejector was fabricated that matched this shape. When tested, the ejector demonstrated superior performance to all those previously tested at Glenn (which were essentially of straight, cylindrical form), achieving a remarkable thrust augmentation of 2. The measured thrust augmentation is shown as a function of ejector length. Also shown are the thrust augmentation values achieved with the straight, cylindrical ejectors of varying diameters. Here, thrust augmentation is plotted as a function of ejector length for several families of ejector diameters. It can be seen that large thrust augmentation values are indeed obtained and that they are sensitive to both ejector length and diameter, particularly the latter. Five curves are shown. Four correspond to straight ejector diameters of 2.2, 3.0, 4.0, and 6.0 in. The fifth curve corresponds to the tapered ejector contoured to bound the emitted vortex. For each curve, there are several data points corresponding to different lengths. The largest value of thrust augmentation is 2.0 for the tapered ejector and 1.81 for the straight ejectors. Regardless of their diameters, all the ejectors trend toward peak performance at a particular leng. That the cross-sectional dimensions of optimal ejectors scaled precisely with the vortex dimensions on three separate pulsed thrust sources demonstrates that the action of the vortex is responsible for the enhanced ejector performance. The result also suggests that, in the absence of a complete understanding of the entrainment and augmentation mechanisms, methods of characterizing starting vortices may be useful for correlating and predicting unsteady ejector performance.

Paxson, Daniel E.↗

NASA NTRSDate not supplied

Development of an Inertial Sensor-based Methodology for Spacesuited Geology Task Assessments during Simulated Lunar Extravehicular Activities

Lunar surface exploration during Artemis missions will require the specific skill set of geology sampling. Apollo astronauts had extensive training and used specialized tools to collect lunar rocks, core samples, pebbles, sand, and dust. The inflexibility of the pressurized Apollo spacesuits forced sampling to be taken at a standstill posture. However, new exploration spacesuits are expected to incorporate advanced materials and joint bearings, allowing for greater mobility and a wider range of functional postures. Thus, science and exploration during Artemis missions will likely involve a variety of standing, squatting, and kneeling postures. In preparation for future lunar exploration missions, NASA provides geologic training to astronauts and other mission personnel. This professional training with a spacesuit in simulated lunar environments will enhance performance and reduce risk of injury to astronauts on the lunar surface. However, anecdotally, untrained or newly trained people wearing prototype planetary spacesuits have been observed to performing motions differently than a trained geologist would when conducting the same geology sampling tasks. Therefore, a tool for evaluating geology postures at extravehicular activity (EVA) training facilities becomes required. In this paper, we introduce a novel inertial measurement unit (IMU)-based method of geology task assessments in spacesuited conditions during simulated lunar EVAs. As a case study, two subjects (one geologist and one non-geologist) participated and donned the Mark III prototype planetary spacesuit during offloading with the spreader bar gimbal in NASA’s Active Response Gravity Offload System (ARGOS). For automated geology task assessments, the spacesuit was instrumented with three wireless IMUs (APDM Opal, OR, USA): one on the chest and one each on the left and right ankle bearings. Then subjects performed geology tasks using various tools (rake, trench, hammer chisel, scoop, and drive tube) for 45 minutes each. The chest IMU measured the torso tilt angle in the sagittal plane. We used an ensemble learning method with the ankle IMUs to discriminate between standing and kneeling activities. IMU data were processed using custom MATLAB (Mathworks, MA, USA) software. In our case study, the developed method was able to discriminate differences in standing and kneeling activity levels between subjects who were all highly experienced with spacesuited testing. Our preliminary data showed one subject maintained the constant and lower range of the upper body tilt angle while both standing and kneeling, while the other subject showed more variation of the upper body tilt angle and preferred bending the upper body rather than changing from standing to kneeling posture and vice versa. While geology experience may be a factor, these results need further investigation as suit sizing and ARGOS offloading configurations have been proven to have a significant influence on suited ARGOS tasks. Also, more subjects will be needed to complete these tasks for validation. IMU-based geology task assessments can provide useful information for geology training programs. Additionally, our IMU-based posture analysis can provide new insights into how to evaluate spacesuited geology task characteristics of astronauts during simulated lunar EVAs.

Kyoung Jae Kim↗

NASA NTRS2026

Performance Evaluation of Intravehicular Activity Spacesuit Without the Use of a Liquid Cooling Garment

The Orion Crew Survival Systems (OCSS) suit is equipped with safety technology that protects the crew during launch and re-entry and Intravehicular Activities (IVA). It was designed to be used with a Liquid Cooling Garment (LCG), an undergarment with tubes that circulate water to remove excess heat from a crew member. The objective of this study is to determine if the Modified Advanced Crew Escape Suit (MACES), which has very similar material, assembly, and pressure characteristics as the OCSS suit, can be used without the LCG to maintain the crew within their heat storage requirements where exceedances can lead to cognitive and physiological impairment. Testing was completed for both hot and cold environments where test subjects wore varying configurations of the MACES suit ensemble without the LCG. The tests were conducted in a temperature and humidity-controlled chamber with four test subjects ranging from extra small to large. Target metabolic rates were reached using an arm ergometer. To represent the different suit configurations seen in the concept of operations, the suit was tested with visor-down, visor-up, and without helmet and gloves. The test data was analyzed to determine how the environment, test subject size, metabolic rate, and suit configuration affected heat storage. Furthermore, the test data was used to correlate the METMAN model, a transient metabolic man program that simulates the heat transfer within a crew member’s body and from a crew member to the surrounding environment. The METMAN correlation showed good agreement between predicted heat storage and test data at the end of the test duration, with a coefficient of determination (R 2 ) value of 0.8999 for visor-down cases and R 2 of 0.8902 for visor-up and helmet off cases. A correlated METMAN model allows for the analysis and prediction of IVA suit performance without an LCG in additional scenarios.

Human Thermal Modeling↗

NASA NTRS2026

Performance Evaluation of Intravehicular Activity Spacesuit Without the Use of a Liquid Cooling Garment

Spacesuit↗

NASA NTRS1992

Fluid mechanics experiments in oscillatory flow. Volume 1: Report

Results of a fluid mechanics measurement program in oscillating flow within a circular duct are presented. The program began with a survey of transition behavior over a range of oscillation frequency and magnitude and continued with a detailed study at a single operating point. Such measurements were made in support of Stirling engine development. Values of three dimensionless parameters, Re(sub max), Re(sub w), and A(sub R), embody the velocity amplitude, frequency of oscillation and mean fluid displacement of the cycle, respectively. Measurements were first made over a range of these parameters which included operating points of all Stirling engines. Next, a case was studied with values of these parameters that are representative of the heat exchanger tubes in the heater section of NASA's Stirling cycle Space Power Research Engine (SPRE). Measurements were taken of the axial and radial components of ensemble-averaged velocity and rms-velocity fluctuation and the dominant Reynolds shear stress, at various radial positions for each of four axial stations. In each run, transition from laminar to turbulent flow, and its reverse, were identified and sufficient data was gathered to propose the transition mechanism. Models of laminar and turbulent boundary layers were used to process the data into wall coordinates and to evaluate skin friction coefficients. Such data aids in validating computational models and is useful in comparing oscillatory flow characteristics to those of fully-developed steady flow. Data were taken with a contoured entry to each end of the test section and with flush square inlets so that the effects of test section inlet geometry on transition and turbulence are documented. Volume 1 contains the text of the report including figures and supporting appendices. Volume 2 contains data reduction program listings and tabulated data (including its graphical presentation).

Seume, J.↗

DOE OSTI2023

Agilent AgileBioFoundry CRADA (Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Explosive Soot Challenge (Final Report)

This project assembled a broad ensemble of modeling and experimentation tools to study the morphological and optical properties of detonation soots in explosive fireballs. A gram-scale hemispherical high explosive was studied in a low-pressure controlled environment using in-situ experimentation with diffusely illuminated visible absorption spectroscopy, particle sizing through light scattering techniques, and post-test collections with subsequent morphological analysis. Hydrocode modeling was performed to replicate the detonation flow observations, and subsequent aerosol kinetics models provided particle size distributions and extinction coefficients from the hydrocode results. Experimentally observed soot morphologies agreed with expectation from the literature - a bimodal distribution was found, brought upon by the particles growing to a size where their inertia and fluid wakes are non-negligible. The aerosol kinetics model did not replicate the observed bimodal size distribution for lack of a coagulation kernel to represent the behavior. To recover particulate optical properties, a spectrally resolved absorption spectroscopy method termed Spectral diffuse back-illuminated extinction imaging (SBI-EI) was developed and implemented on two explosive types. Inverting the absorption spectra using a Kramers-Kronig consistent method yielded the complex index of refraction for the soots produced by the explosives. This method resulted in an unrealistic index of refraction for one of the two explosives, and this is suspected to be due to the model neglecting scattering brought upon by the large particle sizes observed. In addition to the core work, three additional studies were performed in parallel. These investigated the impact of scattering on diffuse absorption spectroscopy, studied how soots oxidate and sublimate in a well-controlled shock tube, and laid the theoretical groundwork for a new collision kernel to replicate the bimodal size distribution from the observations. Summaries of these efforts are included at the end of this report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗