Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structure refinement”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Operando single crystal neutron diffraction reveals insight into the field response mechanisms in the hydrogen-bonded KH 2 PO 4 ferroelectric

The mechanism that facilitates polarization reorientation in KH 2 PO 4 (KDP) was investigated using operando single-crystal neutron diffraction. Diffraction data were measured from a KDP single crystal during the application of alternating electric fields and were then binned into 40 increments to enable field-dependent single-crystal structure refinements. The field-dependent structures are compared with an as-grown crystal to determine how the lattice and atomic sites evolve in response to the applied electric fields. These analyses provide evidence that the reorientation of the macroscopic polarization is facilitated through a cooperative change in hydrogen bonding, which results in the reversal of the spontaneous dipole. In addition, a decrease in secondary extinction near the coercive field indicates that the inversion of the macroscopic polarization is achieved through the nucleation and subsequent growth of new domains.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The Structure of Liquid and Glassy Carbamazepine

To enhance the solubility of orally administered pharmaceuticals, liquid capsules or amorphous tablets are often preferred over crystalline drug products. However, little is known regarding the variation in bonding mechanisms between pharmaceutical molecules in their different disordered forms. In this study, liquid and melt-quenched glassy carbamazepine have been studied using high energy X-ray diffraction and modeled using Empirical Potential Structure Refinement. The results show significant structural differences between the liquid and glassy states. The liquid shows a wide range of structures; from isolated molecules, to aromatic ring correlations and NH-O hydrogen bonding. Upon quenching from the liquid to the glass the number of hydrogen bonds per molecule increases by ~50% at the expense of a ~30% decrease in the close contact (non-bonded) carbon-carbon interactions between aromatic rings. During the cooling process, there is an increase in both singly and doubly hydrogen-bonded adjacent molecules. Although hydrogen-bonded dimers found in the crystalline states persist in the glassy state, the absence of a crystalline lattice also allows small, hydrogen-bonded NH-O trimers and tetramers to form. This proposed model for the structure of glassy carbamazepine is consistent with the results from vibrational spectroscopy and nuclear magnetic resonance.

Benmore, Chris J. (ORCID:0000000170077749)↗
DOE OSTI2025

AUTOIGNITION DELAY TIMES FOR REFORMATE GAS MIXTURES FROM METHANE GAS ENGINES

Methane slip is a prominent issue in natural gas reciprocating engines that are used in transportation and marine applications. The incomplete combustion that results in methane slip can be resolved with the introduction of hydrogen within the combustion mixture to improve methane oxidation and further enable combustion within the engine crevices where methane has previously remained unreacted. Steam methane reforming (SMR) is a common method used to produce hydrogen and can be used to design an onboard device to reduce methane slip from reciprocating engines. The development of this reformer device requires the validation of high-fidelity chemical kinetic models at the low temperatures of the crevice volumes of these engines. In this work, auto-ignition data is obtained using a shock tube at lean (φ—0.714 or λ—1.4) and stoichiometric (φ, λ = 1) equivalence ratios spanning a temperature range of 1042–1234 K at the 80-bar operating pressure of the test engine. Blends of methane, hydrogen, and reformate products from the SMR reaction are shock-heated in synthetic air, with the ignition delay time measured using an OH* chemiluminescence detector at 310 nm and a CH* detector at 430 nm. The experimental results are compared to several state-of-the-art chemical kinetic mechanisms from the literature. In general, most of the mechanisms show very good agreement with experiments at higher temperatures, with simulation results showing little deviation from experiments at lower temperatures. A sensitivity analysis was conducted, and the results reveal that the reaction H2 + CH3O2 = H + CH3O2H has a very significant role in determining low-temperature ignition delay times (IDTs) of SMR mixtures. These findings provide valuable insights into the chemical kinetics governing methane reformate combustion and contribute to the optimization of onboard reformer designs aimed at mitigating methane slip in natural gas-fueled engines.

Fraze, Matthew↗
NASA NTRS1995

An accuracy assessment of Cartesian-mesh approaches for the Euler equations

A critical assessment of the accuracy of Cartesian-mesh approaches for steady, transonic solutions of the Euler equations of gas dynamics is made. An exact solution of the Euler equations (Ringleb's flow) is used not only to infer the order of the truncation error of the Cartesian-mesh approaches, but also to compare the magnitude of the discrete error directly to that obtained with a structured mesh approach. Uniformly and adaptively refined solutions using a Cartesian-mesh approach are obtained and compared to each other and to uniformly refined structured mesh results. The effect of cell merging is investigated as well as the use of two different K-exact reconstruction procedures. The solution methodology of the schemes is explained and tabulated results are presented to compare the solution accuracies.

Coirier, William J.↗
DOE OSTI2026

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗
DOE OSTI2021

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

AMReX: Block-structured adaptive mesh refinement for multiphysics applications

Block-structured adaptive mesh refinement (AMR) provides the basis for the temporal and spatial discretization strategy for a number of Exascale Computing Project applications in the areas of accelerator design, additive manufacturing, astrophysics, combustion, cosmology, multiphase flow, and wind plant modeling. AMReX is a software framework that provides a unified infrastructure with the functionality needed for these and other AMR applications to be able to effectively and efficiently utilize machines from laptops to exascale architectures. AMR reduces the computational cost and memory footprint compared to a uniform mesh while preserving accurate descriptions of different physical processes in complex multiphysics algorithms. AMReX supports algorithms that solve systems of partial differential equations in simple or complex geometries and those that use particles and/or particle–mesh operations to represent component physical processes. In this article, we will discuss the core elements of the AMReX framework such as data containers and iterators as well as several specialized operations to meet the needs of the application projects. In addition, we will highlight the strategy that the AMReX team is pursuing to achieve highly performant code across a range of accelerator-based architectures for a variety of different applications.

Zhang, Weiqun↗
DOE OSTI2022

The structure of sc16 GaP obtained at 17.5 GPa and 1400 K

We report using a laser-heated diamond anvil cell, a powdered sample of gallium phosphide was compressed to 17.5 GPa and heated up to 1400 K. The material obtained was characterized at room temperature using synchrotron x-ray diffraction. Experimental results were compared with first-principles calculations. The polymorph observed assumes the simple cubic structure (sc16) initially reported for GaAs at high pressures. Microdiffraction mapping showed variable grain sizes of the synthesized phase, with the largest grains located in the middle of the heated spot. Structural refinements were performed on selected grains. The structure predicted based on first-principles calculations is in close agreement with the experiments. The two Ga–P bonds show similar lengths in sc16-GaP; however, the bond angles differ, resulting in a distorted tetrahedral coordination geometry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Structure and electronic tunability of acene alkylamine based layered hybrid organic-inorganic perovskites from first principles

Twelve layered hybrid organic-inorganic perovskites combining oligoacene derivatives [phenylmethylammonium (PMA), naphthylmethylammonium (NMA), anthrylmethylammonium (AMA), and tetrylmethylammonium (TMA)] and lead halides (Cl - , Br - , and I - anions) are investigated by first-principles density functional theory (DFT), showing broad, rational tunability of band gap, quantum well type, and spin-dependent energy band properties. Six compounds are known from previous syntheses and are used to devise a computational search space for likely low-energy structures. Among the six known compounds, a refined structure is identified for (NMA) 2 ⁢ PbCl 4 and a new, lower-energy structure is suggested for (AMA) 2 ⁢PbCl 4 . The DFT based search methodology is next applied to predict the likely structures for the six unknown compounds. Computationally predicted energy levels for all 12 compounds from spin-orbit coupled hybrid DFT reveal tunable type I quantum well alignments, with frontier orbitals located on the inorganic component, on the organic component, or on both, as controlled by cation and anion selection. In conclusion, several structures spontaneously break local and global inversion symmetry, causing strong spin splitting of the conduction bands [up to 0.12 eV for (PMA) 2 ⁢PbCl 4 ] and showing potential for spin-dependent transport properties and future spintronic and tunable chiroptical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure↗
DOE OSTI2020

A Possible Radiation-Induced Transition from Monazite-(Ce) to Xenotime-(Y)

This study examines two pegmatitic monazite samples (2a and 4b, these numbers are related to a previous study) to determine their crystal chemistry and effects of internal radiation damage using synchrotron high-resolution powder X-ray diffraction and electron-probe micro-analysis. Both the huttonite and cheralite substitutions are discussed. Rietveld structure refinement of sample 2a shows three different phases [2a = monazite-(Ce), 2b = monazite-(Ce), and 2c = xenotime-(Y)] with distinct structural parameters. The changes among the unit-cell parameters between the two monazite-(Ce) phases is more pronounced in the a followed by the b and c unit-cell parameters. Sample 4a is a single-phase monazite-(Sm) that contains 0.164 apfu Th. Phase 2c with space group I41/amd arises from redistribution of La, Ce, Pr, Nd, Sm, Gd, Dy, Si, and Y atoms from those in monazite (space group P21/n). A possible cause for the phase transition from monazite-(Ce) to xenotime-(Y) is α-radiation events over a long geological time. However, other chemical processes cannot be ruled out as a cause for the transition.

structural variations↗
NASA NTRS1993

An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

Lemke, Max↗
NASA NTRS2007

Topology Synthesis of Structures Using Parameter Relaxation and Geometric Refinement

Typically, structural topology optimization problems undergo relaxation of certain design parameters to allow the existence of intermediate variable optimum topologies. Relaxation permits the use of a variety of gradient-based search techniques and has been shown to guarantee the existence of optimal solutions and eliminate mesh dependencies. This Technical Publication (TP) will demonstrate the application of relaxation to a control point discretization of the design workspace for the structural topology optimization process. The control point parameterization with subdivision has been offered as an alternative to the traditional method of discretized finite element design domain. The principle of relaxation demonstrates the increased utility of the control point parameterization. One of the significant results of the relaxation process offered in this TP is that direct manufacturability of the optimized design will be maintained without the need for designer intervention or translation. In addition, it will be shown that relaxation of certain parameters may extend the range of problems that can be addressed; e.g., in permitting limited out-of-plane motion to be included in a path generation problem.

Hull, P. V.↗
DOE OSTI2022

Ferromagnetic MnBi 4 Te 7 obtained with low-concentration Sb doping: A promising platform for exploring topological quantum states

The tuning of the magnetic phase, chemical potential, and structure is crucial to observe diverse exotic topological quantum states in Mn Bi 2 Te 4 (Bi 2 Te 3 ) m (m = 0–3). Here we show a ferromagnetic (FM) phase with a chiral crystal structure in Mn (Bi 1–x Sb x ) 4 Te 7 , obtained via tuning the growth conditions and Sb concentration. Unlike previously reported Mn (Bi 1–x Sb x ) 4 Te 7 , which exhibits FM transitions only at high Sb doping levels, our samples show FM transitions (T C = 13.5 K) at 15%–27% doping levels. Furthermore, our single-crystal x-ray-diffraction structure refinements find Sb doping leads to a chiral structure with the space group of P3, contrasted with the centrosymmetric $P\bar{3}m1$ crystal structure of the parent compound MnBi 4 Te 7 . Through angle-resolved photoemission spectroscopy measurements, we also demonstrated that the nontrivial band topology is preserved in the Sb-doped FM samples. Given that the nontrivial band topology of this system remains robust for low Sb doping levels, our success in making FM Mn(Bi 1–x Sb x ) 4 Te 7 with x = 0.15, 0.175, 0.2, and 0.27 paves the way for realizing the predicted topological quantum states, such as the axion insulator and Weyl semimetals. Additionally, we also observed magnetic glassy behavior in both antiferromagnetic MnBi 4 Te 7 and FM Mn (Bi 1–x Sb x )4 Te 7 samples, which we believe originates from cluster spin-glass phases coexisting with long-range antiferromagnetic/FM orders. Further, we have also discussed how the antisite Mn ions impact the interlayer magnetic coupling and how FM interlayer coupling is stabilized in this system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Mechanical properties of zeolite-templated carbons from approximate density functional theory calculations

Zeolite-templated carbon (ZTC) is a unique porous carbonaceous material whose structure is ordered at the nanometre scale, enabling a representative periodic description at the atomistic level. Utilizing an existing, well-defined reference model for ZTCs, a structural library of varying compositions was developed by refinement using density-functional tight-binding (DFTB) potentials parameterized for materials science applications. We first determined the quantum chemical-refined structures of models with CH, CHO, CHON, CHOB, and CHOBN compositions with various degrees of heteroatom substitution. These structural models comprise the characteristic morphological features of highly porous carbon materials, such as open-blade surfaces, edges, saddles, and closed-strut formations, spanning a range of curvatures and characteristic sizes. Second, we carried out alternating compression and expansion of the CHO model unit cell to determine the lowest energy structure as well as to obtain its bulk modulus in order to demonstrate a close connection between macroscopic observations and atomic-scale structures. Further, the agreement between experimental measurements and the computational model is remarkable and demonstrates the power of approximate density functional theory as a cost-effective computational tool with chemical accuracy for the investigation of structure/property relationships in real-world carbon-based solids.

03 NATURAL GAS↗
DOE OSTI2024

Hydrogen Bonding in Amorphous Indomethacin

Amorphous Indomethacin has enhanced bioavailability over its crystalline forms, yet amorphous forms can still possess a wide variety of structures. Here, Empirical Potential Structure Refinement (EPSR) has been used to provide accurate molecular models on the structure of five different amorphous Indomethacin samples, that are consistent with their high-energy X-ray diffraction patterns. It is found that the majority of molecules in amorphous Indomethacin are non-bonded or bonded to one neighboring molecule via a single hydrogen bond, in contrast to the doubly bonded dimers found in the crystalline state. The EPSR models further indicate a substantial variation in hydrogen bonding between different amorphous forms, leading to a diversity of chain structures not found in any known crystal structures. The majority of hydrogen bonds are associated with the carboxylic acid group, although a significant number of amide hydrogen bonding interactions are also found in the models. Evidence of some dipole–dipole interactions are also observed in the more structurally ordered models. The results are consistent with a distribution of Z-isomer intramolecular type conformations in the more disordered structures, that distort when stronger intermolecular hydrogen bonding occurs. The findings are supported by 1H and 2H NMR studies of the hydrogen bond dynamics in amorphous Indomethacin.

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

Boosted piezoelectricity with excellent thermal stability in tetragonal NaNbO 3 -based ceramics

The realization of high piezoelectric performance and excellent temperature stability simultaneously in Pb-free ceramics is the key for replacing Pb-containing perovskites in the industry. In this study, large piezoelectric performance (d 33 = 354 pC N –1 ) was achieved in a wide temperature sinterable potassium-free NaNbO 3 –BaTiO 3 –BaSnO 3 system, which is twice more than the piezoelectricity found in NaNbO 3 –BaTiO 3 binary ceramics. Structural refinement of high-energy synchrotron powder diffraction data suggests a single tetragonal structure with P4bm symmetry for the studied NaNbO 3 -based Pb-free ceramic. The results indicate that the small axial ratio favoring polarization reorientation benefits strong piezoelectricity, while the large oxygen octahedron tilt enhances the stability of the P4bm structure during the changing temperature according to the in situ high-energy synchrotron X-ray diffraction measurements and provides the foundation for the excellent thermal stability (20–100 °C) of the piezoelectric properties. Furthermore, a single tetragonal phase with a tiny axial ratio and large oxygen octahedron tilt effectively balances the piezoelectricity and thermal stability in Pb-free systems.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Composite theory applied to elastomers

Reinforced elastomers form the basis for most of the structural or load carrying applications of rubber products. Computer based structural analysis in the form of finite element codes was highly successful in refining structural design in both isotropic materials and rigid composites. This has lead the rubber industry to attempt to make use of such techniques in the design of structural cord-rubber composites. While such efforts appear promising, they were not easy to achieve for several reasons. Among these is a distinct lack of a clearly defined set of material property descriptors suitable for computer analysis. There are substantial differences between conventional steel, aluminum, or even rigid composites such as graphite-epoxy, and textile-cord reinforced rubber. These differences which are both conceptual and practical are discussed.

Clark, S. K.↗