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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

Physics through the 1990s: Atomic, molecular and optical physics

The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

Source record↗
DOE OSTI2021

Understanding the local structure of disordered carbons from cellulose and lignin

An electron microscopy investigation was performed to understand the relationship between the microstructure and properties of carbonized cellulose and lignin (softwood kraft lignin) relative to the structure of the original biomass components. Structure details at micro- and molecular levels were investigated by scanning transmission electron microscopy. Atomic-resolution images revealed the presence of random disordered carbon in carbonized cellulose (C-CNC) and of large domains of well-ordered carbon with graphite sheet structure in carbonized lignin (C-Lignin). These structural differences explain why C-CNC exhibits higher surface area and porosity than C-Lignin. The presence of certain well-ordered carbon in carbonized lignin indicates some of the carbon in lignin are graphitized with heat treatment temperature up to 950 °C. This result is encouraging for future endeavors of attaining acceptable modulus of carbon fiber from lignin given suitable modifications to the chemistry and structure of lignin. The results of this research contribute to an improved understanding of the carbonization mechanism of the key cellulose and lignin components of biomass materials.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

New Dimension in Ab Initio Electronic Structure Theory: Temperature, Pressure, and Chemical Potential

Ab initio electronic structure theory has transformed gas-phase molecular science with its predictive ability. In the attempt to bring such predictive ability to macroscopic systems and condensed matter, the theory must integrate quantum mechanics with statistical thermodynamics, so that thermodynamic functions such as free energy, internal energy, entropy, and chemical potentials are computed as functions of temperature in a systematically converging series of approximations. Here, a general, versatile strategy of elevating ab initio electronic structure theory to nonzero temperatures is introduced and discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Cyclopropenylidenes as Strong Carbene Anchoring Groups on Au Surfaces

The creation of stable molecular monolayers on metallic surfaces is a fundamental challenge of surface chemistry. N-Heterocyclic carbenes (NHCs) were recently shown to form self-assembled monolayers that are significantly more stable than the traditional thiols on Au system. In this study, we theoretically and experimentally demonstrate that the smallest cyclic carbene, cyclopropenylidene, binds even more strongly than NHCs to Au surfaces without altering the surface structure. We deposit bis(diisopropylamino)cyclopropenylidene (BAC) on Au(111) using the molecular adduct BAC–CO 2 as a precursor and determine the structure, geometry, and behavior of the surface-bound molecules through high-resolution X-ray photoelectron spectroscopy, atomic force microscopy, and scanning tunneling microscopy. Our experiments are supported by density functional theory calculations of the molecular binding energy of BAC on Au(111) and its electronic structure. Our work is the first demonstration of surface modification with a stable carbene other than NHC; more broadly, it drives further exploration of various carbenes on metal surfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Structural Models of the Rhodopseudomonas palustris Proteome

This dataset contains the structural models for the primary transcripts of the Rhodopseudomonas palustris proteome. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. palustris proteome to those available in the AlphaFold Protein Structure Database.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Activation dynamics of a water-soluble human mu-opioid receptor

The mu-opioid receptor (MOR), a class A G protein-coupled receptor mediates opioid analgesia and remains a central target for pain therapeutics. While crystal structures of MOR exist, they provide limited insight into the receptor’s dynamic conformational landscape underlying function. Here, we engineered a thermostable water-soluble MOR variant (wsMOR) that retains native-like ligand-binding and activation dynamics. This variant enables high-yield production and detailed solution-phase structural studies that are challenging with membrane-embedded MOR, providing a valuable tool for studying receptor activation and aqueous-phase drug screening. Using a combined computational and experimental approach, we performed long-timescale all-atom molecular dynamics simulations together with neutron scattering and single-molecule FRET, revealing a structurally stable receptor with a diverse ensemble of conformations at different temporal resolutions. In the ligand-free state, wsMOR displayed high conformational flexibility, which decreased upon agonist binding, particularly in transmembrane helix 6, a hallmark of G protein-coupled receptor activation. Positive allosteric modulation and G protein binding further stabilized active-like states. These findings highlight wsMOR’s conformational plasticity across picosecond to millisecond timescales and provide a foundation for structure-guided development of next-generation opioid ligands with improved efficacy and safety.

E, Agyemang [University of Tennessee Knoxville]↗
NASA NTRS1999

Diode Laser Velocity Measurements by Modulated Filtered Rayleigh Scattering

The ability of solid-state lasers to be tuned in operating frequency at MHz rates by input current modulation, while maintaining a relatively narrow line-width, has made them useful for spectroscopic measurements. Their other advantages include low cost, reliability, durability, compact size, and modest power requirements, making them a good choice for a laser source in micro-gravity experiments in drop-towers and in flight. For their size, they are also very bright. In a filtered Rayleigh scattering (FRS) experiment, a diode laser can be used to scan across an atomic or molecular absorption line, generating large changes in transmission at the resonances for very small changes in frequency. The hyperfine structure components of atomic lines of alkali metal vapors are closely spaced and very strong, which makes such atomic filters excellent candidates for sensitive Doppler shift detection and therefore for high-resolution velocimetry. In the work we describe here we use a Rubidium vapor filter, and work with the strong D(sub 2) transitions at 780 nm that are conveniently accessed by near infrared diode lasers. The low power output of infrared laser diodes is their primary drawback relative to other laser systems commonly used for velocimetry. However, the capability to modulate the laser frequency rapidly and continuously helps mitigate this. Using modulation spectroscopy and a heterodyne detection scheme with a lock-in amplifier, one can extract sub-microvolt signals occurring at a specific frequency from a background that is orders of magnitude stronger. The diode laser modulation is simply achieved by adding a small current modulation to the laser bias current. It may also be swept repetitively in wavelength using an additional lower frequency current ramp.

Mach, J. J.↗
DOE OSTI2020

Prediction of chlorine and fluorine crystal structures at high pressure using symmetry driven structure search with geometric constraints

The high-pressure properties of fluorine and chlorine are not yet well understood because both are highly reactive and volatile elements, which have made conducting diamond anvil cell and x-ray diffraction experiments a challenge. Here, we use ab initio methods to search for stable crystal structures of both elements at megabar pressures. We demonstrate how symmetry and geometric constraints can be combined to efficiently generate crystal structures that are composed of diatomic molecules. Furthermore, our algorithm extends the symmetry driven structure search method by adding constraints for the bond length and the number of atoms in a molecule while still maintaining generality. As a method of validation, we have tested our approach for dense hydrogen and reproduced the known molecular structures of Cmca-12 and Cmca-4. We apply our algorithm to study chlorine and fluorine in the pressure range of 10 GPa–4000 GPa while considering crystal structures with up to 40 atoms per unit cell. We predict chlorine to follow the same series of phase transformations as elemental iodine from Cmca to Immm to Fm3¯m, but at substantially higher pressures. We predict fluorine to transition from a C2/c to Cmca structure at 70 GPa, to a novel orthorhombic and metallic structure with P42/mmc symmetry at 2500 GPa, and finally to its cubic analog form with Pm3¯n symmetry at 3000 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2025

Exploiting correlations in multi-coincidence Coulomb explosion patterns for differentiating molecular structures using machine learning

Coulomb explosion imaging (CEI) is a powerful technique for capturing the real-time motion of individual atoms during ultrafast photochemical reactions. CEI generates high-dimensional data with naturally embedded correlations that allow mapping the coordinated motion of nuclei in molecules. This enables reliable separation of competing reaction pathways and makes this approach uniquely suited for characterizing weak reaction channels. However, rich information contained in experimental CEI patterns remains largely underexploited due to challenges in visualizing correlations between multiple observables in multi-dimensional parameter space. Here we present a new approach to CEI of intermediate-sized polyatomic molecules, detecting up to eight ionic fragments in coincidence and leveraging machine-learning-based analysis to identify patterns and correlations in the resulting high-dimensional momentum-space data, enabling robust molecular structure identification and differentiation. Our approach provides high-dimensional background-free data encoding exceptionally rich structural information and establishes an automated, scalable framework for extracting insightful information from the data. As a demonstration, we apply this method to image and distinguish dichloroethylene isomers, showcasing its potential for broader applications in molecular imaging. Our results pave the way for channel-specific analysis of ultrafast structural dynamics in chemically relevant systems, particularly for disentangling mixed reaction pathways and detecting contributions from weak channels and minority species.

Chemical Physics (physics.chem-ph)↗
DOE OSTI2021

Structural and chemical disorder enhance point defect diffusion and atomic transport in Ni 3 Al-based γ' phase

The ordered L1 2 γ' Ni 3 Al intermetallic inclusions are routinely used as strengthening constituents in Ni-based superalloys and recent high-entropy alloys. As there are different metallic elements relative to the alloy matrix, the composition of γ' phase inclusions usually suffers some variations. In this work, we studied the elemental partition and its influence on atomic transport properties in a model (NiCo) 3 Al γ' phase with chemical and structural disorder. Combining the Monte Carlo and molecular static techniques, we first determined the elemental distribution in such compositionally-complexed γ' phase. The results suggest that Co tends to segregate, which profoundly influences defect energetics and diffusion properties. By modeling thermally activated diffusion by molecular dynamics, we found that chemical disorder induced by Co can enhance vacancy diffusion while significantly suppress diffusion via interstitial atom migration, as compared to the stoichiometric γ' Ni 3 Al. We further reveal that these observations are closely related to the defect energetics in these systems. Furthermore, our results explain the effects of disorder, long- and short-range orders on the diffusion properties in multicomponent intermetallic alloys, which helps to understand the stability and, thus, γ'-phase-assisted strengthening at different conditions including annealing and irradiation.

36 MATERIALS SCIENCE↗
NASA NTRS1994

GHRS observations of cool, low-gravity stars. 1: The far-ultraviolet spectrum of alpha Orionis (M2 Iab)

We present far-UV (1200-1930 A) observations of the prototypical red supergiant star alpha Ori, obtained with the Goddard High Resolution Spectrograph (GHRS) on the Hubble Space Telescope (HST). The observations, obtained in both low- (G140L) and medium- (G160/200M) resolution modes, unamibiguously confirm that the UV 'continuum' tentatively seen with (IUE) is in fact a true continuum and is not due to a blend of numerous faint emission features or scattering inside the IUE spectrograph. This continuum appears to originate in the chromospheric of the star at temperatures ranging from 3000-5000 K, and we argue that it is not related to previously reported putative companions or to bright spots on the stellar disk. Its stellar origin is further confirmed by overlying atomic and molecular absorptions from the chromosphere and circumstellar shell. The dominant structure in this spectral region is due to nine strong, broad absorption bands of the fourth-positive A-X system of CO, superposed on this continuum in the 1300-1600 A region. Modeling of this CO absorption indicates that it originates in the circumstellar shell in material characterized by T = 500 K, N(CO) = 1.0 x 10(exp 18) per sq cm, and V(sub turb) = 5.0 km per sec. The numerous chromospheric emission features are attributed mostly to fluorescent lines of Fe II and Cr II (both pumped by Lyman Alpha) and S I lines, plus a few lines of O I, C I, and Si II. The O I and C I UV 2 multiplets are very deficient in flux, compared to both the flux observed in lines originating from common upper levels but with markedly weaker intrinsic strength (i.e., O I UV 146 and C I UV 32) and to the UV 2 line fluxes seen in other cool, less luminous stars. This deficiency appears to be caused by strong self-absorption of these resonance lines in the circumstellar shell and/or upper chromosphere of alpha Ori. Atomic absorption features, primarily due to C I and Fe II are clearly seen in the G160M spectrum centered near 1655 A. These Fe II features are formed at temperatures that can occur only in the chromosphere of the star and are clearly not photospheric or circumstellar in origin.

Carpenter, Kenneth G.↗
DOE OSTI2020

Direct observation of 3D atomic packing in monatomic amorphous materials

Liquids and solids are two fundamental states of matter. Although the structure of crystalline solids has long been solved by crystallography, our understanding of the 3D atomic structure of liquids and amorphous materials remained speculative. In 1952, Frank hypothesized that icosahedral order is the prevalent atomic motif in monatomic liquids. Over the past six decades, there have been a great deal of experimental, computational and theoretical studies to understand the structure of liquids and amorphous materials. A polytetrahedral packing model was proposed to explain the 3D atomic structure of monatomic liquids and amorphous materials, in which icosahedral order is a key feature. The icosahedral order has also been found to play an important role in the structure of metallic glasses and quasicrystals. Here we advance atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. Despite the different chemical composition and synthesis methods, we observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Contrary to the traditional understanding, the pentagonal bipyramids do not assemble full icosahedra, but are closely connected with each other to form networks that extend to medium-range scale. Our molecular dynamic simulations, coupled with experimental results, further reveal that the 3D atomic structure of monatomic liquids is similar to the experimental amorphous material. Moreover, we find that the pentagonal bipyramid networks, prevalent in monatomic liquids, rapidly grow in size and form a fraction of full icosahedra during the quench from a liquid to a metallic glass state, providing a possible new picture of structural evolution through the glass transition.

Yuan, Yakun↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗
DOE OSTI2023

Structural evolution of iodine on approach to the monatomic state

Here, we applied single-crystal x-ray diffraction and Raman spectroscopy in a diamond-anvil cell up to 36 GPa and first-principles theoretical calculations to study the molecular dissociation of solid iodine at high pressure. Unlike previously reported, we find that the familiar Cmce molecular phase transforms to a Cmc2 1 molecular structure at 16 GPa, and then to an incommensurate polymeric Fmmm⁡(00⁢$\gamma$)⁢s⁢00 structure, which can be viewed as a mixture of molecular I 2 and zigzag chains of three iodine atoms, at 20 GPa. The available data are consistent with metallization of iodine at the boundary between the commensurate Cmc⁢2 1 structure and the incommensurate Fmmm⁡(00⁢$\gamma$)s⁢00 structure at 20 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Spiroligomer‐Based Macrocycles for Atomically Precise Membranes

Abstract Here, we report a new class of peptidomimetic macrocycles with well‐defined three‐dimensional structures and low conformational flexibility. They are assembled from fused‐ring spiro‐ladder oligomers (spiroligomers) by modular solid‐phase synthesis. Two‐dimensional nuclear magnetic resonance confirms their shape persistency. Triangular macrocycles of tunable sizes assemble into membranes with atomically precise pores, which exhibit size and shape‐dependent molecular sieving towards a series of structurally similar compounds. The exceptional structural diversity and stability of spiroligomer‐based macrocycles will be explored for more applications.

Xie, Yihui↗
NASA NTRS1993

Theoretical research program to study chemical reactions in AOTV bow shock tubes

The main focus was the development, implementation, and calibration of methods for performing molecular electronic structure calculations to high accuracy. These various methods were then applied to a number of chemical reactions and species of interest to NASA, notably in the area of combustion chemistry. Among the development work undertaken was a collaborative effort to develop a program to efficiently predict molecular structures and vibrational frequencies using energy derivatives. Another major development effort involved the design of new atomic basis sets for use in chemical studies: these sets were considerably more accurate than those previously in use. Much effort was also devoted to calibrating methods for computing accurate molecular wave functions, including the first reliable calibrations for realistic molecules using full CI results. A wide variety of application calculations were undertaken. One area of interest was the spectroscopy and thermochemistry of small molecules, including establishing small molecule binding energies to an accuracy rivaling, or even on occasion surpassing, the experiment. Such binding energies are essential input to modeling chemical reaction processes, such as combustion. Studies of large molecules and processes important in both hydrogen and hydrocarbon combustion chemistry were also carried out. Finally, some effort was devoted to the structure and spectroscopy of small metal clusters, with applications to materials science problems.

Taylor, Peter R.↗