SEARCH · Search NASA
Results for “Structural models”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
What are the current limits on determination of protonation state using neutron macromolecular crystallography?
The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. Here, we observe and discuss systematic map quality deterioration as result of data incompleteness.
Weak data do not make a free lunch, only a cheap meal
Refinement and analysis of four structures with various data resolution cutoffs suggests that at present there are no reliable criteria for judging the diffraction data resolution limit and the condition I/σ(I) = 2.0 is reasonable. However, extending the limit by about 0.2 Å beyond the resolution defined by this threshold does not deteriorate the quality of refined structures and in some cases may be beneficial. Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as R{sub merge} and I/σ(I), optical resolution and the correlation coefficients CC{sub 1/2} and CC*, can be used for judging the internal data quality, whereas the reliability factors R and R{sub free} as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where the I/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.
Atomistic simulation and ab initio study of the defect structure of spinel-related Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}
Graphical abstract: Unit cell of Li0{sub 5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}, showing the lowest energy structure obtained using interatomic potential and DFT ab initio calculations. Large white spheres O{sup 2−}; small light grey spheres Mg{sup 2+} (evenly substituting of Li{sup +} and Fe{sup 3+} at octahedral sites); small dark grey spheres Fe{sup 3+}; small black spheres Li{sup +}. Display Omitted Highlights: ► Defect structure of Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−x}O{sub 4} is studied with atomistic and DFT methods. ► 19 possible defect structure models with ∼60 defect configurations are investigated. ► The most favourable model found is when Mg{sup 2+} ions evenly replace Li{sup +} and octahedral Fe{sup 3+}. ► This defect structure decreases the magnetisation relative to that of Li{sub 0.5}Fe{sub 2.5}O{sub 4}. ► Experimentally-deduced models, at variance with the one obtained here, are discussed. -- Abstract: The position of magnesium ions in Mg{sup 2+}-doped lithium ferrite of the composition Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}, which has been a matter of uncertainty among some experimentalists, is investigated using interatomic potential and ab initio DFT calculations. Among possible 19 defect structure models, some of which have been reported experimentally to be the most favorable, the lowest energy is found for Mg{sup 2+} ions evenly replacing Li{sup +} and Fe{sup 3+} ion on octahedral sites. This gives a decrease in magnetisation for the Mg{sup 2+}-doped ferrite relative to the un-doped lithium ferrite. The results suggest that some experimental observations of increased magnetisation of spinel lithium ferrite on Mg{sup 2+}-doping could be due to substitution of Mg{sup 2+} or Li{sup +} on tetrahedral sites at the high temperatures used in preparation of the solid and/or the presence of undetected defects in the initial precursors.
The crystal structure of a new calcium aluminate phase containing formate
A new calcium aluminate phase containing formate ions was synthesized and its crystal structure determined. This new phase is indicated as M-phase and was firstly observed in Portland cement pastes hydrated in presence of Ca-formate and in excess of water. The crystal structure of the M-phase was successfully solved in the R-3 space group of the trigonal system on the basis of synchrotron X-ray single crystal diffraction data. The structural model was confirmed by Rietveld refinement of the powder diffraction data acquired on the synthesized pure sample. The crystal structure of the M-phase is similar to that of ettringite, being characterized by columns of AlO{sub 6} octahedra alternating with groups of three edge-sharing CaO{sub 7} polyhedra. The formate ions (HCOO){sup −} share two oxygens with Ca polyhedra and are located in the interspace between the columns. The crystal structure of the M-phase testifies the strong interaction occurring between small organic molecules as formate and the calcium aluminate components of Portland cement.
Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach
A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.
Identification of a Novel Drug Lead That Inhibits HCV Infection and Cell-to-Cell Transmission by Targeting the HCV E2 Glycoprotein
We report that Hepatitis C Virus (HCV) infects 200 million individuals worldwide. Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin. Recently, two crystal structures of the core of the HCV E2 protein (E2c) have been determined, providing structural information that can now be used to target the E2 protein and develop drugs that disrupt the early stages of HCV infection by blocking E2’s interaction with different host factors. Using the E2c structure as a template, we have created a structural model of the E2 protein core (residues 421–645) that contains the three amino acid segments that are not present in either structure. Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction. We used surface plasmon resonance detection to screen the ligand set for binding to recombinant E2 protein, and the best binders were subsequently tested to identify compounds that inhibit the infection of Huh-7 cells by HCV. One compound, 281816, blocked E2 binding to CD81 and inhibited HCV infection in a genotype-independent manner with IC50’s ranging from 2.2 µM to 4.6 µM. 281816 blocked the early and late steps of cell-free HCV entry and also abrogated the cell-to-cell transmission of HCV. Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.
Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders
We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural model of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.
Beta decay rates of neutron-rich nuclei
Heavy element nucleosynthesis models involve various properties of thousands of nuclei in order to simulate the intricate details of the process. By necessity, as most of these nuclei cannot be studied in a controlled environment, these models must rely on the nuclear structure models for input. Of all the properties, the beta-decay half-lives are one of the most important ones due to their direct impact on the resulting abundance distributions. Currently, a single large-scale calculation is available based on a QRPA calculation with a schematic interaction on top of the Finite Range Droplet Model. In this study we present the results of a large-scale calculation based on the relativistic nuclear energy density functional, where both the allowed and the first-forbidden transitions are studied in more than 5000 neutron-rich nuclei.
Global energy sector emission reductions and bioenergy use: overview of the bioenergy demand phase of the EMF-33 model comparison
We present an overview of results from 11 integrated assessment models (IAMs) that participated in the 33rd study of the Stanford Energy Modeling Forum (EMF-33) on the viability of large-scale deployment of bioenergy for achieving long-run climate goals. The study explores future bioenergy use across models under harmonized scenarios for future climate policies, availability of bioenergy technologies, and constraints on biomass supply. This paper provides a more transparent description of IAMs that span a broad range of assumptions regarding model structures, energy sectors, and bioenergy conversion chains. Without emission constraints, we find vastly different CO 2 emission and bioenergy deployment patterns across models due to differences in competition with fossil fuels, the possibility to produce large-scale bio-liquids, and the flexibility of energy systems. Imposing increasingly stringent carbon budgets mostly increases bioenergy use. A diverse set of available bioenergy technology portfolios provides flexibility to allocate bioenergy to supply different final energy as well as remove carbon dioxide from the atmosphere by combining bioenergy with carbon capture and sequestration (BECCS). Sector and regional bioenergy allocation varies dramatically across models mainly due to bioenergy technology availability and costs, final energy patterns, and availability of alternative decarbonization options. Although much bioenergy is used in combination with CCS, BECCS is not necessarily the driver of bioenergy use. We find that the flexibility to use biomass feedstocks in different energy sub-sectors makes large-scale bioenergy deployment a robust strategy in mitigation scenarios that is surprisingly insensitive with respect to reduced technology availability. However, the achievability of stringent carbon budgets and associated carbon prices is sensitive. Constraints on biomass feedstock supply increase the carbon price less significantly than excluding BECCS because carbon removals are still realized and valued. Incremental sensitivity tests find that delayed readiness of bioenergy technologies until 2050 is more important than potentially higher investment costs.
Modification of Quark-Gluon Distributions in Nuclei by Correlated Nucleon Pairs
We extend the QCD Parton Model analysis using a factorized nuclear structure model incorporating individual nucleons and pairs of correlated nucleons. Our analysis of high-energy data from lepton deep-inelastic scattering, Drell-Yan, and W and Z boson production simultaneously extracts the universal effective distribution of quarks and gluons inside correlated nucleon pairs, and their nucleus-specific fractions. Such successful extraction of these universal distributions marks a significant advance in our understanding of nuclear structure properties connecting nucleon- and parton-level quantities. Published by the American Physical Society 2024
Beta decay rates of neutron-rich nuclei
Heavy element nucleosynthesis models involve various properties of thousands of nuclei in order to simulate the intricate details of the process. By necessity, as most of these nuclei cannot be studied in a controlled environment, these models must rely on the nuclear structure models for input. Of all the properties, the beta-decay half-lives are one of the most important ones due to their direct impact on the resulting abundance distributions. In this study we present the results of a large-scale calculation based on the relativistic nuclear energy density functional, where both the allowed and the first-forbidden transitions are studied in more than 5000 neutron-rich nuclei. Aside from the astrophysical applications, the results of this calculation can also be employed in the modeling of the electron and antineutrino spectra from nuclear reactors.
Determining the ballistic threshold velocity for a composite structure using multiple failure models
A composite structure, such as a laminated composite panel, for example, comprises one or more layers or “plies” embedded in a matrix material or otherwise fixed together in an arrangement, commonly referred to as a “stack up.” Each material in the structure has a corresponding material failure model (MFM) defining the physical characteristics of that material. A ballistic threshold velocity computing device obtains the MFMs for each material in the composite structure, generates a predicted ballistic velocity threshold velocity for each MFM, and then generates a parametric model to compute a composite ballistic velocity threshold velocity for the composite structure.
Hydrothermal synthesis and crystal structure of a new lithium copper bismuth oxide, LiCuBiO{sub 4}
A new lithium copper bismuth oxide, LiCuBiO{sub 4} was prepared by hydrothermal reaction using NaBiO{sub 3}0.1*4H{sub 2}O. The crystal structural model of this compound was refined by using synchrotron X-ray powder diffraction data. This bismuthate has the LiCuSbO{sub 4} related structure with the orthorhombic cell (Space group: Pnma) of a=10.9096(9), b=5.8113(5) and c=5.0073(4) Å, and the final R-factors were R{sub wp}=4.84 and R{sub p}=3.58%. This compound is the first example of a lithium copper bismuthate containing Bi{sup 5+}. An antiferromagnetic ordering of Cu{sup 2+} moment was observed at 6 K. - Graphical abstract: In the crystal structure of LiCuBiO{sub 4} all metal atoms are coordinated octahedrally by six O atoms and LiO{sub 6} and CuO{sub 6} octahedra form the one-dimensional chains by edge-sharing along the b-axis. The LiO{sub 6} and CuO{sub 6} chains form the layer by face-sharing in the bc plane. The Bi atoms are placed in that interlayer and BiO{sub 6} octahedra are edge-sharing with LiO{sub 6} and CuO{sub 6} octahedra. - Highlights: • A new lithium copper bismuth oxide, LiCuBiO{sub 4} is prepared by hydrothermal reaction. • The crystal structure of LiCuBiO{sub 4} is closely related with that of LiCuSbO{sub 4}. • This new compound exhibits an antiferromagnetic ordering of Cu{sup 2+} moment at 6 K.
Combining Experimental and Theoretical Techniques to Gain an Atomic Level Understanding of the Defect Binding Mechanism in Hard Carbon Anodes for Sodium Ion Batteries
Sodium ion batteries (NIBs) are an attractive alternative to lithium–ion batteries in applications that require large–scale energy storage due to sodium's high natural abundance and low cost. Hard carbon (HC) is the most promising anode material for NIBs; however, there is a knowledge gap in the understanding of the sodium binding mechanism that prevents a rational design of HC. This study tunes sucrose–derived HC via synthesis temperature then evaluates the structural, physical, and electrochemical properties. Neutron total scattering is used to generate structural models by fitting pair distribution functions (PDF) with a combination of molecular dynamics and reverse Monte Carlo methods. From this model, the number and type of structural features are identified, quantified, and correlated to the galvanostatic charge/discharge. A method of PDF “fingerprinting” binding sites using Na probe atoms is developed and analyzing these PDFs reveals an atomistic view of ion binding sites responsible for “defect” storage mechanisms. Combining these techniques results in an atomic–level study that provides a big picture of the Na–binding mechanism in NIBs, which allows for more precise tuning of the structure–property relationships in the future. Finally, the methodologies developed will also enable new strategies for the analysis of amorphous functional materials.
Uncertainty in Simulating Wheat Yields Under Climate Change
Anticipating the impacts of climate change on crop yields is critical for assessing future food security. Process-based crop simulation models are the most commonly used tools in such assessments1,2. Analysis of uncertainties in future greenhouse gas emissions and their impacts on future climate change has been increasingly described in the literature3,4 while assessments of the uncertainty in crop responses to climate change are very rare. Systematic and objective comparisons across impact studies is difficult, and thus has not been fully realized5. Here we present the largest coordinated and standardized crop model intercomparison for climate change impacts on wheat production to date. We found that several individual crop models are able to reproduce measured grain yields under current diverse environments, particularly if sufficient details are provided to execute them. However, simulated climate change impacts can vary across models due to differences in model structures and algorithms. The crop-model component of uncertainty in climate change impact assessments was considerably larger than the climate-model component from Global Climate Models (GCMs). Model responses to high temperatures and temperature-by-CO2 interactions are identified as major sources of simulated impact uncertainties. Significant reductions in impact uncertainties through model improvements in these areas and improved quantification of uncertainty through multi-model ensembles are urgently needed for a more reliable translation of climate change scenarios into agricultural impacts in order to develop adaptation strategies and aid policymaking.
Age and structure of a model vapour-deposited glass
Glass films prepared by a process of physical vapour deposition have been shown to have thermodynamic and kinetic stability comparable to those of ordinary glasses aged for thousands of years. A central question in the study of vapour-deposited glasses, particularly in light of new knowledge regarding anisotropy in these materials, is whether the ultra-stable glassy films formed by vapour deposition are ever equivalent to those obtained by liquid cooling. Here we present a computational study of vapour deposition for a two-dimensional glass forming liquid using a methodology, which closely mimics experiment. We find that for the model considered here, structures that arise in vapour-deposited materials are statistically identical to those observed in ordinary glasses, provided the two are compared at the same inherent structure energy. We also find that newly deposited hot molecules produce cascades of hot particles that propagate far into the film, possibly influencing the relaxation of the material.
X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex
Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.