Search NASA⌕ Search

SEARCH · Search NASA

Results for “test tube ensemble”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

4 records
All sourcesNASA NTRSDOE OSTI
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↗
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↗