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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Frustration- and doping-induced magnetism in a Fermi–Hubbard simulator

Geometrical frustration in strongly correlated systems can give rise to a plethora of novel ordered states and intriguing magnetic phases, such as quantum spin liquids. Promising candidate materials for such phases can be described by the Hubbard model on an anisotropic triangular lattice, a paradigmatic model capturing the interplay between strong correlations and magnetic frustration. However, the fate of frustrated magnetism in the presence of itinerant dopants remains unclear, as well as its connection to the doped phases of the square Hubbard model. Here we investigate the local spin order of a Hubbard model with controllable frustration and doping, using ultracold fermions in anisotropic optical lattices continuously tunable from a square to a triangular geometry. At half-filling and strong interactions U/t ≈ 9, we observe at the single-site level how frustration reduces the range of magnetic correlations and drives a transition from a collinear Néel antiferromagnet to a short-range correlated 120° spiral phase. Away from half-filling, the triangular limit shows enhanced antiferromagnetic correlations on the hole-doped side and a reversal to ferromagnetic correlations at particle dopings above 20%, hinting at the role of kinetic magnetism in frustrated systems. Furthermore, this work paves the way towards exploring possible chiral ordered or superconducting phases in triangular lattices and realizing t–t' square lattice Hubbard models that may be essential to describe superconductivity in cuprate materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1995

The effect of plasma heating on sublimation-driven flow in Io's atmosphere

The atmospheric flow on Io is numerically computed in a flat 2-D axisymmetric geometry for a sublimation atmosphere on the trailing hemisphere subjected to plasma bombardment, UV heating, and IR cooling. Calculations are performed for subsolar vapor pressures of approximately 6.5 x 10(exp -3) Pa (approximately 3 x 10(exp 18) SO2/sq cm) and 6.8 x 10(exp -4) Pa (approximately 4 x 10(exp 17) SO2/sq cm); the latter approximates the vapor pressure of F. P. Fanale et al. (1982). The amount of plasma energy deposited in the atmosphere is 20% of the plasma flow energy due to corotation (J. A. Linker et al., 1988). It is found that plasma heating significantly inflates the upper atmosphere, increasing both the exobase altitude and the amount of surface covered by more than an exospheric column of gas. This in turn controls the supply of the Io plasma torus (M. A. McGrath and R. E. Johnson, 1987). The horizontal flow of mass and energy is also important in determining the exobase altitude; and it is shown that IR cooling can be important, although our use of the equilibrium, cool-to-space approximation for a pure SO2 gas (E. Lellouch et al., 1992) may overestimate this effect. The calculated exobase altitudes are somewhat lower than those suggested by McGrath and Johnson (1987) for supplying the torus, indicating the details of the plasma energy deposition and sputter ejection rate near the exobase, as well as the IR emission from this region need to be examined. In addition, the molecules sublimed (or sputtered) from the surface are transported to the exobase in times short compared to the molecular photodissociation time. Therefore, the exobase is dominated by molecular species and the exobase is supplied by a small region of the surface.

Wong, Mau C.↗
DOE OSTI2025

The Remarkable I 2 O 3 Molecule: A New View from Theory

Atmospheric iodine chemistry has garnered increasing attention as a result of increased iodine emissions. A key subset of this chemistry involves iodine oxides (I 2 O 2–5 ), which serve as precursors to particle formation. Among these, I 2 O 3 is the simplest iodine oxide involved in particle formation, but it has remained undetected in the atmosphere. Previous theoretical studies have characterized this peculiar molecule, primarily using energies to refine geometries obtained at low levels of theory. Due to the reemerging interest in I 2 O 3 , this study presents geometries optimized at the CCSD(T)/aug-cc-pwCVTZ-PP level of theory─marking the first instance, to the best of our knowledge, where this system has been studied exclusively with CCSD(T). Harmonic vibrational frequencies were computed at the same level of theory. Final energetics were obtained using the very high level CCSDT(Q) method with basis sets up to quintuple-zeta cardinality (aug-cc-pwCV5Z-PP) and extrapolated to the CBS limit to yield CCSDT(Q)/CBS//CCSD(T)/aug-cc-pwCVTZ-PP energies. These energies include harmonic zero-point vibrational energy corrections and scalar relativistic energy corrections. Additionally, this study discovers new isomers along the I 2 O 3 potential energy surface, a novel contribution to the field. The performance of different computational methods and DFT functionals commonly used in atmospheric chemistry is also assessed relative to high-level theoretical methods.

basis sets↗
DOE OSTI2025

Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree

Hydroxynitrile lyase fromHevea brasiliensis(HbHNL) and the esterase SABP2 fromNicotiana tabacumshare the α/β-hydrolase fold, a Ser–His–Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions inHbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineeredHbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C α atoms, and even smaller r.m.s.d.s within the active-site region. Both HNL40 and HNL71 show a restored oxyanion hole and an additional tunnel connecting the active site to the protein surface. This work demonstrates the essential role of distant, indirectly acting residues to catalysis in α/β-hydrolase enzymes.

Biochemistry & Molecular Biology↗
DOE OSTI2024

High-Density Capacitive Energy Storage in Low-Dielectric-Constant Polymer PMMA/2D Mica Nanofillers Heterostructure Composite

The ubiquitous, rising demand for energy storage devices with ultra-high storage capacity and efficiency has drawn tremendous research interest in developing energy storage devices. Dielectric polymers are one of the most suitable materials used to fabricate electrostatic capacitive energy storage devices with thin-film geometry with high power density. In this work, we studied the dielectric properties, electric polarization, and energy density of PMMA/2D Mica nanocomposite capacitors where stratified 2D nanofillers are interfaced between the multiple layers of PMMA thin films using two heterostructure designs of the capacitors, PMMA/2D Mica/PMMA (PMP) and PMMA/2D Mica/PMMA/2D Mica/PMMA (PMPMP). The incorporation of a 2D Mica nanofiller in the low-dielectric-constant PMMA leads to an enhancement in the dielectric constant, with ∆ε ~ 15% and 53% for PMP and PMPMP heterostructures at room temperature. Additionally, a significant improvement in discharged energy density was measured for the PMPMP capacitor (Ud ~ 38 J/cm3 at 825 MV/m) compared to the pristine PMMA (Ud ~ 9.5 J/cm3 at 522 MV/m) and PMP capacitors (Ud ~ 19 J/cm3 at 740 MV/m). This excellent capacitive and energy storage performance of the PMMA/2D Mica heterostructure nanocomposite may inform the fabrication of thin-film, high-density energy storage capacitor devices for potential applications in various platforms.

Biochemistry & Molecular Biology↗
NASA NTRS2003

CO2 Acquisition Membrane (CAM)

The objective of CAM is to develop, test, and analyze thin film membrane materials for separation and purification of carbon dioxide (CO2) from mixtures of gases, such as those found in the Martian atmosphere. The membranes are targeted toward In Situ Resource Utilization (ISRU) applications that will operate in extraterrestrial environments and support future unmanned and human space missions. A primary application is the Sabatier Electrolysis process that uses Mars atmosphere CO2 as raw material for producing water, oxygen, and methane for rocket fuel and habitat support. Other applications include use as an inlet filter to collect and concentrate Mars atmospheric argon and nitrogen gases for habitat pressurization, and to remove CO2 from breathing gases in Closed Environment Life Support Systems (CELSS). CAM membrane materials include crystalline faujasite (FAU) zeolite and rubbery polymers such as silicone rubber (PDMS) that have been shown in the literature and via molecular simulation to favor adsorption and permeation of CO2 over nitrogen and argon. Pure gas permeation tests using commercial PDMS membranes have shown that both CO2 permeance and the separation factor relative to other gases increase as the temperature decreases, and low (Delta)P(Sub CO2) favors higher separation factors. The ideal CO2/N2 separation factor increases from 7.5 to 17.5 as temperature decreases from 22 C to -30 C. For gas mixtures containing CO2, N2, and Ar, plasticization decreased the separation factors from 4.5 to 6 over the same temperature range. We currently synthesize and test our own Na(+) FAU zeolite membranes using standard formulations and secondary growth methods on porous alumina. Preliminary tests with a Na(+) FAU membrane at 22 C show a He/SF6 ideal separation factor of 62, exceeding the Knudsen diffusion selectivity by an order of magnitude. This shows that the membrane is relatively free from large defects and associated non-selective (viscous flow) transport mechanisms. The Membrane Test Facility (MTF) has been developed to measure membrane permeance over a wide range of temperature and pressure. The facility uses two volume compartments separated by the membrane that are instrumented to measure temperature, delta pressure across the membrane, and gas composition. A thermal shroud supports and encloses the membrane, and provides temperature control. Methods were developed to determine membrane permeance using the first order decay of the pressure difference between the sealed compartments, using the total pressure for pure gases, and partial pressure of each species in gas mixtures. The technique provides an end-to-end measurement of gas permeance that includes concentration polarization effects. Experiments have shown that in addition to membrane permeance properties, the geometry and design of associated structures play an important role in how membrane systems will function on Mars.

Mason, Larry W.↗
NASA NTRS2004

Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen

Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of erosion of various interior locations was compared with the erosion that would occur external to the spacecraft. Results of one cavity model indicate that, at depths into a two-dimensional cavity that are equal to 10 cavity widths, the erosion on the walls of the cavity is less than that on the top surface by over 2 orders of magnitude. Wall erosion near the surface of a cavity depends on which wall is receiving direct atomic oxygen attack. However, deep in the cavity little difference is present. Testing of various cavity models such as these gives spacecraft designers an indication of the level of threat to sensitive interior surfaces for different geometries. Even though the Monte Carlo model is two-dimensional, it can be used to provide qualitative information about spacecraft openings that are three-dimensional by offering reasonable insight as to the nature of the attenuation of damage that occurs within a spacecraft in low Earth orbit. As shown, there is more erosion on the side seeing direct atomic oxygen attack until a depth of approximately 5 times the width of the opening, where the erosion is the same on both sides.

Banks, Bruce A.↗
NASA NTRSDate not supplied

The VATMOS-SR Mission Concept: DSMC Studies of the Gas Sampling

VATMOS-SR (Venus ATMOSpheric - Sample Return) is a small spacecraft mission concept that would return a gas sample from the upper atmosphere of Venus to Earth for scientific analysis. This could be the first sample return mission for an extra-terrestrial atmosphere and potentially the first sample return from an Earth-sized planet. The VATMOS-SR mission concept consists of a SmallSat atmospheric sampling probe (45 deg. sphere/cone geometry, <1 m diameter) that is designed to skim through the Venus upper atmosphere and acquire gas samples below the homopause altitude (around ~110 km altitude), where the different atmospheric gases are mixed. The velocity of the spacecraft where sampling would occur is expected to be between ~10.5 km/s and ~13.1 km/s, depending on the trajectory chosen. This presentation will discuss hypervelocity sampling in the upper atmosphere of Venus with respect to the VATMOS-SR mission concept. VATMOS-SR would enable critical atmospheric measurements to form a complete picture of how, why, and when Venus evolved to be so different from Earth and Mars. The abundances and isotopic compositions of volatile elements (such as N, C, S, O, and the noble gases) in planetary atmospheres record volatile delivery during accretion, outgassing from planetary interiors, and atmospheric loss to space. Precise and accurate determinations of volatile atmospheric signatures are the key to understanding the origins and geodynamical evolution of Venus compared to the other terrestrial planets. Hypersonic sampling poses unique technical and scientific challenges. To ensure it is possible to relate the composition of the sampled gases to the free stream atmospheric composition, large-scale numerical simulations are employed to model the flow through the VATMOS-SR sampling system. In particular, an emphasis is placed on quantifying noble gas isotopic fractionation that occurs during the sample acquisition and transfer process to determine how measured isotopic ratios of noble gases in the sample compared to actual isotopic ratios in the Venusian atmosphere. The Direct Simulation Monte Carlo (DSMC) code SPARTA, an open-source software package developed by Sandia National Laboratories, is used in this work. SPARTA, based on Bird’s DSMC method, is a molecular-level gas-kinetic technique. As SPARTA is able to model hypervelocity reacting flows in strong chemical and thermal non-equilibrium, this software package is well suited to determine relevant flow properties for the VATMOS-SR mission concept and to numerically quantify the expected level of elemental and/or isotopic fractionation in the sample acquired by VATMOS-SR. This presentation will show results from 3D simulations correlating the noble gas isotopic fractionation in the gas acquired at hypervelocity speeds to its ambient atmosphere value. In particular, emphasis will be placed on Xenon isotopes of masses 128 and 130, as precise measurements of that ratio would yield comparison to Earth’s atmosphere. Additionally, sensitivity studies that quantify the uncertainties due to the freestream parameters, as well as the modeling parameters, will be performed.

direct simulation Monte Carlo↗
NASA NTRSDate not supplied

Direct Simulation Monte Carlo Studies of the Gas Sampling for the VATMOS-SR Mission Concept

VATMOS-SR (Venus ATMOSpheric - Sample Return) is a small spacecraft mission concept which would return a gas sample from the upper atmosphere of Venus to Earth for scientific analysis. This could be the first sample return mission for an extra-terrestrial atmosphere, and potentially the first sample return from an Earth-sized planet. The VATMOS-SR mission concept consists of a SmallSat atmospheric sampling probe (45 deg. sphere/cone geometry, <1 m diameter) that is designed to skim through the Venus upper atmosphere and acquire gas samples below the homopause altitude (around ~110 km altitude), where the different atmospheric gases are mixed. The velocity of the spacecraft where sampling would occur is expected to be between ~10.5 km/s and ~13.1 km/s, depending on the trajectory chosen. This presentation will discuss hypervelocity sampling in the upper atmosphere of Venus, with respect to the VATMOS-SR mission concept. VATMOS-SR would enable critical atmospheric measurements to form a full picture of how, why, and when Venus evolved to be so different from Earth and Mars. The abundances and isotopic compositions of volatile elements (such as N, C, S, O and the noble gases) in planetary atmospheres record volatile delivery during accretion, outgassing from planetary interiors, and atmospheric loss to space. Precise and accurate determinations of atmospheric volatile signatures are the key to understanding the origins and geodynamical evolution of Venus compared to the other terrestrial planets. Hypersonic sampling poses unique technical and scientific challenges. To ensure it is possible to relate the composition of the sampled gases to the free stream atmospheric composition, large-scale numerical simulations are employed to model the flow through the VATMOS-SR sampling system. In particular, an emphasis is placed on quantifying noble gas isotopic fractionation that occurs during the sample acquisition and transfer process in order to determine how measured isotopic ratios of noble gases in the sample compare to actual isotopic ratios in the Venusian atmosphere. The Direct Simulation Monte Carlo (DSMC) code SPARTA, an open source software package developed by Sandia National Laboratories, is used in this work. SPARTA, based on Bird’s DSMC method, is a molecular-level gas-kinetic technique. As SPARTA is able to model hypervelocity reacting flows in strong chemical and thermal non-equilibrium, this software package is well suited to determine relevant flow properties for the VATMOS-SR mission concept, and to numerically quantify the expected level of elemental and/or isotopic fractionation in the sample acquired by VATMOS-SR. This presentation will show results from 3D simulations correlating the noble gas isotopic fractionation in the gas acquired at hypervelocity speeds to its ambient atmosphere value. In particular, emphasis will be placed at Xenon isotopes of masses 128 and 130, as precise measurements of that ratio would yield a comparison to Earth’s atmosphere. Additionally, sensitivity studies that quantify the uncertainties due to the freestream parameters as well as the modeling parameters will be performed.

direct simulation Monte Carlo↗
DOE OSTI2022

Quantum simulation of quantum phase transitions using the convex geometry of reduced density matrices

Transitions of many-particle quantum systems between distinct phases at absolute-zero temperature, known as quantum phase transitions, require an exacting treatment of particle correlations. Here in this work, we present a general quantum-computing approach to quantum phase transitions that exploits the geometric structure of reduced density matrices. While typical approaches to quantum phase transitions examine discontinuities in the order parameters, the origin of phase transitions—their order parameters and symmetry breaking—can be understood geometrically in terms of the set of two-particle reduced density matrices (2-RDMs). The convex set of 2-RDMs provides a comprehensive map of the quantum system including its distinct phases as well as the transitions connecting these phases. Because 2-RDMs can potentially be computed on quantum computers at nonexponential cost, even when the quantum system is strongly correlated, they are ideally suited for a quantum-computing approach to quantum phase transitions. We compute the convex set of 2-RDMs for a Lipkin-Meshkov-Glick spin model on IBM superconducting-qubit quantum processors. Even though computations are limited to few-particle models due to device noise, comparisons with a classically solvable 1000-particle model reveal that the finite-particle quantum solutions capture the key features of the phase transitions including the strong correlation and the symmetry breaking.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Thermodynamics and Mechanism of a Photocatalyzed Stereoselective [2 + 2] Cycloaddition on a CdSe Quantum Dot

Colloidal quantum dots (QDs) have shown promise over the last few decades for a range of applications including single photon emission, in vivo imaging and photocatalysis. Recent experiments demonstrated that QDs impart stereoselectivity to triplet excited-state [2+2] cycloaddition reactions of alkenes photocatalyzed by the QD through self-assembly of the reagent molecules on the QD surface, but these experiments did not reveal the precise geometries of surface-bound molecules or their interactions with surface atoms. Here, a theoretical mechanistic approach is used to study such interactions for [2+2] cycloadditions of 4-vinylbenzoic acid derivatives on CdSe QDs. Spin-polarized periodic density functional theory (DFT) and non-periodic DFT calculations are deployed to determine the origin of the selectivity for the syn diastereomer of the resultant tetrasubstituted cyclobutane product via atomistic modelling of the CdSe surface and substrates, and determination of the thermodynamic energies of reactions for each step, the intermolecular interactions between the substrates, and the triplet state reaction paths. The calculations indicate that reaction selectivity arises from preferred binding of pairs through intermolecular interactions of substrate molecules on the QD surface in a syn-precursor structure followed by dimerization after triplet excitation. Further, these mechanisms are generalizable to other metal-enriched QD surfaces that have a similar surface structure to CdSe, such as InSe or CdTe. Design principles for anti diastereomer derivatives are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Emergent Magnetism with Continuous Control in the Ultrahigh-Conductivity Layered Oxide PdCoO 2

The current challenge to realizing continuously tunable magnetism lies in our inability to systematically change properties, such as valence, spin, and orbital degrees of freedom, as well as crystallographic geometry. Here, we demonstrate that ferromagnetism can be externally turned on with the application of low-energy helium implantation and can be subsequently erased and returned to the pristine state via annealing. We find that this high level of continuous control is made possible by targeting magnetic metastability in the ultrahigh-conductivity, nonmagnetic layered oxide PdCoO 2 where local lattice distortions generated by helium implantation induce the emergence of a net moment on the surrounding transition metal octahedral sites. These highly localized moments communicate through the itinerant metal states, which trigger the onset of percolated long-range ferromagnetism. The ability to continuously tune competing interactions enables tailoring precise magnetic and magnetotransport responses in an ultrahigh-conductivity film and will be critical to applications across spintronics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

An evaluation for geometries, formation enthalpies, and dissociation energies of diatomic and triatomic (C, H, N, O), NO 3 , and HNO 3 molecules from the PAW DFT method with PBE and optB88-vdW functionals

The structural geometries, formation enthalpies, and dissociation energies of all diatomic and triatomic molecules consisting of the four basic elements C, H, N, and/or O are calculated using the projector augmented wave density functional theory (DFT) method with the Perdew–Burke–Ernzerhof and optB88-vdW exchange-correlation functionals. The calculations are also extended to two larger molecules NO 3 and HNO 3 , which consist of four and five atoms, respectively. In total, 82 molecules or isomers are considered in the calculations. The geometric parameters including 42 bond lengths and 15 bond angles of these molecules calculated using the planewave DFT method are highly satisfactory, relative to the available experimental data. The error analysis is also performed for 49 formation enthalpies and 138 dissociation energies (including 51 atomization energies as well as the corresponding bond dissociation energies). The results are also compared with the previous data from various atomic-orbital-based methods for molecules and from similar or different planewave DFT methods for various solids and other molecules. This provides an informative and instructive evaluation especially for calculating the large-size material systems containing these small molecules as well as for developing the DFT methods further.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2003

Effect of Molding and Machining on Neoflon CTFE M400H Polychlorotrifluoroethylene Rod Stock and Valve Seat Properties

Since 1997 numerous fires have been reported to the Food and Drug Administration involving cylinder valves installed on medical use oxygen cylinders sold and operated within the United States. All of the cylinder valves in question had polychlorotrifluoroethylene (PCTFE) valve seats. Subsequent failure analysis showed that the main seat was the primary source of ignition. A review of the incidents involving cylinder valve fires indicated three possible ignition mechanisms: contaminant promotion, flow friction, and resonance. However, gas purity analysis showed that uncombusted, residual oxygen was within specification. Infrared and energy dispersive spectroscopy further showed that no contaminants or organic compounds were present in the remaining, uncombusted valve seat material or on seat plug surfaces. Therefore, contaminant-promoted ignition did not appear to be responsible for the failures. Observations of extruded material along the outer edge of the coined or loaded seat area produced by cylinder overuse or poppet overload led to concerns that accelerated gas flow across a deformed seat surface could generate enough localized heating to ignite the polymeric seat. Low molecular weight or highly amorphous quick-quenched PCTFE grades might be expected to be especially prone to this type of deformation. Such a failure mechanism has been described as flow friction; however, the corresponding mechanistic parameters are poorly understood. Subsequent revelation of low-temperature dimensional instability by thermomechanical analysis (TMA) in a variety of PCTFE sheet and rod stock samples led to new concerns that PCTFE valve seats could undergo excessive expansion or contraction during service. During expansion, additional extrusion and accompanying flow friction could occur. During contraction, a gap between the seal and adjacent metal surfaces could form. Gas flowing past the gap could, in turn, lead to resonance heating and subsequent ignition as described in ASTM Guide for Evaluation Nonmetallic Materials for Oxygen Service (G 63). Attempts to uncover the origins of the observed dimensional instability were hindered by uncertainties about resin grade, process history, and post-process heat history introduced by machining, annealing, and sample preparation. An approach was therefore taken to monitor property changes before and after processing and machining using a single, well-characterized lot of Neoflon CTFE.1 M400H resin. A task group consisting of the current PCTFE resin supplier, two molders, and four valve seat manufacturers was formed, and phased testing on raw resin, intermediate rod stock, and finished valve seats initiated. The effect of processing and machining on the properties of PCTFE rod stock and oxygen gas cylinder valve seats was then determined. Testing focused on two types of extruded rod stock and one type of compression-molded rod stock. To accommodate valve seat manufacturer preferences for certain rod stock diameters, two representative diameters were used (4.8 mm (0.1875 in.) and 19.1 mm (0.75 in.)). To encompass a variety of possible sealing configurations, seven different valve seat types with unique geometries or machining histories were tested. The properties investigated were dimensional stability as determined by TMA, specific gravity, differential scanning calorimetry (DSC), compressive strength, zero strength time, and intrinsic viscosity. Findings are discussed in the context of polymer structure-process-property relationships whenever possible.

Waller, Jess M.↗
NASA NTRS1995

Modeling of a possible conformational change associated with the catalytic mechanism in the hammerhead ribozyme

Here we describe a possible model of the cleavage mechanism in the hammerhead ribozyme. In this model, the 2' hydroxyl of C17 is moved into an appropriate orientation for an in-line attack on the G1.1 phosphate through a change in its sugar pucker from C3' endo to C2' endo. This conformational change in the active site is caused by a change in the uridine turn placing the N2 and N3 atoms of G5 of the conserved core in hydrogen bonding geometry with the N3 and N2 atoms on the conserved G16.2 residue. The observed conformational change in the uridine turn suggests an explanation for the conservation of G5. In the crystal structure of H.M. Pley et al., Nature 372, 68-74 (1994), G5 is situated 5.3A away from G16.2. However, the uridine turn is sufficiently flexible to allow this conformational change with relatively modest changes in the backbone torsion angles (average change of 14.2 degrees). Two magnesium ions were modeled into the active site with positions analogous to those described in the functionally similar Klenow fragment 3'-5' exonuclease (L.S. Beese and T.A. Steitz, EMBO J. 10, 25-33 (1991)), the Group I intron (T.A. Steitz and J.A. Steitz, P.N.A.S. U.S.A. 90, 6498-6502 (1993); R.F. Setlik et al., J. Biomol. Str. Dyn. 10, 945-972 (1993)) and other phosphotransferases. Comparison of this model with one in which the uridine turn conformation was not changed showed that although the changes in the C17 sugar pucker could be modeled, insufficient space existed for the magnesium ions in the active site.

Non-NASA Center↗
DOE OSTI2023

NbTaV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution ternary alloys niobium-tantalum-vanadium (Nb-Ta-V). The first-principle code that has been used to run the calculations is the closed-source Vienna Ab-Initio Simulation Package (VASP). The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 8. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 10,500 randomized atomic structures over 105 chemical compositions. The calculations have been collected on NERSC-Perlmutter using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for ternary alloys is AXBYCZ, where A, B, and C refer to the constituents, and X, Y, and Z are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. 0.POSCAR: input file that defines the atomic structure of a system 3. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 4. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 6. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 7. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 8. OUTCARL: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 10. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 11. vasprun.xml: contains similar information to OUTCAR, but in an xml format. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗
NASA NTRS1997

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

NASA Discipline Exobiology↗