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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

The electronic characterization of biphenylene—Experimental and theoretical insights from core and valence level spectroscopy

In this paper, we provide detailed insights into the electronic structure of the gas phase biphenylene molecule through core and valence spectroscopy. By comparing results of X-ray Photoelectron Spectroscopy (XPS) measurements with ΔSCF core-hole calculations in the framework of Density Functional Theory (DFT), we could decompose the characteristic contributions to the total spectra and assign them to non-equivalent carbon atoms. As a difference with similar molecules like biphenyl and naphthalene, an influence of the localized orbitals on the relative XPS shifts was found. The valence spectrum probed by photoelectron spectroscopy at a photon energy of 50 eV in conjunction with hybrid DFT calculations revealed the effects of the localization on the electronic states. Using the transition potential approach to simulate the X-ray absorption spectroscopy measurements, similar contributions from the non-equivalent carbon atoms were determined from the total spectrum, for which the slightly shifted individual components can explain the observed asymmetric features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

New X-ray insight into oxygen intercalation in epitaxial graphene grown on 4H-SiC(0001)

Efficient control of intercalation of epitaxial graphene by specific elements is a way to change properties of the graphene. Results of several experimental techniques, such as X-ray photoelectron spectroscopy, micro-Raman mapping, reflectivity, attenuated total reflection, X-ray diffraction, and X-ray reflectometry, gave a new insight into the intercalation of oxygen in the epitaxial graphene grown on 4H-SiC(0001). These results confirmed that oxygen intercalation decouples the graphene buffer layer from the 4H-SiC surface and converts it into the graphene layer. However, in contrast to the hydrogen intercalation, oxygen does not intercalate between carbon planes (in the case of few layer graphene) and the interlayer spacing stays constant at the level of 3.35–3.32 Å. Moreover, X-ray reflectometry showed the presence of an oxide layer having the thickness of about 0.8 Å underneath the graphene layers. Apart from the formation of the nonuniform thin oxide layer, generation of defects in graphene caused by oxygen was also evidenced. Last but not least, water islands underneath defected graphene regions in both intercalated and non-intercalated samples were most probably revealed. These water islands are formed in the case of all the samples stored under ambient laboratory conditions. Water islands can be removed from underneath the few layer graphene stacks by relevant thermal treatment or by UV illumination.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Pulsed high-magnetic-field experiments: New insights into the magnetocaloric effect in Ni-Mn-In Heusler alloys

The present pulsed high-magnetic-field study on Ni{sub 50}Mn{sub 35}In{sub 15} gives an extra insight into the thermodynamics of the martensitic transformation in Heusler shape-memory alloys. The transformation-entropy change, ΔS, was estimated from field-dependent magnetization experiments in pulsed high magnetic fields and by heat-capacity measurements in static fields. We found a decrease of ΔS with decreasing temperature. This behavior can be understood by considering the different signs of the lattice and magnetic contributions to the total entropy. Our results further imply that the magnetocaloric effect will decrease with decreasing temperature and, furthermore, the martensitic transition is not induced anymore by changing the temperature in high magnetic fields.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

New insight into the helium-induced damage in MAX phase Ti{sub 3}AlC{sub 2} by first-principles studies

In the present work, the behavior of He in the MAX phase Ti{sub 3}AlC{sub 2} material is investigated using first-principle methods. It is found that, according to the predicted formation energies, a single He atom favors residing near the Al plane in Ti{sub 3}AlC{sub 2}. The results also show that Al vacancies are better able to trap He atoms than either Ti or C vacancies. The formation energies for the secondary vacancy defects near an Al vacancy or a C vacancy are strongly influenced by He impurity content. According to the present results, the existence of trapped He atoms in primary Al vacancy can promote secondary vacancy formation and the He bubble trapped by Al vacancies has a higher tendency to grow in the Al plane of Ti{sub 3}AlC{sub 2}. The diffusion of He in Ti{sub 3}AlC{sub 2} is also investigated. The energy barriers are approximately 2.980 eV and 0.294 eV along the c-axis and in the ab plane, respectively, which means that He atoms exhibit faster migration parallel to the Al plane. Hence, the formation of platelet-like bubbles nucleated from the Al vacancies is favored both energetically and kinetically. Our calculations also show that the conventional spherical bubbles may be originated from He atoms trapped by C vacancies. Taken together, these results are able to explain the observed formation of bubbles in various shapes in recent experiments. This study is expected to provide new insight into the behaviors of MAX phases under irradiation from electronic structure level in order to improve the design of MAX phase based materials.

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

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900–1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture’s self-diffusion coefficients, viscosity, and ionic conductivity.

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

Nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass: Insights from molecular dynamics simulations

We have carried out classical molecular dynamics simulations in order to get insight into the atomistic mechanisms of the deformation during nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass. In terms of the glass hardness, we have found that the primary factor affecting the decrease of hardness after irradiation is depolymerization rather than free volume, and we argue that this is a general trend applicable to other borosilicate glasses with similar compositions. We have analyzed the changes of the short- and medium-range structures under deformation and found that the creation of oxygen triclusters is an important mechanism in order to describe the deformation of highly polymerized borosilicate glasses and is essential in the understanding of the folding of large rings under stress. We have equally found that the less polymerized glasses present a higher amount of relative densification, while the analysis of bond-breaking during the nanoindentation has showed that shear flow is more likely to appear around sodium atoms. The results provided in this study can be proven to be useful in the interpretation of experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Insight into ethylene interactions with molybdenum suboxide cluster anions from photoelectron spectra of chemifragments

We present that recent studies on reactions between Mo x O y - cluster anions and H 2 O/C 2 H 4 mixtures revealed a complex web of addition, hydrogen evolution, and chemifragmentation reactions, with chemifragments unambiguously connected to cluster reactions with C 2 H 4 . To gain insight into the molecular-scale interactions along the chemifragmentation pathways, the anion photoelectron (PE) spectra of MoC 2 H 2 - , MoC 4 H 4 - , MoOC 2 H 2 - , and MoO 2 C 2 H 2 - formed directly in Mo x O y - + C 2 H 4 (x > 1; y ≥ x) reactions, along with supporting CCSD(T) and density functional theory calculations, are presented and analyzed. The complexes have spectra that are all consistent with η 2- acetylene complexes, though for all but MoC 4 H 4 - , the possibility that vinylidene complexes are also present cannot be definitively ruled out. Structures that are consistent with the PE spectrum of MoC 2 H 2 - differ from the lowest energy structure, suggesting that the fragment formation is under kinetic control. The PE spectrum of MoO 2 C 2 H 2 - additionally exhibits evidence that photodissociation to MoO 2 - + C 2 H 2 may be occurring. In conclusion, the results suggest that oxidative dehydrogenation of ethylene is initiated by Lewis acid/base interactions between the Mo centers in larger clusters and the π orbitals in ethylene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular insights into ionic liquid/aqueous interface of phosphonium based phase-separable ionic liquids

Phosphonium based phase-separable ionic liquids (PSILs) are promising green solvents for dissolution of cellulose and lignin, a necessary step for conversion of biomass to fuels and chemicals. The knowledge of interfacial behavior of ionic liquid/solvent systems is critical for designing efficient separation processes. Here, molecular dynamics simulations are carried out for aqueous interface of tetraalkylphosphonium ionic liquids with chloride and acetate as anions to investigate IL miscibility with water. The transition zone from miscible to immiscible behavior was observed for alkyl chain lengths of 6 to 8. Emulsion phase was observed for [P8888]+ ion and multiple IL/water interface was observed for [P12121212]+ phosphonium cation. IL/water interface is observed to be enriched with solvated anions with phosphorous atom oriented towards the aqueous phase. The potential of mean force calculations suggest that as the alkyl chain of the phosphonium cations increase, so does the driving force for aggregation of cations in the aqueous phase. Due to the difference in the molecular shape and size, anions are better solvated by the water molecules, and these ions diffuse into the aqueous phase. Furthermore, the analysis of selected pair interactions provides insights into the nature of intermolecular forces and the role of the alkyl side chains on the interfacial properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting metal–metal interactions. II. Accelerating generalized schemes through physical insights

Operando-computational frameworks that integrate descriptors for catalyst stability within catalyst screening paradigms enable predictions of rates and selectivity on chemically faithful representations of nanoparticles under reaction conditions. These catalyst stability descriptors can be efficiently predicted by density functional theory (DFT)-based models. The alloy stability model, for example, predicts the stability of metal atoms in nanoparticles with site-by-site resolution. In this work, we use physical insights to present accelerated approaches of parameterizing this recently introduced alloy-stability model. These accelerated approaches meld quadratic functions for the energy of metal atoms in terms of the coordination number with linear correlations between model parameters and the cohesive energies of bulk metals. By interpolating across both the coordination number and chemical space, these accelerated approaches shrink the training set size for 12 fcc p- and d-block metals from 204 to as few as 24 DFT calculated total energies without sacrificing the accuracy of our model. We validate the accelerated approaches by predicting adsorption energies of metal atoms on extended surfaces and 147 atom cuboctahedral nanoparticles with mean absolute errors of 0.10 eV and 0.24 eV, respectively. This efficiency boost will enable a rapid and exhaustive exploration of the vast material space of transition metal alloys for catalytic applications.

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

Constrained non-negative matrix factorization enabling real-time insights of in situ and high-throughput experiments

Non-negative matrix factorization (NMF) is an appealing class of methods for performing unsupervised learning on streaming spectral data, particularly in time-sensitive applications such as in situ characterization of materials. These methods seek to decompose a dataset into a small number of components and weights that can compactly represent the underlying signal while effectively reconstructing the observations with minimal error. However, canonical NMF methods have no underlying requirement that the reconstruction uses components or weights that are representative of the true physical processes. In this work, we demonstrate how constraining a subset of the NMF weights or components as rigid priors, provided as known or assumed values, can provide significant improvement in revealing true underlying phenomena. We present a PyTorch-based method for efficiently applying constrained NMF and demonstrate its application to several synthetic examples. Our implementation allows an expert researcher-in-the-loop to provide and dynamically adjust the constraints during a live experiment involving streaming spectral data. Such interactive priors allow researchers to specify known or identified independent components, as well as functional expectations about the mixing or transitions between the components. We further demonstrate the application of this method to measured synchrotron x-ray total scattering data from in situ beamline experiments. In such a context, constrained NMF can result in a more interpretive and scientifically relevant decomposition than canonical NMF or other decomposition techniques. As a result, the details of the method are provided, along with general guidance for employing constrained NMF in the extraction of critical information and insights during time-sensitive experimental applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Analytic insights into nonlocal energy transport: Steady state Fokker Planck theory in arbitrary Z plasmas

The generation of energetic electrons in laser fusion in an important issue. The electrons may either arise from a laser plasma instability, or from the uncoupled high temperature tail of a Maxwellian distribution. To study these in a laser fusion context, it is important to find a method accurate enough to be useful, and simple enough to be incorporated into a radiation hydrodynamics numerical simulation, the main workhorse for studying the laser fusion target. That is why analytic insights become important, they allow one to simplify the Fokker Planck theory so that a solution of it can be incorporated into a radiation hydrodynamic simulation. This work develops and analyzes a steady state Fokker Planck theory for plasmas of arbitrary Z. It develops a method of solving the simplified Fokker Planck method with a technique called sparse eigenfunction analysis. As a result, this method appears to work reasonably well when compared to the experimental results from the Rochester/NIF on plastic spherical targets with and without a silicon layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Atomistic insight into the effects of electrostatic fields on hydrocarbon reaction kinetics

Reactive Molecular Dynamics (MD) and Density Functional Theory (DFT) computations are performed to provide insight into the effects of external electrostatic fields on hydrocarbon reaction kinetics. By comparing the results from MD and DFT, the suitability of the MD method in modeling electrodynamics is first assessed. Results show that the electric field-induced polarization predicted by the MD charge equilibration method is in good agreement with various DFT charge partitioning schemes. Then, the effects of oriented external electric fields on the transition pathways of non-redox reactions are investigated. Results on the minimum energy path suggest that electric fields can cause catalysis or inhibition of oxidation reactions, whereas pyrolysis reactions are not affected due to the weaker electronegativity of the hydrogen and carbon atoms. MD simulations of isolated reactions show that the reaction kinetics is also affected by applied external Lorentz forces and interatomic Coulomb forces since they can increase or decrease the energy of collision depending on the molecular conformation. In addition, electric fields can affect the kinetics of polar species and force them to align in the direction of field lines. These effects are attributed to energy transfer via intermolecular collisions and stabilization under the external Lorentz force. The kinetics of apolar species is not significantly affected mainly due to the weak induced dipole moment even under strong electric fields. The dynamics and reaction rates of species are studied by means of large-scale combustion simulations of n-dodecane and oxygen mixtures. Results show that under strong electric fields, the fuel, oxidizer, and most product molecules experience translational and rotational acceleration mainly due to close charge transfer along with a reduction in their vibrational energy due to stabilization. This study will serve as a basis to improve the current methods used in MD and to develop novel methodologies for the modeling of macroscale reacting flows under external electrostatic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Mechanistic insights into c-di-GMP–dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa

Significance Pseudomonas aeruginosa , an opportunistic pathogen that can cause fatal chronic infections, relies on the intracellular second-messenger c-di-GMP to form robust multicellular biofilms during host tissue colonization. c-di-GMP is sensed directly by the transcription regulator FleQ, which inversely regulates flagellar motility and exopolysaccharide secretion to secure a planktonic to sessile life-form transition. FleQ belongs to the diverse family of AAA+ ATPase enhancer-binding proteins, but how its noncanonical function on transcriptional regulation is controlled by c-di-GMP remains enigmatic. Here, we report structural and functional data that identify an unusual mode of c-di-GMP recognition accompanied by a major quaternary structure reorganization. Our analyses offer a consensus to previous studies and unique insights into the mechanism of action of FleQ and FleQ-like proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Significance Modern industrial and agricultural practices generate large quantities of aromatic pollutants; however, these waste products can be converted into fine chemicals, fuels, and plastics through biocatalytic pathways. The bacterial world can inform such utilization strategies as certain strains of soil and marine bacteria metabolize environmentally derived aromatics. Many of these metabolic pathways involve aryl intermediates that require demethylation to facilitate modification and ring opening for assimilation into the tricarboxylic acid (TCA) cycle. Aryl demethylases, which catalyze this reaction, are poorly understood, making their utilization in biotechnology difficult. We provide the structural and mechanistic characterization of a single-domain aryl demethylase, LigM, which employs a tyrosine-dependent mechanism. Insights from this work will inform synthetic biology approaches to convert underutilized aromatics into higher value compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural insights into lipoprotein N-acylation by Escherichia coli apolipoprotein N-acyltransferase

Gram-negative bacteria express a diverse array of lipoproteins that are essential for various aspects of cell growth and virulence, including nutrient uptake, signal transduction, adhesion, conjugation, sporulation, and outer membrane protein folding. Lipoprotein maturation requires the sequential activity of three enzymes that are embedded in the cytoplasmic membrane. First, phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) recognizes a conserved lipobox motif within the prolipoprotein signal sequence and catalyzes the addition of diacylglycerol to an invariant cysteine. The signal sequence is then cleaved by signal peptidase II (LspA) to give an N-terminal S-diacylglyceryl cysteine. Finally, apolipoprotein N-acyltransferase (Lnt) catalyzes the transfer of the sn-1-acyl chain of phosphatidylethanolamine to this N-terminal cysteine, generating a mature, triacylated lipoprotein. Although structural studies of Lgt and LspA have yielded significant mechanistic insights into this essential biosynthetic pathway, the structure of Lnt has remained elusive. Here, we present crystal structures of wild-type and an active-site mutant of Escherichia coli Lnt. The structures reveal a monomeric eight-transmembrane helix fold that supports a periplasmic carbon–nitrogen hydrolase domain containing a Cys–Glu–Lys catalytic triad. Two lipids are bound at the active site in the structures, and we propose a putative phosphate recognition site where a chloride ion is coordinated near the active site. Based on these structures and complementary cell-based, biochemical, and molecular dynamics approaches, we propose a mechanism for substrate engagement and catalysis by E. coli Lnt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Here, all eight cysteines of the CTD form four disulfide bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗