Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ATOMIC MODELS”

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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Atomic data and spectral modeling constraints from high-resolution X-ray observations of the Perseus cluster with Hitomi

Here, the Hitomi Soft X-ray Spectrometer spectrum of the Perseus cluster, with ~5 eV resolution in the 2–9 keV band, offers an unprecedented benchmark of the atomic modeling and database for hot collisional plasmas. It reveals both successes and challenges of the current atomic data and models. The latest versions of AtomDB/APEC (3.0.8), SPEX (3.03.00), and CHIANTI (8.0) all provide reasonable fits to the broad-band spectrum, and are in close agreement on best-fit temperature, emission measure, and abundances of a few elements such as Ni. For the Fe abundance, the APEC and SPEX measurements differ by 16%, which is 17 times higher than the statistical uncertainty. This is mostly attributed to the differences in adopted collisional excitation and dielectronic recombination rates of the strongest emission lines. We further investigate and compare the sensitivity of the derived physical parameters to the astrophysical source modeling and instrumental effects. The Hitomi results show that accurate atomic data and models are as important as the astrophysical modeling and instrumental calibration aspects. Substantial updates of atomic databases and targeted laboratory measurements are needed to get the current data and models ready for the data from the next Hitomi-level mission.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Defect‐Tailoring Mediated Electron–Hole Separation in Single‐Unit‐Cell Bi 3 O 4 Br Nanosheets for Boosting Photocatalytic Hydrogen Evolution and Nitrogen Fixation

Abstract Solar photocatalysis is a potential solution to satisfying energy demand and its resulting environmental impact. However, the low electron–hole separation efficiency in semiconductors has slowed the development of this technology. The effect of defects on electron–hole separation is not always clear. A model atomically thin structure of single‐unit‐cell Bi 3 O 4 Br nanosheets with surface defects is proposed to boost photocatalytic efficiency by simultaneously promoting bulk‐ and surface‐charge separation. Defect‐rich single‐unit‐cell Bi 3 O 4 Br displays 4.9 and 30.9 times enhanced photocatalytic hydrogen evolution and nitrogen fixation activity, respectively, than bulk Bi 3 O 4 Br. After the preparation of single‐unit‐cell structure, the bismuth defects are controlled to tune the oxygen defects. Benefiting from the unique single‐unit‐cell architecture and defects, the local atomic arrangement and electronic structure are tuned so as to greatly increase the charge separation efficiency and subsequently boost photocatalytic activity. This strategy provides an accessible pathway for next‐generation photocatalysts.

Di, Jun↗
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Predicted Melt Curve and Liquid Shear Viscosity of RDX up to 30 GPa

Recent grain-scale simulations of HMX and TATB have shown that predictions for hot spot formation in high explosives are particularly sensitive to accurate determinations of the pressure-dependent melt curve and the shear viscosity of the liquid phase. These physics terms are poorly constrained beyond ambient pressure for the explosive RDX. Here we adopt an all-atom modeling approach using molecular dynamics (MD) simulations to predict the melt curve of RDX near to detonation conditions (30 GPa) and determine the shear viscosity of the liquid as a function of temperature and pressure above the melt curve. Phase-coexistence simulations were used to determine the melt curve, which is predicted to vary by almost 1100 K as the pressure increases from 0 GPa to 30 GPa. Equilibrium MD simulations and the Green-Kubo formalism were used to obtain the pressure-temperature-dependent shear viscosity. The shear viscosity of RDX is predicted to be of similar magnitude to the viscosity of TATB at low GPa-range pressures, and to be roughly an order of magnitude lower than the viscosity of HMX. The temperature dependence of the shear viscosity is Arrhenius at a given pressure, and the exponential pre-factor and activation term exhibit a strong, yet complicated, pressure dependence. An empirical pressure-temperature dependent function for RDX shear viscosity is developed that simultaneously captures a wide range of MD predictions while taking an analytic form that extrapolates smoothly beyond the fitted regime. The relative strength of the pressure and temperature dependencies of these two physics terms is found to be of similar magnitude for RDX, HMX, and TATB, which motivates incorporating these results in future RDX grain-scale modeling.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Effects of Galactic Irradiation on Thermal and Electronic Transport in Tungsten

The impact of irradiation on the thermal and electronic properties of materials is a persistent puzzle, particularly defect formation at the atomic and nanoscales. This work examines the nanoscale effects of low-energy irradiation on tungsten (W), focusing on defect-induced modifications to thermal and electronic transport. Using the site-projected thermal conductivity (SPTC) method [A. Gautam et al. PSS-RRL, 2400306, 2024], bulk and twin-grain boundary W with vacancy defects based on the Norgett–Robinson–Torrens displacements per atom model is analyzed. SPTC provides a detailed prediction of postcascade spatial thermal conductivity distribution. Electronic conductivity activity is estimated using the “N 2 method” [K. Nepal et al. Carbon, 119711, 2025] to explore the consequences of vacancies and grain boundaries, highlighting the defect-dependent nature of charge transport behavior. These findings offer high-resolution insights into irradiation-driven transport phenomena, with implications for space-exposed materials and nanoscale thermal/electronic management.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Theoretical assessment of the nuclear quantum effects on polymer crystallinity via perturbation theory and dynamics

As seen in experiments with poly(3-hexylthiophene), substitution of hydrogen with deuterium on the main chain alone decreases crystallinity. To understand this effect, a general formalism for analysis of the dipole moments and polarizabilities incorporating quantum nuclei, is developed in this paper. The formalism, based on quantum dynamics of the proton/deuteron and on the perturbative analysis of the dipole interaction energy, accounts for the anharmonicity of a potential energy surface and for the anisotropy of molecular dipole moments. The formalism is implemented within the Discrete Variable Representation and the Density Functional Theory describing, respectively, the quantum proton/deuteron on the thiophene ring and the electronic structure of the 27-atom model polymer chain, embedded into a larger crystalline environment. Finally, the isotope effect is mainly attributed to the differences in the zero-point energy of the CH/CD bonds and to the isotope-dependence of the dipole-dipole inter-chain interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Revealing the Atomic Structures of Exposed Lateral Surfaces for Polymorphic Manganese Dioxide Nanowires

Polymorphic 1D MnO 2 nanostructures are widely applied in fields such as catalysis, sensing, and energy storage with the functionality mainly determined by the atomic patterns of their laterally exposed facets, which largely remain unclear so far. Herein, by high‐resolution transmission electron microscopy (HRTEM) imaging directly along their axial directions, the atomic structures of the outmost lateral facets of polymorphic MnO 2 nanowires are disclosed. To generalize the findings, four most commonly seen phases with characteristic tunnel structures are targeted, i.e., β‐, γ‐, α‐, and todorokite(t)‐MnO 2 , which are synthesized conventionally using a hydrothermal method reported in the literature. Axially imaging these MnO 2 nanowires via HRTEM, the {hkl} facets covering the lateral surfaces are accurately indexed, the atomic pattern of each {hkl} facet is revealed, and it is further coupled with the outmost tunnel configuration that can significantly affect the physicochemical property of MnO 2 materials via tunnel‐driven mass adsorption/transport. This work provides a reliable reference for atomic modeling of MnO 2 to benefit the pursuit of its structure–property relationship; in addition, it can benefit surface engineering strategies to better rationalize the facet growth control with optimized functionality.

Yuan, Yifei↗
DOE OSTI2022

Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.

Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.

Chinnam, Naga Babu↗
DOE OSTI2017

Influence of Asymmetric Cyclic Loading on Structural Evolution and Deformation Behavior of Cu-5 at.% Zr Alloy: An Atomistic Simulation-Based Study

Molecular dynamics (MD) simulation-based studies of tensile test and structural evolution of Cu-5 at.% Zr alloy under asymmetric cyclic loading (i.e., ratcheting behavior) considering various stress ratios such as − 0.2, − 0.4 and − 0.6 for different temperatures, viz.≈ 100, 300 and 500 K have been performed using embedded atom model Finnis–Sinclair potential. According to obtained stress–strain response from MD calculation, Cu-5 at.% Zr alloy specimen is pristine in nature as sudden drop in stress just after yield stress and subsequent elastic type deformation are observed for this alloy. Predicted ratcheting strain by MD simulation for Cu-5 at.% Zr alloy varies from 4.5 to 5%. Significant increase in ratcheting strain has been observed with the increase in temperature. Slight reduction in crystallinity is identified at the middle of the each loading cycle from the performed radial distribution function analysis and cluster analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Displacement Threshold Energy and Recovery in an Al-Ti Nanolayered System with Intrinsic Point Defect Partitioning

A method is established and validated using molecular dynamics (MD) to determine the displacement threshold energies as Ed in nanolayered, multilayered systems of dissimilar metals. The method is applied to specifically oriented nanolayered films of Al-Ti where the crystal structure and interface orientations are varied in atomic models and Ed is calculated. Methods for defect detection are developed and discussed based on prior research in the literature and based on specific crystallographic directions available in the nanolayered systems. These are compared and contrasted to similar calculations in corresponding bulk materials, including fcc Al, fcc Ti, hcp Al, and hcp Ti. In all cases, the calculated Ed in the multilayers are intermediate to the corresponding bulk values but exhibit some important directionality. In the nanolayer, defect detection demonstrated systematic differences in the behavior of Ed in each layer. Importantly, collision cascade damage exhibits significant defect partitioning within the Al and Ti layers that is hypothesized to be an intrinsic property of dissimilar nanolayered systems. This type of partitioning could be partly responsible for observed asymmetric radiation damage responses in many multilayered systems. In addition, a pseudo-random direction was introduced to approximate the average Ed without performing numerous simulations with random directions.

Al-Ti↗
DOE OSTI2020

Silica nanocluster binding rate coefficients from molecular dynamics trajectory calculations

Oxide nanoparticle growth from vapor phase precursors occurs in high temperature aerosol reactors first via the formation of nanoclusters, which are nanometer-scale condensed-phase species composed of 10 1 -10 2 atoms. The binding rate for nanoclusters, defined as the rate at which two nanoclusters collide with and stick to one another, is hence of interest in predicting nanoparticle size distribution functions in an aerosol. We have utilized molecular dynamics (MD) trajectory calculations to determine the homogeneous (equal-sized) and heterogeneous (disparate-sized) binding rate coefficients of SiO2 (silica) nanoclusters composed of 18, 144, and 333 atoms. MD trajectory calculations incorporated all-atom models of nanoclusters using a combined Born–Huggins–Mayer-Lennard-Jones potential model, which accounts for both short range interactions and electrostatic interactions. MD calculations were utilized to determine the binding probability as a function of both initial relative velocity and impact parameter; integration of the binding probability across impact parameter and relative velocity space yields the binding rate coefficient. MD trajectory calculations reveal that the most common type of encounters between nanoclusters leading to binding are grazing collisions, i.e. instances where collision would not occur without induced dipole potential influences. The resulting binding rate coefficients are found to be extremely weakly dependent on system temperature, which is in contrast to the use of rate coefficient models which are the product of a hard-sphere collision rate coefficient and a constant enhancement factor (leading to a rate coefficient proportional to the square root of temperature). Enhancement factors defined from MD trajectory calculations fall in the range of 3–9 as system temperature decreases from 1500 K to 300 K. Furthermore, such large values suggest that potential interactions need to be considered when modeling oxide nanocluster growth in the gas phase.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Assessment of uranium nitride interatomic potentials

Uranium mononitride (UN) is a promising nuclear fuel due to its high fissile density, high thermal conductivity, and suitability for reprocessing. In this study, two uranium nitride interatomic potentials are assessed: Tseplyaev and Starikov's angular-dependent potential and Kocevski et al.'s embedded atom model potential. Predictions of the thermophysical and elastic properties of UN, UN 2 , and α- and β-U 2 N 3 computed using both potentials are assessed and compared to available experimental data. Notably, the Tseplyaev potential performs better with the energetic aspects of UN, e.g., specific heat capacity and point defect formation energies, whereas the Kocevski potential performs better with the structural aspects of UN, e.g., thermal expansion as well as with the elastic properties. The reasons why the Kocevski potential underestimates the UN specific heat are explained by examining the UN phonon properties modeled using both potentials. The Kocevski potential shows better identification of the mechanical stability ranges of UN, UN 2 , and α- and β-U 2 N 3 , reasonably predicting the melting point of UN and predicting stable structures for UN 2 and α- and β-U 2 N 3 . On the other hand, the Tseplyaev potential predicts a premature phase change of both UN and UN 2 and cannot stabilize α- nor β-U 2 N 3 . However, the Kocevski potential cannot predict a stable α-U phase and is thus not suitable for the calculation of formation energies for non-stoichiometric point defects.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2017

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electrons inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase V o Proton Channel

The molecular mechanism of transmembrane proton translocation in rotary motor ATPases is not fully understood. Here in this paper, we report the 3.5-Å resolution cryoEM structure of the lipid nanodisc-reconstituted V o proton channel of the yeast vacuolar H + -ATPase, captured in a physiologically relevant, autoinhibited state. The resulting atomic model provides structural detail for the amino acids that constitute the proton pathway at the interface of the proteolipid ring and subunit a. Based on the structure and previous mutagenesis studies, we propose the chemical basis of transmembrane proton transport. Moreover, we discovered that the C terminus of the assembly factor Voa1 is an integral component of mature V o . Voa1’s C-terminal transmembrane α helix is bound inside the proteolipid ring, where it contributes to the stability of the complex. Our structure rationalizes possible mechanisms by which mutations in human V o can result in disease phenotypes and may thus provide new avenues for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Alteration of intersubunit acid–base pair interactions at the quasi-threefold axis of symmetry of Cucumber mosaic virus disrupts aphid vector transmission

In the atomic model of Cucumber mosaic virus (CMV), six amino acid residues form stabilizing salt bridges between subunits of the asymmetric unit at the quasi-threefold axis of symmetry. To evaluate the effects of these positions on virion stability and aphid vector transmissibility, six charged amino acid residues were individually mutated to alanine. All of the six engineered viruses were viable and exhibited near wild type levels of virion stability in the presence of urea. Aphid vector transmissibility was nearly or completely eliminated in the case of four of the mutants; two mutants demonstrated intermediate aphid transmissibility. For the majority of the engineered mutants, second-site mutations were observed following aphid transmission and/or mechanical passaging, and one restored transmission rates to that of the wild type. CMV capsids tolerate disruption of acid–base pairing interactions at the quasi-threefold axis of symmetry, but these interactions are essential for maintaining aphid vector transmissibility. - Highlights: ► Amino acids between structural subunits of Cucumber mosaic virus affect vector transmission. ► Mutant structural stability was retained, while aphid vector transmissibility was disrupted. ► Spontaneous, second-site mutations restored aphid vector transmissibility.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Understanding How Isotopes Affect Charge Transfer in P3HT/PCBM: A Quantum Trajectory-Electronic Structure Study with Nonlinear Quantum Corrections

The experimentally observed effect of selective deuterium substitution on the open circuit voltage for a blend of poly(3-hexylthiophene)(P3HT) and [6,6]-phenyl-C 61 - butyric acid methyl ester (PCBM) (Nat. Commun. 5:3180, 2014) is explored using a 221-atom model of a polymer-wrapped PCBM molecule. We describe the protonic and deuteronic wavefunctions for the H/D isotopologues of the hexyl side chains within a Quantum Trajectory/Electronic Structure approach where the dynamics is performed with newly developed nonlinear corrections to the quantum forces, necessary to describe the nuclear wavefunctions; the classical forces are generated with a Density Functional Tight Binding method. We used the resulting protonic and deuteronic time-dependent wavefunctions to assess the effects of isotopic substitution (deuteration) on the energy gaps relevant to the charge transfer for the donor and acceptor electronic states. Furthermore, while the isotope effect on the electronic energy levels is found negligible, the quantum-induced fluctuations of the energy gap between the charge transfer and charge separated states due to nuclear wavefunctions may account for experimental trends by promoting charge transfer in P3HT/PCBM and increasing charge recombination on the donor in the deuterium substituted P3HT/PCBM.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Ab Initio Computation of Rotationally-Averaged Pump–Probe X-ray and Electron Diffraction Signals

We develop a new algorithm for the computation of the rotationally averaged elastic molecular diffraction signal for the cases of perpendicular or parallel pump–probe geometries. The algorithm first collocates the charge density from an arbitrary ab initio wave function onto a Becke quadrature grid [A. Becke, J. Chem. Phys. 1988, 88, 2457], providing a high-fidelity multiresolution representation of the charge density. A double sum is then performed over the Becke grid points, and the interaction between points computed using the scattering kernels of Williamson and Zewail [J. C. Williamson and A. H. Zewail, J. Phys. Chem. 1994, 98, 2766]. These kernels analytically average over the molecular orientations with the cos 2 γ selection factor appropriate for one-photon dipole absorption in a perpendicular pump–probe geometry. We demonstrate that the method is converged with small grids containing <500 points/atom. We implement the algorithm on a GPU for increased efficiency and emonstrate the algorithm for molecules with up to a few dozen atoms. We explore the accuracy of the independent atom model (IAM) by comparison with our new and more accurate method. We also investigate the possibility of detecting signatures of electronic transitions in polyatomic pump–probe diffraction experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗