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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.

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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
NASA NTRS1984

Molecular clouds and galactic spiral structure

Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

Dame, T. M.↗
DOE OSTI2024

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold ; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.

Bragagnolo, Nicholas↗
DOE OSTI2024

Development of Transformational Solvents for CO2 Separations

The primary objective of this CRADA activity is to use a combined molecular modeling and experimental validation approach to refine and develop transformational solvents for carbon capture. PNNL’s role on this project is currently funded by the Department of Energy’s (DOE) Office of Fossil Energy (OFE). PNNL is developing advanced molecular modeling based on their CO2BOLs solvent platform as a demonstration solvent for the activity; the model was developed and compared against measured data for CO2BOL derivatives. Here, a CRADA with PNNL and GE will leverage their current molecular models and apply them to solvent classes that operate on carbamate chemistry, specifically GE’s aminosilicone solvent class. The molecular models will be used to predict physical and thermodynamic properties, such as viscosity, as a means to predict advanced formulations with reduced viscosity compared to current aminosilicone derivatives, enabling optimized thermodynamic and kinetic metrics for economical carbon capture for this class of materials. Together, PNNL and GE will develop a comprehensive means of linking molecular modeling parameters to intermediate physical properties as a means to improve solvent performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Insights into the Thermal Expansion of Amorphous Polymers

Here, we investigated the thermal expansion of amorphous polystyrene (PS) and poly(methyl methacrylate) (PMMA) homopolymers using the temperature dependence of spatial electron-density correlations. The strong and broad X-ray interference maxima arising from inter- and intramolecular correlation distances were distinct, maintaining their shape during the heating of the samples to 250 °C. Three maxima characteristic of electron density correlations between the backbones, substituents along the chain, and repeat-units were observed. A remarkable temperature dependence was identified in the largest correlation distances arising from the intermolecular interactions. Based on the temperature dependence of the correlation distances, the coefficients of molecular expansion were very close to the coefficients of thermal expansion. This study provides a simple yet accurate way to correlate macroscopic volume expansions with the molecular expansion obtained from wide-angle X-ray scattering (WAXS) data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1979

The spectrum of the Becklin-Neugebauer source in Orion from 3.3 to 5.5 microns

Spectra of the Becklin-Neugebauer source in Orion and the associated nebula are presented covering the complete range from 3.3-5.5 microns with a resolution of 1.2 kaysers. The data were taken in December 1976 and February 1978. Atomic hydrogen emission lines of Brackett-alpha and Pfund-beta are seen, as well as molecular CO absorptions. No other features intrinsic to BN were detected. The December 1976 data show an anomalously high intensity for Pfund-beta line. Theoretical considerations are presented which suggest that Pfund-beta radiation arises in a small dense region, with the transition possibly lasing.

Smith, H. A.↗
DOE OSTI2023

Connecting suborganismal data to bioenergetic processes: killifish embryos exposed to a dioxin-like compound

A core challenge for ecological risk assessment is to integrate molecular responses into a chain of causality to organismal or population level outcomes. Bioenergetic theory may be a useful approach for integrating suborganismal responses to predict organismal level responses that influence population dynamics. In this work, we describe a novel application of Dynamic Energy Budget (DEB), theory in the context of a toxicity framework (Adverse Outcome Pathways, AOP) to make quantitative predictions of chemical exposures to individuals, starting from suborganismal data. We use early life stage exposure of Fundulus heteroclitus to dioxin-like chemicals (DLCs) and connect AOP Key Events (KEs) to DEB processes through “damage” that is produced at a rate proportional to the internal toxicant concentration. We use transcriptomic data of fish embryos exposed to DLCs to translate molecular indicators of damage into changes in DEB parameters (damage increases somatic maintenance costs) and use DEB models to predict sublethal and lethal effects of young fish. By changing a small subset of model parameters, we predict the evolved tolerance to DLCs in some wild F. heteroclitus populations, a data set not used in model parameterization. The differences in model parameters points to reduced sensitivity and altered damage repair dynamics as contributing to this evolved resistance. Our methodology has potential extrapolation to untested chemicals of ecological concern.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Determining best practices for using genetic algorithms in molecular discovery

Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this tutorial, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection method, mutation rate, and convergence criteria, on key GA performance metrics. Here, we show that using a self-termination method with a minimum Spearman’s rank correlation coefficient of 0.8 between generations maintained for 50 consecutive generations along with a population size of 32, a 50% elitism rate, three-way tournament selection, and a 40% mutation rate provides the best balance of finding the overall champion, maintaining good coverage of elite targets, and improving relative speedup for general use in molecular design GAs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

One thousand soils for molecular understanding of belowground carbon cycling

While significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray computed tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Physics-informed graph neural networks for predicting cetane number with systematic data quality analysis

Designing alternative fuels for advanced compression ignition engines necessitates a predictive model for cetane number (CN). In this study, the physics-informed graph neural networks are introduced for a reliable CN prediction by considering molecular features pertinent to the physical properties of molecules that affect CN. The reliability of measured data is another key factor to consider for improving the predictive model. Various experimental instruments for measuring CN exist, including standard and non-standard methods. In this regard, a systematic data quality analysis was carried out for the total 630 CNs collected from literature and new measurements in this study using Advanced Fuel Ignition Delay Analyzer (AFIDA). The results from this data curation process were reflected in the model by imposing lower sample weights on the data coming from less reliable measurement techniques. This approach effectively maximized the prediction accuracy while incorporating data from all available sources. Using the sample weights decreased the mean absolute error (MAE) up to 0.8 CN units. The accuracy was also improved by introducing the CN-related physical properties (the number of hydrogen bond donors and acceptors); the test set MAE is 5.74 and 7.01 for the model with and without such properties, respectively. Investigating molecular structural effects on CN was also carried out to gain chemical insights into factors used to design new fuel candidates. The dimensionality reduction analysis of feature vectors showed a clear clustering in terms of functional groups and CN and the structural effect derived from the model was consistent with the physicochemical insights. Finally, this physics-informed model and data curation would be helpful for accurate CN prediction and inform rational fuel design.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1990

Molecular clouds without detectable CO

The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to ben an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is then only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase

Blitz, Leo↗
NASA NTRS1991

Theoretical studies of important processes in planetary and comet atmospheres

The dissociative recombination (DR) of the AB(+) molecular ion with an electron has been shown to be an important component in the detailed interpretation of planetary ionosphere data. A first principles theoretical approach is developed for calculating the DR cross sections and rates for AB(+) molecular ions. The calculations focus on O2(+) and N2(+) DR, and are the first to include the indirect DR mechanism (Ryberg vibrational levels below v = 0 level of ion) for a molecule larger than H2(+). The importance of electron capture width in calculating the cross sections and rates is also examined. Electron capture widths are given for all states of O2 that are of importance to DR (lowest 10 vibrational levels of ion). Knowledge of the details of dissociative recombination will be needed for interpretation of data from future interplanetary and comet atmospheric studies.

Guberman, Steven L.↗
NASA NTRS1973

Role of gas-surface interactions in the reduction of OGO 6 neutral-particle mass spectrometer data

Data obtained with the quadrupole mass spectrometer aboard the OGO 6 satellite show the effects of significant surface interaction processes, including nearly complete recombination of incoming atomic oxygen on the walls of the instrument antechamber plus absorption and desorption of oxygen and carbon monoxide. The observed data are fit by solving the time-dependent continuity equations accounting for production and loss of atomic oxygen, molecular oxygen, and (in the case of mass 28) carbon monoxide. The surface parameters that best fit the data are selected and applied to the determination of ambient densities and their estimated errors.

Hedin, A. E.↗
NASA NTRS1973

Role of gas-surface interactions in the reduction of Ogo 6 neutral particle mass spectrometer data.

Data obtained with the quadrupole mass spectrometer aboard the Ogo 6 satellite show the effects of significant surface interaction processes, including nearly complete recombination of incoming atomic oxygen on the walls of the instrument antechamber plus adsorption and desorption of oxygen and carbon monoxide. The observed data are fit by solving the time-dependent continuity equations accounting for production and loss of atomic oxygen, molecular oxygen, and (in the case of mass 28) carbon monoxide. The surface parameters that best fit the data are selected and applied to the determination of ambient densities and their estimated errors.

Hedin, A. E.↗
NASA NTRS1975

A study of molecular contamination

Contamination kinetics of typical space materials were studied using several techniques, including ellipsometry. Data were obtained on contaminant deposition rates, sticking coefficients, and reevaporation of the contamination. Materials studied included silicone sealants, a thermal control paint, and a graphite laminate as contaminant sources, and gold coated surfaces, a thermal control paint and a second surface mirror material as the contaminees. Both deposition and reevaporation rates were found to be nonlinear with time, and followed an exponential decay. A hypothesis is presented that the nonlinear behavior was a result of disproportionation of the molecular weight fractions of the polymers. The measured sticking coefficients were found to vary substantially with temperature over narrow ranges. Simulated space radiation was found to reduce the evaporation rates of contaminants by several orders of magnitude.

Allen, T. H.↗
DOE OSTI2026

Thermal exchange-correlation functionals: Capturing quantum electron behavior in warm, dense plasmas

We summarize and give perspective upon recent progress in developing non-empirical constraint-based thermal (i.e., free energy) exchange-correlation (XC) density functionals essential for accurate description of the quantum behavior of electrons in warm, dense plasmas. After delineating the critical role of ground-state functionals for zero-temperature, time-dependent DFT, we outline the underpinnings of local density approximation, generalized gradient approximation (GGA), and meta-GGA XC free-energy functionals. Two basic thermalization principles for upgrading ground-state XC functionals to successful thermal ones are emphasized. Then, we turn to a long-standing challenge, assessment of the accuracy of well-founded functionals. Unlike the ground state, there are a few exact results for large T and P. An exception is path integral Monte Carlo (PIMC) data for dense H/D and He plasmas. For those, we did ab initio molecular dynamics simulations under selected thermodynamic conditions employing five thermal XC functionals: two approximate thermal GGAs, fully thermal GGA, an approximate meta-GGA, and fully thermal meta-GGA. Comparisons with the PIMC data show that functionals thermalized by augmenting a non-thermal functional with a lower-level thermal contribution are inferior to functionals with thermal XC and spatial inhomogeneity effects taken into account at the same level of refinement. We believe this and similar evidence should be convincing to the high-energy density physics community of the necessity of use of proper thermal XC functionals in simulation studies of finite-temperature quantum effects in warm, dense plasmas.

Ab-initio molecular dynamics↗