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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
NASA NTRS1990

A CO survey of regions around 34 open clusters. II - Physical properties of cataloged molecular clouds

The physical properties of the 148 molecular clouds found in a CO survey of regions around 34 young open clusters have been examined. Expressions are given for the cloud size spectrum and the mass spectrum. The mass-radius relation implies that clouds of all size larger than a few pc have about the same mean volume density. Power laws with slopes of 0.6 and 3 describe, respectively, the relations of CO linewidth and cloud mass to cloud size. The clouds are distinctly nonspherical and appear to be randomly oriented with respect to the Galactic plane. The observations can be explained by a model for molecular clouds in which clouds are ensembles of dense clumps of gas. Based on such a model, it is shown that molecular clouds are perturbed on a time scale short compared to the time required for them to reestablish virial equilibrium.

Leisawitz, D.↗
DOE OSTI2020

Art and Science of the Cellular Mesoscale

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2017

A Hybrid Line List for CH4 and Hot Methane Continuum

Molecular line lists (a catalogue of transition frequencies and line strengths) are important for modelling absorption and emission processes in atmospheres of different astronomical objects, such as cool stars and exoplanets. In order to be applicable for high temperatures, line lists for molecules like methane must contain billions of transitions, which makes their direct (line-by-line) application in radiative transfer calculations impracticable. Here we suggest a new, hybrid line list format to mitigate this problem, based on the idea of temperature-dependent absorption continuum. Methods. The line list is partitioned into a large set of relatively weak lines and a small set of important, stronger lines. The weaker lines are then used either to construct a temperature-dependent (but pressure-independent) set of intensity cross sections or are blended into a greatly reduced set of super-lines. The strong lines are kept in the form of temperature independent Einstein A coefficients. Results. A line list for methane is constructed as a combination of 17 million strong absorption lines relative to the reference absorption spectra and a background methane continuum in two temperature-dependent forms, of cross sections and super-lines. This approach eases the use of large high temperature line lists significantly as the computationally expensive calculation of pressure dependent profiles only need to be performed for a relatively small number of lines. Both the line list and cross sections were generated using a new 34 billion methane line list (34 to10), which extends the 10to10 line list to higher temperatures (up to 2000 K). The new hybrid scheme can be applied to any large line lists containing billions of transitions. We recommend to use super-lines generated on a high resolution grid based on resolving power R = 1,000,000 to model the molecular continuum as a more flexible alternative to the temperature dependent cross sections.

Line Profiles↗
DOE OSTI2021

Can machine learning predict fuel properties accurately?

High-potential molecules derived from biomass sources may suitably replace or supplement traditional nonrenewable hydrocarbon fuels to reduce pollution and fuel processing cost. Experimental property testing of these bioproducts is usually conducted years after initial bench-scale experiments, due to high experimental costs and/or high volume requirements. However, neglecting to conduct property testing early in the pathway development cycle can lead to investments spent on scaling-up production of bioproducts and biofuels that do not perform as expected. Instead, machine-learning techniques can be used to develop quantitative structure–property relationships for molecules using a relatively large training set of molecular descriptor data. For this study, we compiled measured properties, IR spectra, and molecular descriptors of bio-based molecules from databases and published studies for training models of bioproduct properties. We trained regression models with molecular descriptors and will compare results of different estimators. This study describes the first steps towards a performance prediction tool for bio-based alternative fuels. Keywords: Machine learning, biofuels, jet fuels, fuel properties

Mayer, Morgan A.↗
NASA NTRS2015

Elastic and Piezoelectric Properties of Boron Nitride Nanotube Composites: Finite Element Model - Part II

This paper is the second part of a two-part series where the first part presents a molecular dynamics model of a single Boron Nitride Nanotube (BNNT) and this paper scales up to multiple BNNTs in a polymer matrix. This paper presents finite element (FE) models to investigate the effective elastic and piezoelectric properties of (BNNT) nanocomposites. The nanocomposites studied in this paper are thin films of polymer matrix with aligned co-planar BNNTs. The FE modelling approach provides a computationally efficient way to gain an understanding of the material properties. We examine several FE models to identify the most suitable models and investigate the effective properties with respect to the BNNT volume fraction and the number of nanotube walls. The FE models are constructed to represent aligned and randomly distributed BNNTs in a matrix of resin using 2D and 3D hollow and 3D filled cylinders. The homogenisation approach is employed to determine the overall elastic and piezoelectric constants for a range of volume fractions. These models are compared with an analytical model based on Mori-Tanaka formulation suitable for finite length cylindrical inclusions. The model applies to primarily single-wall BNNTs but is also extended to multi-wall BNNTs, for which preliminary results will be presented. Results from the Part 1 of this series can help to establish a constitutive relationship for input into the finite element model to enable the modeling of multiple BNNTs in a polymer matrix.

Kim, H. Alicia↗
DOE OSTI2021

Effects of interaction strength of associating groups on linear and star polymer dynamics

A small number of associating groups incorporated onto a polymer backbone have dramatic effects on the mobility and viscoelastic response of the macromolecules in melts. These associating groups assemble, driving the formation of clusters, whose lifetime affects the properties of the polymers. In this study, we probe the effects of the interaction strength on the structure and dynamics of two topologies, linear and star polymer melts, and further investigate blends of associative and non-associating polymers using molecular dynamics simulations. Polymer chains of approximately one entanglement length are described by a bead–spring model, and the associating groups are incorporated in the form of interacting beads with an interaction strength between them that is varied from 1 to 20 k B T. We find that, for all melts and blends, interaction of a few k B T between the associating groups drives cluster formation, where the size of the clusters increases with increasing interaction strength. These clusters act as physical crosslinkers, which slow the chain mobility. Blends of chains with and without associating groups macroscopically phase separate for interaction strength between the associating groups of a few k B T and above. For weakly interacting associating groups, the static structure function S(q) is well fit by functional form predicted by the random phase approximation where a clear deviation occurs as phase segregation takes place, providing a quantitative assessment of phase segregation.

36 MATERIALS SCIENCE↗
NASA NTRS1995

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

NASA Discipline Exobiology↗
DOE OSTI2022

Competing ionization and dissociation in the H 2 gerade system

A numerically solvable two-dimensional (2D) model, employed by the authors to study the dissociative recombination of H$^+_2$ in the ungerade symmetry, is extended to describe the collision process in the gerade symmetry of H$_2$. In this symmetry, the ionization and dissociation processes are driven primarily by the direct, curve-crossing mechanism. The model is represented by a set of three coupled electronic channels in 2D, in the space of $\textit{s, p, d}$ partial waves of the colliding electron. In this work, we demonstrate that the Born-Oppenheimer properties of the H$_2$ molecule in the relevant range of internuclear distances can be described by such a model. The molecular rotational degrees of freedom are accounted for by the rotational frame transformation. The numerical solution of the model is discussed, and the resulting rovibrationally inelastic and dissociative recombination cross sections are compared with the available data.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation

As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. In this work, using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl 2 on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The effect of ion pairing on speciation and transport in ion exchange membranes at varying hydration levels: A four-state model

Understanding ion pairing in ion exchange membranes (IEMs) is essential for advancing IEM applications in energy and environmental technologies. Here, this study introduces a four-state molecular dynamics model to quantify speciation and transport within Nafion-117, specifically examining the role of ion pairing in monovalent and divalent counterions (NaCl, Na 2 SO 4 , and MgSO 4 ). By analyzing radial distribution functions (RDFs) and molecular snapshots, we distinguish ion pairing modes and classify counterions into four states: condensed counterion, condensed ion pair, free ion pair, and free counterion. A key finding is that while divalent counterions (e. g., Mg 2+ ) maintain stable speciation across hydration levels, monovalent counterions (e.g., Na + ) show notable speciation shifts with hydration. Both monovalent and divalent counterions are not diffusive when condensed onto the polymer (sorbed to membrane functional groups). In contrast, free counterions are diffusive across all hydration levels. To evaluate the overall diffusivity of counterions, four-state fractions and diffusivities are computed, each contributing to counterion transport. The condensed/free ion speciation for multivalent sulfate salts aligns with previous revisions to the Donnan-Manning framework that include ion pairing, thereby validating its relevance to established membrane theories. The four-state model's diffusivity results support several current ion exchange assumptions, including that the condensed counterions are immobile, while uncondensed counterions are mobile. The four-state model offers insights into contact ion pairing within IEMs, highlighting its potential even when undetected in aqueous solution experiments. This work advances the theoretical understanding of counterion speciation in IEMs while identifying model limitations that suggest avenues for refinement, such as distinguishing water-mediated ion pairs between fully hydrated ions.

Ion exchange membranes↗
NASA NTRS1993

CO(J = 1-0) line emission from giant molecular clouds

Numerical models of the (C-12)O (J = 1-0) line emission from giant molecular clouds (GMCs) have been constructed. Line profiles are presented for both microturbulent and macroturbulent clouds. The observed width of the CO (J = 1-0) line cannot be physically interpreted as a microturbulent gas velocity dispersion. Microturbulent models produce emission with a wide range of profile shapes and brightness temperatures at line center over a cloud mass range of 100 to 10 exp 6 solar masses. Macroturbulent models produce smooth, centrally peaked profiles. Clumpy GMC models can produce peak brightness temperatures over about 6 K provided that clump densities are larger than 1000/cu cm. If there are no significant velocity gradients, photoelectric heating dominates in the region where the CO line arises. The observed relation between cloud mass and CO luminosity can be constructed from theoretical models.

Wolfire, Mark G.↗
NASA NTRS2002

Molecular Line and Continuum Opacities for Modeling of Extrasolar Giant Planet and Cool Stellar Atmospheres

The molecular line and continuum opacities are investigated in the atmospheres of cool stars and Extrasolar Giant Planets (EGPs). Using a combination of ab inito and experimentally derived potential curves and dipole transition moments, accurate data have been calculated for rovibrationally-resolved oscillator strengths and photodissociation cross sections in the B' (sup 2)Sigma+ (left arrow) X (sup 2)Sigma+ and A (sup 2)Pi (left arrow) X (sup 2)Sigma+ band systems in MgH. We also report our progress on the study of the electronic structure of LiCl and FeH.

Weck, P. F.↗
DOE OSTI2024

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Potential pathogenicity determinants identified from structural proteomics of SARS-CoV and SARS-CoV-2

Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest non-conservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure-dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Main and Satellite Features in the Ni 2p XPS of NiO

The origin and assignment of the complex main and satellite XPS features of the cations in ionic compounds has been the subject of extensive theoretical studies using different methods. There is agreement that within a molecular orbital model one needs to take into account different types of configurations. Specifically, those where a core electron is removed but no other configuration changes are made and those where in addition to ionization there are also shake or charge transfer changes to the ionic configuration. However, there are strong disagreements about the assignment of XPS features to these configurations. The present work is directed toward resolving the origin of main and satellite features for the Ni 2p XPS of NiO based on ab initio molecular orbital wavefunctions for a cluster model of NiO. A major problem in earlier ab initio XPS studies of ionic compounds has been the use of a common set of orbitals that was not able to properly describe all the ionic configurations that contribute to the full XPS spectra. This is resolved in the present work by using orbitals that are optimized for averages of the occupations of the different configurations that contribute to the XPS. The approach of using State Averaged orbitals is validated through comparisons between different averages and through use of higher order excitations in the wavefunctions for the ionic states. It represents a major extension of our earlier work on the main and satellite features of the Fe 2p XPS of Fe 2 O 3 and proves the reliability and the generality of the assignments of the character and origin of the different features of the XPS obtained with orbitals optimized for State Averages. These molecular orbital methods permit the characterization of the ionic states in terms of the importance of shake excitations and of the coupling of ionization of 2p 1/2 and 2p 3/2 spin-orbit split sub shells. Further, the work lays the foundation for definitive assignments of the character of main and satellite XPS features and points to their origin in the electronic structure of the material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1972

Experimental models of communication at the molecular and microsystemic levels.

Communication at both the macromolecular and the (supramacromolecular) microsystemic levels has been demonstrated in artificial polymers and artificial systems. These phenomena are models for communication in evolving and contemporary systems. The significance of a combination of communication at the two levels is emphasized.

Fox, S. W.↗
NASA NTRS1995

MODTRAN3: An update and recent validations against airborne high resolution interferometer measurements

MODTRAN, the Moderate Resolution Atmospheric Radiance and Transmittance Model, encompasses all the capabilities of LOWTRAN 7, the widely used 20 cm(exp -1) resolution radiance code, but incorporates a much more sensitive molecular band model with 2 cm(exp -1) resolution. MODTRAN contains many important elements that other band model based radiative transfer codes do not incorporate. It shares with FASCODE: spherical geometry, single and multiple scattering default atmospheric profile descriptors (gases, aerosols, clouds, fogs, and rain), and molecular continua (H2O, CO2, O3, O2, N2). In addition, it can calculate the solar/lunar direct and scattered radiation. MODTRAN3 was released to the general public in November 1994. It has several important features that the previous version, MODTRAN2, does not have. Chloro-fluorocarbon (CFC) and related heavy molecules (whose spectroscopic properties first appear on the HITRAN92 data base as temperature-dependent cross sections) have been incorporated into pseudo-band models, with provision for using both default and user supplied profiles. The addition of SO2 and O2 in the UV, along with upgraded ozone Chappuis bands in the visible is also part of MODTRAN3. An improved multiple scattering algorithm, the DIScrete Ordinate Radiative Transfer (DISORT) has also been incorporated into MODTRAN3. MODTRAN is very fast: simple timing runs of MODTRAN3 vs. FASCOD3 show an improvement of more than a factor of 100 for a typical 500 cm(exp -1) spectral interval and comparable vertical layering. Speed is an important consideration in heating/cooling rates calculations, where a large number of radiative transfer calculations are needed. The MODTRAN3 used in this study is based on HITRAN92, but as mentioned, above, it will be upgraded to HITRAN94 upon its release at the end of 1994. MODTRAN has been adopted by: some researchers in the AVIRIS program as one radiative transfer code to derive surface reflectance from AVIRIS measurements. The accuracy of the code is very important because any errors in the radiative transfer calculation will directly translate into errors in the derived surface reflectance. In this paper, the new solar irradiance calculated by Kurucz, which is adopted in MODTRAN3, will be presented. Recent validations of MODTRAN3 with airborne high resolution interferometer measurements over ocean will be discussed. Good agreeement between model calculations and measurements was achieved.

Anderson, Gail P.↗