Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular modelling”

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.

At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Resveratrol Ameliorates Lipopolysaccharide-Induced Sudden Sensorineural Hearing Loss in In Vitro Model through Multitarget Antiapoptotic Mechanism Based on Network Pharmacology and Molecular Docking

Objective. To explore the effects of resveratrol (RSV) on hair cell apoptosis caused by sudden sensorineural hearing loss (SSNHL) and its effect on lipopolysaccharide-induced apoptosis of HEI-OC1 cells. Methods. We used the network pharmacology method to screen molecules related to RSV for the treatment of SSNHL and analyzed these molecules and their enriched biological processes and signaling pathways through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis. We selected hub genes related to apoptosis using protein-protein interaction (PPI) analysis for in vitro and molecular docking verification. Results. Eighty overlapping genes were identified as potential targets for RSV treatment of SSNHL. Further GO analysis showed that the biological processes were mainly related to toxicity, cell proliferation, and lipopolysaccharide reactions. KEGG analysis showed that the AGE-RAGE signaling pathway in diabetic complications, Kaposi’s sarcoma-associated herpesvirus infection, FoxO signaling pathway, PI3K-Akt signaling pathway, and other inflammatory signaling pathways were concentrated. AKT1, STAT3, JUN, TNF, TP53, MAPK3, CASP3, and VEGFA were screened as HUB genes using PPI analysis. The apoptosis-related proteins TNF, CASP3, AKT1, and TP53 were selected for in vitro experiments, which showed that mRNA was significantly different before and after RSV intervention, confirming that the corresponding protein receptors could bind well with RSV. Conclusion. RSV mainly affects the prognosis of SSNHL through anti-inflammatory effects and may improve hair cell apoptosis caused by inflammatory factors through multitargeted interventions involving TNF, CASP3, AKT1, and TP53.

Ye, Shiming↗
DOE OSTI2020

Polymer Retention Evaluation in a Heavy Oil Sand for a Polymer Flooding Application on Alaska’s North Slope

For a polymer flooding field trial in a heavy oil reservoir on Alaska’s North Slope, polymer retention is a key parameter. Because of the economic impact of retention, this parameter was extensively studied using field core material and conditions. Several important findings were noted. Polymer retention based on effluent viscosity measurements can be overestimated unless the correct (non-linear) relation between polymer concentration and viscosity is used. Polymer degradation (either mechanical or oxidative) can also lead viscosity-based measurements to overestimate retention. Inaccessible pore volume (IAPV) can be overestimated if insufficient brine is flushed through the sand between polymer banks. Around 100 pore volumes (PV) of brine may be needed to displace mobile polymer to approach a true residual resistance factor and properly measure IAPV. Even for a sand pack with kwsor = 20 mD, IAPV was zero for HPAM with molecular weight (Mw) of 18 million g/mol. Fine-grain particles (<20 μm) strongly impacted polymer retention values. Native NB#1 sand with a significant component of particles <20 μm exhibited 290 μg/g, while the same sand exhibited 28 μg/g after these small particles were removed. Polymer retention did not necessarily correlate with mineral composition. The NB#1, NB#3, and OA sands had similar elemental and clay compositions, but the NB#1 sand exhibited ~10 times higher retention than the NB#3 sand. Polymer retention did not necessarily correlate with permeability. NB#1 sand exhibited much higher retention than OA sand, even though NB#1 sand was twice as permeable as OA sand. No evidence of chromatographic separation of HPAM molecular weights was found in our experiments. Although retention tended to be greater without a residual oil saturation (than at Sor), the effect was not strong. Aging a core (with high oil saturation) at 60°C reduced HPAM retention by a factor of two. As expected, under similar conditions, polymer retention was greater for a higher Mw HPAM (18 million g/mol) than for a lower Mw HPAM (10-12 million g/mol). In many cases with high polymer retention values (e.g., 240 μg/g), polymer arrival at the end of the core was relatively quick, but achieving the injected concentration occurred gradually over many pore volumes. This effect was not due chromatographic separation of polymer molecular weights. Results from modeling of this behavior was consistent with concentrationdependent polymer retention. The form assumed for the retention function in a simulator can have an important impact on the timing and magnitude of the oil response from a polymer flood. Field-based observations can underestimate polymer retention, depending on when the tracer and polymer concentrations were measured and the assumptions made about reservoir heterogeneity.

Wang, Dongmei↗
DOE OSTI2020

Mechanistic Understanding of Silver Sorbent Aging Processes in Off-Gas Treatment

The effect of aging in various off-gas streams including dry air, humid air, 1% NO/N 2 , 2% NO 2 /air, and a gas mixture consisting of 99.25% humid air (dew point: -15 °C), 0.25% NO/N 2 , and 0.5% NO 2 /air in terms of concentration on reduced silver exchanged mordenite (Ag 0 Z) and silver functionalized silica aerogel (Ag 0 -aerogel) were studied in this project. Utilizing simple and sophisticated experimental information combined with molecular and macroscopic mechanistic modeling, this project has significantly advanced the current understanding of aging for silver bearing adsorbents in nuclear-fuel-reprocessing off-gas streams. In addition, this project has produced models that can be utilized to predict the influence of adsorbent aging on the uptake kinetics and capacity of aged adsorbents for iodine and iodine-containing organic compounds. The results of the study have been published in the open literature, and can be used to help DOE better predict the removal of radioactive gases from nuclear-fuel-reprocessing off-gas streams.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

DRIFT: Diffusivity Regulation of Isotopes by nanoconFinementT

Spontaneous isotope fractionation has been reported under nanoconfinement conditions in naturally occurring systems, but the origin of this phenomena is currently unknown. Two existing hypotheses have been proposed, one based on changes in the solvation environment of the isotopes that reduces the non-mass dependent hydrodynamics contribution to diffusion. The other is that isotopes have mass-dependent surface adsorption, varying their total diffusion through nanoconfined channels. To investigate these hypotheses, benchtop experiments, nuclear magnetic resonance (NMR) spectroscopy, and molecule scale modeling were applied. Classical molecular dynamics simulations identified that the Na + and Cl - hydration shells across the three different salt solutions ( 22 Na 35 Cl, 23 Na 35 Cl, 24 Na 35 Cl) did not vary as a function of the Na + isotope, but that there was a significant pore size effect, with larger hydration shells at larger pore sizes. Additionally, while total adsorption times did not vary as a function of the Na + isotope or pore size, the free ion concentration, or those adsorbed on the surface for <5% of the simulation time did exhibit isotope dependence. Experimentally, challenges occurred developing a repeatable experiment, but NMR characterization of water diffusion rates through ordered alumina membranes was able to identify the existence of two distinct water environments associated with water inside and outside the pore. Further NMR studies could be used to confirm variation in hydration shells and diffusion rates of dissolved ions in water. Ultimately, mass-dependence adsorption is a primary driver of variations in isotope diffusion rates, rather than variation in hydration shells that occur under nanoconfinement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Predicting Fuel Properties and Emissions for Advanced Biofuels for Diesel Engines (CRADA Final Report)

The project will investigate variations in biofuel composition and optimize performance in combustion for conventional and future compression ignition engines. It will evaluate a variety of bio-derived molecules in the diesel range that can be produced using technology in ExxonMobil’s portfolio as well as fuels that cover the range of potential molecular structures for robust model development. Changes in fuel/air premixing and stratification in advanced engines could alter the relationship between fuel properties and performance in comparison to current generation spray combustion approaches. NREL experience in fuel and combustion modeling will enable development of general rules for predicting performance of a wide range of biofuel options.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

New Methods for Predicting Non-Born-Oppenheimer Chemistry

Current methods for modeling non-adiabatic molecular dynamics face fundamental limitations when treating geometric phase effects: quantum mechanical phenomena where nuclear wavepackets acquire phase shifts when encircling conical intersections. Existing approaches either neglect these effects entirely or rely on potential energy surfaces arising from the Born-Oppenheimer approximation, which introduce artificial singularities and can overestimate geometric phase contributions. This project developed a new theoretical framework based on exact factorization (XF) methods to overcome these limitations. We derived mathematical formulations for hybrid quantum-classical XF dynamics that selectively treat critical nuclear degrees of freedom quantum mechanically while propagating others classically. This approach addresses the computational intractability that has previously limited exact methods to toy systems. Key innovations include a new approach to systematically identifying nuclear coordinates requiring quantum treatment, as well as novel implementation strategies that interface with existing quantum chemistry codes. The project also developed a proof-of-concept code for treating Jahn-Teller systems and creation of educational materials on non-adiabatic dynamics geared at the graduate level. The theoretical framework developed will enable future systematically improvable calculations of nuclear quantum effects in realistic molecular systems, filling a critical gap in non-adiabatic dynamics methods. This foundation supports future development of predictive tools for designing energy-relevant photochemical processes where quantum coherence effects may be exploited to control reaction outcomes.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Perspectives on biorefineries in microbial production of fuels and chemicals

Microbes drive our complex biosphere by regulating the global ecosystem through cycling elements and energy. Humankind has barely begun leveraging this biotransformation capacity to impact global economies and ecologies. Advances in genetic engineering, molecular analysis, metabolic flux modeling, microbial consortia/biome mapping and engineering, cell-free bioproduction, artificial intelligence/machine learning and the ever expanding -omics frontiers have set the stage for paradigm changes to how humankind produces, uses, transforms, and recycles carbon and energy through microbes. Harnessing this enormous potential could drive a global bioeconomy and manage carbon at a planetary level but requires understanding and application at a grand scale across a broad range of science and engineering disciplines. The penultimate manifestation of these advances is the “bio-refinery”, which is often referenced, but is a long way from being fully developed as a global carbon management platform. Broadening the feed stocks, processing operations, and product portfolio to a sequential cascade optimizing the conversion as a whole instead of limited outputs could greatly advance deployment and stability of a bioeconomy.

09 BIOMASS FUELS↗
DOE OSTI2023

Characterizing Families of Spectral Similarity Scores and Their Use Cases for Gas Chromatography–Mass Spectrometry Small Molecule Identification

Metabolomics provides a unique snapshot into the world of small molecules and the complex biological processes that govern the human, animal, plant, and environmental ecosystems encapsulated by the One Health modeling framework. However, this “molecular snapshot” is only as informative as the number of metabolites confidently identified within it. The spectral similarity (SS) score is traditionally used to identify compound(s) in mass spectrometry approaches to metabolomics, where spectra are matched to reference libraries of candidate spectra. Unfortunately, there is little consensus on which of the dozens of available SS metrics should be used. This lack of standard SS score creates analytic uncertainty and potentially leads to issues in reproducibility, especially as these data are integrated across other domains. In this work, we use metabolomic spectral similarity as a case study to showcase the challenges in consistency within just one piece of the One Health framework that must be addressed to enable data science approaches for One Health problems. Here, using a large cohort of datasets comprising both standard and complex datasets with expert-verified truth annotations, we evaluated the effectiveness of 66 similarity metrics to delineate between correct matches (true positives) and incorrect matches (true negatives). We additionally characterize the families of these metrics to make informed recommendations for their use. Our results indicate that specific families of metrics (the Inner Product, Correlative, and Intersection families of scores) tend to perform better than others, with no single similarity metric performing optimally for all queried spectra. This work and its findings provide an empirically-based resource for researchers to use in their selection of similarity metrics for GC-MS identification, increasing scientific reproducibility through taking steps towards standardizing identification workflows.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

The repulsive 1 Sigma g/+/ He2 potential obtained from total cross sections

An improved apparatus for obtaining short-range molecular potentials is described. The setup is a refined version of that used by Jordan-Amdur and by Leonas. The ion source is provided with a mass analyzing magnet, the capacitance manometer in the scattering cell is calibrated with a McCleod gauge, and the detection unit substitutes a Channeltron multiplier for the thermopile. The measured ground-state He-He potential for radii between 0.49 and 1.56 A is approximately V(r) = 215 x exp(-3.95r) eV, which is 25% higher than the earlier experiments. The result is supported by molecular orbital and statistical model calculations.

Foreman, P. B.↗
NASA NTRS1975

Viscous-shock-layer solutions with radiation and ablation injection for Jovian entry

This paper presents results that describe the flow field and surface response conditions for a planetary probe entering the atmosphere of Jupiter. The results are obtained with a viscous-shock-layer analysis which includes mass injection, radiative transfer, diffusion, and viscous effects. Radiative transfer is calculated with an existing nongray radiation model that accounts for molecular band, atomic line, and continuum transitions. Particular emphasis is given to the effect of mass injection on the stagnation and downstream flow. Results for both specified and coupled mass injection are obtained for a carbon heat shield.

Moss, J. N.↗
NASA NTRS1976

Wind enhanced planetary escape: Collisional modifications

The problem of thermal escape is considered in which both the effects of thermospheric winds at the exobase and collisions below the exobase are included in a Monte Carlo calculation. The collisions are included by means of a collisional relaxation layer of a background gas which models the transition region between the exosphere and the thermosphere. The wind effects are considered in the limiting cases of vertical and horizontal flows. Two species are considered: terrestrial hydrogen and terrestrial helium. In the cases of terrestrial hydrogen the escape fluxes were found to be strongly filtered or throttled by collisions at high exospheric temperatures. The model is applied to molecular hydrogen diffusing through a methane relaxation layer under conditions possible on Titan. The results are similar to the case of terrestrial hydrogen with wind enhanced escape being strongly suppressed by collisions. It is concluded that wind enhanced escape is not an important process on Titan.

Curtis, S. A.↗
NASA NTRS1979

Preliminary results from the University of Denver infrared spectrometer - 1977 intertropical convergence zone experiment

The Denver University Infrared Spectrometer (DUIRS) is a liquid-helium-cooled emission radiometer designed to study minor atmospheric constituents. DUIRS flew on 12 data flights during the 1977 Intertropical Convergence Zone experiment. No data were obtained on the flight from Wallops Island to Panama because of a power failure or on the return flight to Wallops Island because of a cryogen line freeze-up. The data coverage on the nine vertical profile flights that were flown before the freeze-up are shown. Typical spectra and variations as a function of U-2 (research aircraft) altitude are also shown. Radio metric data and rawinsonde temperature data were used to perform band model calculations to obtain molecular number densities in the column above the aircraft at each altitude.

Barker, D. B.↗
NASA NTRS1979

Close-coupling calculations with an INDOX/1s static potential, semiclassical exchange, and a semi-empirical polarisation potential for electron-CO2 elastic scattering and rotational excitation

A semiempirical molecular-orbital method for modelling the effective potential for electron-molecule scattering is applied to elastic scattering and rotational excitation of CO2 at 20 eV impact energy. Agreement with experiment is reasonably good. The calculated rotationally summed integral cross section is 67.8 a sub 0 squared.

Onda, K.↗
NASA NTRS1979

Effects of probe shape change on flow phenomena during Jovian entry

The effects of probe shape change on the flow phenomena around a Jovian entry body is investigated. The initial body shapes considered are: 45-degree sphere cone, 35-degree hyperboloid, and 45-degree ellipsoid. The radiating shock-layer flow is assumed to be axisymmetric, inviscid, and in chemical and local thermodynamic equilibrium. The radiative transfer is calculated with an existing nongray radiation model that accounts for molecular band, atomic line, and continuum transitions. The results indicate that the shock-standoff distance, shock temperature and density, wall pressure distribution and radiative heating to the body are influenced significantly because of the probe shape change. The effect of shape change on radiative heating of the afterbody was considerably larger for the sphere cone and ellipsoid than for the hyperboloid. For the peak heating conditions, the net radiative heating to the body was found to be highest for the ellipsoid

Tiwari, S. N.↗
NASA NTRS1981

Influence of nonequilibrium radiation and shape change on aerothermal environment of a Jovian entry body

The influence of nonequilibrium radiative energy transfer and the effect of probe configuration changes on the flow phenomena around a Jovian entry body are investigated. The radiating shock layer flow is assumed to be axisymmetric, viscous, laminar and in chemical equilibrium. The radiative transfer equations are derived under nonequilibrium conditions which include multilevel energy transitions. The equilibrium radiative transfer analysis is performed with an existing nongray radiation model which accounts for molecular band, atomic line, and continuum transitions. The nonequilibrium results are obtained with and without ablation injection in the shock layer. The nonequilibrium results are found to be greatly influenced by the temperature distribution in the shock layer. In the absence of ablative products, the convective and radiative heating to the entry body are reduced under nonequilibrium conditions. The influence of nonequilibrium is found to be greater at higher entry altitudes. With coupled ablation and carbon phenolic injection, 16 chemical species are used in the ablation layer for radiation absorption. Equilibrium and nonequilibrium results are compared under peak heating conditions.

Tiwari, S. N.↗
NASA NTRS1980

Interior structure of Saturn inferred from Pioneer 11 gravity data

The structure of Saturn is studied via a fourth-order theory for rotating planets and equations of state for the envelope which depend parametrically on the helium abundance, on the starting temperature for the adiabat, and on adopted forms of the pressure-density curve in the region of transition from molecular to metallic hydrogen. Models are constrained by the values of J2 and J4 obtained from the Pioneer-Saturn celestial mechanics experiment. Equations of state are tested by computing Jupiter models, which can now be subjected to a more stringent comparison with observed zonal harmonics. It is found that Saturn has a low-density hydrogen-helium envelope with no evidence for enhancement of H2O, CH4, or other abundant compounds. Such compounds are presumably located near the core. The helium mass abundance for Saturn's envelope appears to be in the range of approximately 0.12 to 0.19, but this result is very model-dependent. The helium abundance in the envelope of Jupiter is apparently very similar to that of Saturn.

Hubbard, W. B.↗