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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

In this work, we have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å 2 , a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (S CD ) profiles calculated from the simulations were in relatively good agreement with S CD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å 2 resulted in good agreement between the simulation and experimental scattering form factors, but not with S CD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models

Cell doubling times of the purple bacterium Rhodobacter sphaeroides during photosynthetic growth are determined experimentally and computationally as a function of illumination. For this purpose, energy conversion processes in an intracytoplasmic membrane vesicle, the chromatophore, are described based on an atomic detail structural model. The cell doubling time and its illumination dependence are computed in terms of the return-on-investment (ROI) time of the chromatophore, determined computationally from the ATP production rate, and the mass ratio of chromatophores in the cell, determined experimentally from whole cell absorbance spectra. The ROI time is defined as the time it takes to produce enough ATP to pay for the construction of another chromatophore. The ROI time of the low light-growth chromatophore is 4.5–2.6 h for a typical illumination range of 10–100 μmol photons m –2 s –1 , respectively, with corresponding cell doubling times of 8.2–3.9 h. Finally, when energy expenditure is considered as a currency, the benefit-to-cost ratio computed for the chromatophore as an energy harvesting device is 2–8 times greater than for photovoltaic and fossil fuel-based energy solutions and the corresponding ROI times are approximately 3–4 orders of magnitude shorter for the chromatophore than for synthetic systems.

09 BIOMASS FUELS↗
DOE OSTI2020

Orientation and Conformation of Proteins at the Air–Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. Here in this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2022

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Determining Relative f and d Orbital Contributions to M–Cl Covalency in MCl 6 2– (M = Ti, Zr, Hf, U) and UOCl 5 – Using Cl K-Edge X-ray Absorption Spectroscopy and Time-Dependent Density Functional Theory

Chlorine K-edge X-ray absorption spectroscopy (XAS) and ground-state and time-dependent hybrid density functional theory (DFT) were used to probe electronic structure for O{sub h}-MCl{sub 6}{sup 2-}(M = Ti, Zr, Hf, U) and C{sub 4v}-UOCl{sub 5}{sup -}, and to determine the relative contributions of valence 3d, 4d, 5d, 6d, and 5f orbitals in M-Cl bonding. Spectral interpretations were guided by time-dependent DFT calculated transition energies and oscillator strengths, which agree well with the experimental XAS spectra. The data provide new spectroscopic evidence for the involvement of both 5f and 6d orbitals in actinide-ligand bonding in UCl{sub 6}{sup 2-}. For the MCl{sub 6}{sup 2-}, where transitions into d orbitals of t{sub 2g} symmetry are spectroscopically resolved for all four complexes, the experimentally determined Cl 3p character per M-Cl bond increases from 8.3(4)% (TiCl{sub 6}{sup 2-}) to 10.3(5)% (ZrCl{sub 6}{sup 2-}), 12(1)% (HfCl{sub 6}{sup 2-}), and 26 18(1)% (UCl{sub 6}{sup 2-}). Chlorine K-edge XAS spectra of UOCl{sub 5}{sup -} provide additional insights into the transition assignments by 27 lowering the symmetry to C{sub 4v}, where five pre-edge transitions into both 5f and 6d orbitals are observed. For UCl{sub 6}{sup 2-}, the XAS data 28 suggest that orbital mixing associated with the U 5f orbitals is considerably lower than that of the U 6d orbitals. For both UCl{sub 6}{sup 2-}29 and UOCl{sub 5}{sup -}, the ground-state DFT calculations predict a larger 5f contribution to bonding than is determined experimentally. 30 These findings are discussed in the context of conventional theories of covalent bonding for d- and f-block metal complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Mass Spectrometric Determination of Site-Specific O -Acetylation in Rhamnogalacturonan I Oligomers

O-acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify O-acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses smaller sample amounts, faces challenges due to O-acetyl migration between monosaccharide positions. The multiple steps in pectin sample analysis can further promote O-acetyl migration, especially near free hydroxyl groups. Moreover, during tandem MS, O-acetyl groups may detach, complicating the accurate tracking. This study presents an approach to lock O-acetyl groups by introducing trideuteroacetyl and propionyl substituents onto free hydroxyls of RG-I or partially acetylated RG-I. By combining matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization (ESI) MS with MS/MS or tandem mass spectrometry (MSn), we devised a way to determine the monosaccharide sequence in the oligomer and the precise positions of O-acetyl groups in partially acetylated RG-I. This method enables the study of the regiospecificity of recombinant pectin O-acetyltransferases and can be applied to other oligosaccharides to determine acyl positions.

O-acetylation↗
DOE OSTI2012

The Molecular Volcano Revisited: Determination of Crack Propagation and Distribution During the Crystallization of Nanoscale Amorphous Solid Water Films.

Temperature programmed desorption (TPD) is utilized to determine the length distribution of cracks formed through amorphous solid water (ASW) during crystallization. This distribution is determined by monitoring how the thickness of an ASW overlayer alters desorption of an underlayer of O2. As deposited the ASW overlayer prevents desorption of O2. During crystallization, cracks form through the ASW overlayer and open a path to vacuum which allows O2 to escape in a rapid episodic release known as the 'molecular volcano'. Sufficiently thick ASW overlayers further trap O2 resulting in a second O2 desorption peak commensurate with desorption of the last of the ASW overlayer. The evolution of this trapping peak with overlayer thickness is the basis for determining the distribution of crystallization induced cracks through the ASW. Reflection adsorption infrared spectroscopy (RAIRS) and TPD of multicomponent parfait structures of ASW, O2 and Kr indicate that a preponderance of these cracks propagate down from the outer surface of the ASW.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

The Pingding segment of the Altyn Tagh Fault (91 °E): Holocene slip-rate determination from cosmogenic radionuclide dating of offset fluvial terraces

Morphochronologic slip-rates on the Altyn Tagh Fault (ATF) along the southern front of the Pingding Shan at ~90.5°E are determined by cosmogenic radionuclide (CRN) dating of seven offset terraces at two sites. The terraces are defined based upon morphology, elevation and dating, together with fieldwork and high-resolution satellite analysis. The majority of the CRN model ages fall within narrow ranges (<2 ka) on the four main terraces (T1, T2, T3 and T3'), and allow a detailed terrace chronology. Bounds on the terrace ages and offsets of 5 independent terraces yield consistent slip-rate estimates. The long-term slip-rate of 13.9 ± 1.1 mm/yr is defined at the 95% confidence level, as the joint rate probability distribution of the rate derived from each independent terrace. It falls within the bounds of all the rates defined on the central Altyn Tagh Fault between the Cherchen He (86.4°E) and Akato Tagh (~88°E) sites. This rate is ~10 mm/yr less than the upper rate determined near Tura at ~87°E, in keeping with the inference of an eastward decreasing rate due to progressive loss of slip to thrusts branching off the fault southwards but it is greater than the 9 ± 4 mm/yr rate determined at ~90°E by GPS surveys and other geodetic short-term rates defined elsewhere along the ATF. Whether such disparate rates will ultimately be reconciled by a better understanding of fault mechanics, resolved transient deformations during the seismic cycle or by more accurate measurements made with either approach remains an important issue.

58 GEOSCIENCES↗
DOE OSTI2015

Determining the location and nearest neighbours of aluminium in zeolites with atom probe tomography

Zeolite catalysis is determined by a combination of pore architecture and Brønsted acidity. As Brønsted acid sites are formed by the substitution of AlO4 for SiO4 tetrahedra, it is of utmost importance to have information on the number as well as the location and neighbouring sites of framework aluminium. Unfortunately, such detailed information has not yet been obtained, mainly due to the lack of suitable characterization methods. Here we report, using the powerful atomic-scale analysis technique known as atom probe tomography, the quantitative spatial distribution of individual aluminium atoms, including their three-dimensional extent of segregation. Ultimately, using a nearest-neighbour statistical analysis, we precisely determine the short-range distribution of aluminium over the different T-sites and determine the most probable Al–Al neighbouring distance within parent and steamed ZSM-5 crystals, as well as assess the long-range redistribution of aluminium upon zeolite steaming.

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

Determination of band alignment in the single-layer MoS 2 /WSe 2 heterojunction

The emergence of two-dimensional electronic materials has stimulated proposals of novel electronic and photonic devices based on the heterostructures of transition metal dichalcogenides. Here we report the determination of band offsets in the heterostructures of transition metal dichalcogenides by using microbeam X-ray photoelectron spectroscopy and scanning tunnelling microscopy/spectroscopy. We determine a type-II alignment between MoS 2 and WSe 2 with a valence band offset value of 0.83 eV and a conduction band offset of 0.76 eV. First-principles calculations show that in this heterostructure with dissimilar chalcogen atoms, the electronic structures of WSe 2 and MoS 2 are well retained in their respective layers due to a weak interlayer coupling. Moreover, a valence band offset of 0.94 eV is obtained from density functional theory, consistent with the experimental determination.

36 MATERIALS SCIENCE↗
DOE OSTI2018

MRP3 is a sex determining gene in the diatom Pseudo-nitzschia multistriata

A broad diversity of sex-determining systems has evolved in eukaryotes. However, information on the mechanisms of sex determination for unicellular microalgae is limited, including for diatoms, key-players of ocean food webs. Here we report the identification of a mating type (MT) determining gene for the diatom Pseudo-nitzschia multistriata . By comparing the expression profile of the two MTs, we find five MT-biased genes, of which one, MRP3 , is expressed exclusively in MT+ strains in a monoallelic manner. A short tandem repeat of specific length in the region upstream of MRP3 is consistently present in MT+ and absent in MT– strains. MRP3 overexpression in an MT– strain induces sex reversal: the transgenic MT– can mate with another MT– strain and displays altered regulation of the other MT-biased genes, indicating that they lie downstream. Our data show that a relatively simple genetic program is involved in defining the MT in P. multistriata.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Abstract Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Three rate-determining protein roles in photosynthetic O 2 -evolution addressed by time-resolved experiments on genetically modified photosystems

Light-driven water splitting by plants, algae and cyanobacteria is pivotal for global bioenergetics and biomass formation. A manganese cluster bound to the photosystem II proteins catalyzes the complex reaction at high rate, but the rate-determining factors are insufficiently understood. Here we trace the oxygen-evolution transition by time-resolved polarography and infrared spectroscopy for cyanobacterial photosystems genetically modified at two strategic sites, complemented by computational chemistry. Our results highlight three rate-determining roles of the protein environment of the metal cluster: acceleration of proton-coupled electron transfer, acceleration of substrate-water insertion after O 2 -formation, and balancing of rate-determining enthalpic and entropic contributions. Whereas in general the substrate-water insertion step may be unresolvable in time-resolved experiments, here it likely becomes traceable because of deceleration by genetic modification. Our results may stimulate new time-resolved experiments on substrate-water insertion in photosynthesis, clarification of enthalpy-entropy compensation in enzyme catalysis, and knowledge-guided development of inorganic catalyst materials.

Bioenergetics↗
DOE OSTI2025

Numerically exact configuration interaction at quadrillion-determinant scale

The combinatorial growth of configuration interaction (CI) has long limited this formally exact quantum chemistry method to only the smallest molecules. Here, we report a numerically exact CI calculation exceeding one quadrillion (10 15 ) determinants, made possible by a lossless categorical compression strategy within the small-tensor-product distributed active space (STP-DAS) framework. This approach overcomes the traditional memory bottlenecks of CI by a numerically exact compression of the wavefunction representation and reformulating the most computationally demanding matrix–vector operations. Using this method, we performed a fully relativistic CI calculation of the ground state of HBrTe with over 10 15 complex-valued determinants in just 34.5 h on 1000 computing nodes—the largest CI calculation ever reported. We further achieved fast computation for systems with hundreds of billions of determinants on only a few compute nodes. Extensive benchmarks confirm that the method retains full numerical exactness while cutting memory and computational cost by orders of magnitude. Compared to previous state-of-the-art CI calculations, this work achieves a 1000 times increase in CI space, a 10 6 -fold increase in floating-point operations performed, and a 10 6 -fold improvement in computational speed.

Computational chemistry↗
DOE OSTI2021

Determining the three-dimensional atomic structure of an amorphous solid

Amorphous solids such as glass, plastics and amorphous thin films are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells 1-4 . However, owing to the lack of long-range order, the three-dimensional (3D) atomic structure of amorphous solids has so far eluded direct experimental determination 5-15 . Here we develop an atomic electron tomography reconstruction method to experimentally determine the 3D atomic positions of an amorphous solid. Using a multi-component glass-forming alloy as proof of principle, we quantitatively characterize the short- and medium-range order of the 3D atomic arrangement. We observe that, although the 3D atomic packing of the short-range order is geometrically disordered, some short-range-order structures connect with each other to form crystal-like superclusters and give rise to medium-range order. We identify four types of crystal-like medium-range order-face-centred cubic, hexagonal close-packed, body-centred cubic and simple cubic-coexisting in the amorphous sample, showing translational but not orientational order. These observations provide direct experimental evidence to support the general framework of the efficient cluster packing model for metallic glasses 10,12-14,16 . Finally, we expect that this work will pave the way for the determination of the 3D structure of a wide range of amorphous solids, which could transform our fundamental understanding of non-crystalline materials and related phenomena.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Determining the gluonic gravitational form factors of the proton

The proton is one of the main building blocks of all visible matter in the Universe. Among its intrinsic properties are its electric charge, mass and spin. These properties emerge from the complex dynamics of its fundamental constituents—quarks and gluons—described by the theory of quantum chromodynamics. The electric charge and spin of protons, which are shared among the quarks, have been investigated previously using electron scattering. An example is the highly precise measurement of the electric charge radius of the proton. By contrast, little is known about the inner mass density of the proton, which is dominated by the energy carried by gluons. Gluons are hard to access using electron scattering because they do not carry an electromagnetic charge. Here we investigated the gravitational density of gluons using a small colour dipole, through the threshold photoproduction of the J/ψ particle. We determined the gluonic gravitational form factors of the proton from our measurement. Here we used a variety of models and determined, in all cases, a mass radius that is notably smaller than the electric charge radius. In some, but not all cases, depending on the model, the determined radius agrees well with first-principle predictions from lattice quantum chromodynamics. This work paves the way for a deeper understanding of the salient role of gluons in providing gravitational mass to visible matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Determination of the Raman polarizability tensor in the optically anisotropic crystal potassium dihydrogen phosphate and its deuterated analog

Abstract The Raman tensor of the dominant A 1 modes of the nonlinear optical crystalline material potassium dihydrogen phosphate and its 70% deuterated analog have been ascertained. Challenges in determining the A 1 mode tensor element values based on previous reports have been resolved using a specially designed experimental setup that makes use of spherical crystal samples. This novel experimental design enabled the determination of measurement artifacts, including polarization rotation of the pump and/or scattered light propagating through the sample and the contribution of additional overlapping phonon modes, which have hindered previous efforts. Results confirmed that the polarization tensor is diagonal, and matrix elements were determined with high accuracy.

36 MATERIALS SCIENCE↗