Search NASA⌕ Search

SEARCH · Search NASA

Results for “Conformal 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.

At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS1987

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

NASA Discipline Exobiology↗
DOE OSTI2022

Hydration Free Energies of Polypeptides from Popular Implicit Solvent Models versus All-Atom Simulation Results Based on Molecular Quasichemical Theory

Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT)-an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecular solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions and thus provides a convenient framework to investigate the assumptions in implicit solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit solvent models for polyglycine and polyalanine solutes covering a range of chain lengths and conformations. The hydration free energies or the differences in hydration free energies between conformers obtained from the implicit solvent models do not agree with explicit solvent results, with the deviations being largest for the group additive EEF1 and ABSINTH models. GB/SA does better in capturing the qualitative trends seen in explicit solvent results. Finally, analysis founded on QCT reveals the critical importance of the cooperativity of hydration that is inherent in the hydrophilic and hydrophobic contributions to hydration-physics that is not well captured in additive models but somewhat better accounted for by means of a dielectric in the GB/SA approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2019

A Multi-Physics Study on High-Specific Power Li-O2 Batteries for Electric Aircraft

Commercialization of lithium-air batteries faces many challenges, such as electrolyte decomposition, short cycle life, low energy and power density, etc. However, commercialization of Li-O2 batteries for aeronautics is much more challenging due to additional safety constraints on cyclability and performance (high specific power and specific energy). For this presentation, we will discuss inter-related aspects of physics-based modeling of a pack: cell and battery model calibration. In addition, we will evaluate and present optimal battery designs for high discharge current density, high discharge time, and low battery mass using simulation-based optimization.The Finite Element Model (FEM) used to simulate a Li-O2 cell is based on the work of Bevara [1]. The different aspects of the model are based on: porous electrode theory and concentrated electrolyte theory; quantum tunneling model for the resistance of conformal layer of discharge product (Li2O2) [1]; Butler-Volmer kinetics for electrochemical reaction; Fick's diffusion for oxygen transport; and an oxygen dissolution model is applied at the air/electrolyte interface [2]. The electrolyte properties such as ion conductivity, ion diffusion, oxygen diffusion, and mass density of the electrolyte were taken from Molecular Dynamics (MD) simulations [3]; while the other model parameters, which includes mass of cell components, were calibrated to match experiments at high discharge current densities. The cell mass includes the anode, cathode, separator, electrolyte, and other components (such as current collector). This calibrated model is used to perform parametric studies on cathode thickness, porosity, tortuosity, carbon particle size, electrolyte transport and material properties, partial pressure of oxygen, discharge time, and discharge current density to study optimal designs for high specific power and energy. References:1. Bevara, V. & Andrei, P. (2014), J. Electrochem. Soc. 161 (14), A2068-A2079.2.Mehta, M. & Andrei, P. (2015), J. Power Sources. 286, 299-308.3.Liyana-Arachchi, T.; Haskins, J.; Burke, C.; Diederichsen, K.; McCloskey, B.; & Lawson, J. (2018), J. Phys. Chem. B. 122 (36), 8548 - 8559.4.Choi, W.; Kikumoto, H.; Choudhary, R. & Ooka, R. (2018), Applied Energy, 209, 306-321.

Mehta, Mohit↗
NASA NTRS1993

Wind tunnel investigations of forebody strakes for yaw control on F/A-18 model at subsonic and transonic speeds

Wind tunnel investigations have been conducted of forebody strakes for yaw control on 0.06-scale models of the F/A-18 aircraft at free-stream Mach numbers of 0.20 to 0.90. The testing was conducted in the 7- by 10-Foot Transonic Tunnel at the David Taylor Research Center and the Langley 7- by 10-Foot High-Speed Tunnel. The principal objectives of the testing were to determine the effects of the Mach number and the strake plan form on the strake yaw control effectiveness and the corresponding strake vortex induced flow field. The wind tunnel model configurations simulated an actuated conformal strake deployed for maximum yaw control at high angles of attack. The test data included six-component forces and moments on the complete model, surface static pressure distributions on the forebody and wing leading-edge extensions, and on-surface and off-surface flow visualizations. The results from these studies show that the strake produces large yaw control increments at high angles of attack that exceed the effect of conventional rudders at low angles of attack. The strake yaw control increments diminish with increasing Mach number but continue to exceed the effect of rudder deflection at angles of attack greater than 30 degrees. The character of the strake vortex induced flow field is similar at subsonic and transonic speeds. Cropping the strake planform to account for geometric and structural constraints on the F-18 aircraft has a small effect on the yaw control increments at subsonic speeds and no effect at transonic speeds.

Erickson, Gary E.↗
DOE OSTI2021

Anisotropic Coarse-Grained Model for Conjugated Polymers: Investigations into Solution Morphologies

The optoelectronic properties of conjugated polymers are dictated by the interplay of multiscale structural features, including intrachain dihedrals, interchain pi-pi stacking, and the complex mesoscale morphology. While much is known about the structures of polymers with isotropically interacting monomers, little is known about polymers with strongly anisotropic backbone monomers, a class of materials to which conjugated polymers belong. Fundamental understanding is further complicated when the semiflexible and molecularly heterogeneous nature of conjugated polymers is taken into account. We present an anisotropic coarse-grained (CG) model for conjugated polymers that incorporates key molecular features (monomer anisotropy, intermonomer dihedrals, and side chains). Finally, the model is employed to characterize the single-chain conformational properties of conjugated polymers, revealing a rich temperature-dependent conformational landscape. These studies provide a critical link between CG molecular descriptors and conformational ordering in conjugated polymers.

36 MATERIALS SCIENCE↗
NASA NTRS1997

Frozen-Flux Modelling for Epochs 1915 and 1980

The frozen-flux hypothesis for the Earth's liquid core assumes that convective terms dominate diffusive terms in the induction equation governing the behaviour of the magnetic field at the surface of the core. While highly plausible on the basis of estimates of physical parameters, the hypothesis has been questioned. To study this hypothesis, we improve the method which tests the consistency of magnetic observations with the hypothesis by constructing simple, flux-conserving core-field models fitting the data at pairs of epochs. We introduce a new approach that fixes the patch configurations at each of the two epochs before inversion, so that each configuration is consistent with its respective data set but possesses the same patch topology. We expand upon the inversion algorithm, using quadratic programming to maintain the proper flux sign within patches; the modelling calculations are also extended to include data types that depend non-linearly on the model. Every test of a hypothesis depends on the characterization of the observational uncertainties; we undertake a thorough review of this question. For main-field models, the primary source of uncertainty comes from the crustal field. We base our analysis on statistical models of the crustal magnetization, adjusted to bring it into better conformity with our data set. The noise model permits us to take into account the correlations between the measurements and requires that a different weighting be given to horizontal and vertical components. It also indicates that the observations should be fit more closely than has been the practice heretofore. We apply the revised method to Magsat data from 1980 and survey and observatory data from 1915.5, two data sets believed to be particularly difficult to reconcile with the frozen-flux hypothesis. We compute a pair of simple, flux-conserving models that fit the averaged data from each epoch. We therefore conclude that present knowledge of the geomagnetic fields of 1980 and 1915.5 is consistent with the frozen-flux hypothesis.

OBrien, Michael S.↗
NASA NTRS1985

Computers in Aerospace Conference, 5th, Long Beach, CA, October 21-23, 1985, Technical Papers

Among the topics discussed are: access control models for a distributed CAIS-conforming system; a knowledge-based advisory system for casualty procedures; and automated interactive simulation modeling system. Consideration is also given to: reusable software concepts and software development methodologies; the electronic device aspects of neutral network memories; an expert system for automated satellite anomaly resolution; and the use of automatic programming techniques for fault-tolerant computing systems. Among additional topics discussed are: systems approaches to software fault tolerance; a Space Shuttle navigation validation system; and a vision-based road following system for an autonomous land vehicle.

Source record↗
NASA NTRS1990

Obtaining an equivalent beam

In modeling a complex structure the researcher was faced with a component that would have logical appeal if it were modeled as a beam. The structure was a mast of a robot controlled gantry crane. The structure up to this point already had a large number of degrees of freedom, so the idea of conserving grid points by modeling the mast as a beam was attractive. The researcher decided to make a separate problem of of the mast and model it in three dimensions with plates, then extract the equivalent beam properties by setting up the loading to simulate beam-like deformation and constraints. The results could then be used to represent the mast as a beam in the full model. A comparison was made of properties derived from models of different constraints versus manual calculations. The researcher shows that the three-dimensional model is ineffective in trying to conform to the requirements of an equivalent beam representation. If a full 3-D plate model were used in the complete representation of the crane structure, good results would be obtained. Since the attempt is to economize on the size of the model, a better way to achieve the same results is to use substructuring and condense the mast to equivalent end boundary and intermediate mass points.

Butler, Thomas G.↗
DOE OSTI2026

The Molecular Structures of Liquid and Glassy Nifedipine and Felodipine and Their Incorporation into PVP

Background: Amorphous drug formulations are commonly used to improve the solubility and bioavailability of poorly soluble molecular pharmaceuticals, yet less is known about their molecular conformations and local bonding interactions than their crystalline phases. Methods: High-energy X-ray diffraction structure factor measurements have been made on liquid and glassy nifedipine (NIF), felodipine (FEL), NIF 1:3 polyvinylpyrrolidone (PVP), and FEL 1:3 PVP wt.% mixtures. The corresponding X-ray pair distribution functions have been interpreted using empirical potential structure refinement using different models and density functional theory conformer calculations. Results: In both NIF and FEL, the NH···O inter-molecular hydrogen bonds between the pyridyl nitrogen and ester carbonyls are found to be considerably weaker than those observed in the crystalline polymorphs. For nifedipine, it is proposed that either inter-molecular NH…ON nitro bonds are present and/or a fraction (<20%) of conformational changes, with the aryl ring flipped, occur in the liquid state. For felodipine, the models indicate significant disorder associated with the methyl and ethyl side chains in the liquid state, with the main peak intensity at 3.0 Å arising from intra-molecular Cl-Cl atom pairs. When nifedipine molecules are incorporated into PVP, our models show they possess stronger NH···O bonds to the PVP polymer than felodipine molecules, which have stronger affinity for bonding to the polymer than to other felodipine molecules. Conclusions: The amorphous forms of both NIF and FEL show much weaker hydrogen bonding than found in their crystalline phases. Liquid NIF also exhibits configurations which are not observed in the crystal phases.

Amorphous Solid Dispersion↗
DOE OSTI2023

GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production

GRB2 is an adaptor protein required for facilitating cytoplasmic signaling complexes from a wide array of binding partners. GRB2 has been reported to exist in either a monomeric or dimeric state in crystal and solution. GRB2 dimers are formed by the exchange of protein segments between domains, otherwise known as “domain-swapping”. Swapping has been described between SH2 and C-terminal SH3 domains in the full-length structure of GRB2 (SH2/C–SH3 domain-swapped dimer), as well as between α-helixes in isolated GRB2 SH2 domains (SH2/SH2 domain-swapped dimer). Interestingly, SH2/SH2 domain-swapping has not been observed within the full-length protein, nor have the functional influences of this novel oligomeric conformation been explored. We herein generated a model of full-length GRB2 dimer with an SH2/SH2 domain-swapped conformation supported by in-line SEC–MALS–SAXS analyses. This conformation is consistent with the previously reported truncated GRB2 SH2/SH2 domain-swapped dimer but different from the previously reported, full-length SH2/C-terminal SH3 (C–SH3) domain-swapped dimer. Our model is also validated by several novel full-length GRB2 mutants that favor either a monomeric or a dimeric state through mutations within the SH2 domain that abrogate or promote SH2/SH2 domain-swapping. GRB2 knockdown and re-expression of selected monomeric and dimeric mutants in a T cell lymphoma cell line led to notable defects in clustering of the adaptor protein LAT and IL-2 release in response to TCR stimulation. These results mirrored similarly-impaired IL-2 release in GRB2-deficient cells. These studies show that a novel dimeric GRB2 conformation with domain-swapping between SH2 domains and monomer/dimer transitions are critical for GRB2 to facilitate early signaling complexes in human T cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS

Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation of Listeria actin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics.

Sargent, Rachel [Department of Chemistry and Bioch↗
DOE OSTI2021

Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy of solute in solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of conformational entropy of solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal/mol for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

25 ENERGY STORAGE↗
DOE OSTI2023

Comparative Study of High-Resolution LysB29(Nε-myristoyl) des(B30) Insulin Structures Display Novel Dynamic Causal Interrelations in Monomeric-Dimeric Motions

The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic β-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with type 1 diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here, we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 Å resolution at cryogenic temperature. We computationally further investigated our crystal structure’s monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ), obtained at elevated pH, provides electrostatically triggered minor movements in the equilibrium between alternate conformational substates compared to the previous structure, suggesting it might induce an intermediate state in the dissociation pathway of the insulin detemir’s hexamer:dihexamer equilibrium. Supplemented with orientational cross-correlation analysis by a Gaussian network model (GNM), this alternate oligomeric conformation offers the distinct cooperative motions originated by loose coupling of distant conformational substates of a protracted insulin analog that has not been previously observed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Missing components in ΛCDM from DESI Y1 baryonic acoustic oscillation measurements: Insights from redshift remapping

We explore transformations of the Friedman-Lemaître-Robertson-Walker (FLRW) metric and cosmological parameters that align with observational data while aiming to gain insights into potential extensions of standard cosmological models. We modified the FLRW metric by introducing a scaling factor, e 2Θ(a) –the cosmological scaling function (CSF), which alters the standard relationship between cosmological redshift and the cosmic scale factor without affecting angular measurements or cosmic microwave background (CMB) anisotropies. Using data from DESI Year 1, Pantheon+ supernovae, and the Planck CMB temperature power spectrum, we constrained both the CSF and cosmological parameters through a Markov chain Monte Carlo approach. Our results indicate that the CSF model fits observational data with a lower Hubble constant (although it is compatible with the value given by Planck 2018 within 1σ) and is predominantly dark matter dominated. Additionally, the CSF model produces temperature and lensing power spectra similar to those predicted by the standard model, though with lower values in the CSF model at large scales. We also checked that when fitting a CSF model without dark energy to the data, we obtain a more negative conformal function. This suggests that the CSF model may offer hints about missing elements and opens up a new avenue for exploring physical interpretations of cosmic acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Counterions under a Surface-Adsorbed Cationic Surfactant Monolayer: Structure and Thermodynamics

The surface adsorption of ionic surfactants is fundamental for many widespread phenomena in life sciences and for a wide range of technological applications. However, direct atomic-resolution structural experimental studies of noncrystalline surface-adsorbed films are scarce. Thus, even the most central physical aspects of these films, such as their charge density, remain uncertain. Consequently, theoretical models based on contradicting assumptions as for the surface films' ionization are widely used for the description and prediction of surface thermodynamics. We employ X-ray reflectivity to obtain the angstrom Ångström-scale surface-normal structure of surface-adsorbed films of the cationic surfactant cetyltrimethylammonium bromide (CTAB) in aqueous solutions at several different temperatures and concentrations. In conjunction with published neutron reflectivity data, we determine the surface-normal charge distribution due to the dissociated surfactants' headgroups. The distribution appears to be inconsistent with the Gouy-Chapman model yet consistent with a compact Stern layer model of condensed counterions. Here, the experimental surfactant adsorption thermodynamics conforms well to classical, Langmuir and Kralchevsky, adsorption models. Furthermore, the Kralchevsky model correctly reproduces the observed condensation of counterions, allowing the values of the adsorption parameters to be resolved, based on the combination of the present data and the published surface tension measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1972

Influence of a detailed model of man on proton depth/dose calculation

The development of a detailed radiation shielding model of man is discussed. This model will be used to plan for manned space missions in which sensitive human tissues may be subjected to excessive radiation. The model has two configurations: standing and seated. More than 2500 individual elements were used to depict the external conformation, skeleton, and principal organs. The model is briefly described and several examples of its application to mission planning are given.

Kase, P. G.↗