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

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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering

Abstract IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Science & Technology - Other Topics↗
DOE OSTI2024

Effective many-body interactions in reduced-dimensionality spaces through neural network models

Accurately describing properties of challenging problems in physical sciences often requires complex mathematical models that are unmanageable to tackle head on. Therefore, developing reduced-dimensionality representations that encapsulate complex correlation effects in many-body systems is crucial to advance the understanding of these complicated problems. However, a numerical evaluation of these predictive models can still be associated with a significant computational overhead. To address this challenge, in this paper we discuss a combined framework that integrates recent advances in the development of active-space representations of coupled cluster (CC) downfolded Hamiltonians with neural network approaches. The primary objective of this effort is to train neural networks to eliminate the computationally expensive steps required for evaluating hundreds or thousands of Hugenholtz diagrams, which correspond to multidimensional tensor contractions necessary for evaluating a many-body form of downfolded effective Hamiltonians. Using small molecular systems (the H 2 O and HF molecules) as examples, we demonstrate that training neural networks employing effective Hamiltonians for a few nuclear geometries of molecules can accurately interpolate or extrapolate their forms to other geometrical configurations characterized by different intensities of correlation effects. We also discuss differences between effective interactions that define CC downfolded Hamiltonians with those of bare Hamiltonians defined by Coulomb interactions in the active spaces. Published by the American Physical Society 2024

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Planar 2D wireframe DNA origami

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2008

Simplified Modeling of Oxidation of Hydrocarbons

A method of simplified computational modeling of oxidation of hydrocarbons is undergoing development. This is one of several developments needed to enable accurate computational simulation of turbulent, chemically reacting flows. At present, accurate computational simulation of such flows is difficult or impossible in most cases because (1) the numbers of grid points needed for adequate spatial resolution of turbulent flows in realistically complex geometries are beyond the capabilities of typical supercomputers now in use and (2) the combustion of typical hydrocarbons proceeds through decomposition into hundreds of molecular species interacting through thousands of reactions. Hence, the combination of detailed reaction- rate models with the fundamental flow equations yields flow models that are computationally prohibitive. Hence, further, a reduction of at least an order of magnitude in the dimension of reaction kinetics is one of the prerequisites for feasibility of computational simulation of turbulent, chemically reacting flows. In the present method of simplified modeling, all molecular species involved in the oxidation of hydrocarbons are classified as either light or heavy; heavy molecules are those having 3 or more carbon atoms. The light molecules are not subject to meaningful decomposition, and the heavy molecules are considered to decompose into only 13 specified constituent radicals, a few of which are listed in the table. One constructs a reduced-order model, suitable for use in estimating the release of heat and the evolution of temperature in combustion, from a base comprising the 13 constituent radicals plus a total of 26 other species that include the light molecules and related light free radicals. Then rather than following all possible species through their reaction coordinates, one follows only the reduced set of reaction coordinates of the base. The behavior of the base was examined in test computational simulations of the combustion of heptane in a stirred reactor at various initial pressures ranging from 0.1 to 6 MPa. Most of the simulations were performed for stoichiometric mixtures; some were performed for fuel/oxygen mole ratios of 1/2 and 2.

Bellan, Josette↗
DOE OSTI2024

Utilizing Quantum Cascade Lasers for Ultranarrow Velocity Resolution and Quantum-State Selectivity in Molecular Beam Scattering and Spectroscopy

Here, we demonstrate the capability of a narrow linewidth quantum cascade laser (QCL) to selectively excite a very narrow velocity range of nitric oxide (σ ≤ 7(3) m/s) with a pure ro-vibrational quantum state. By implementing a counter-propagating geometry, the molecules are selectively excited according to the Doppler shift of the ro-vibrational transition frequency such that the velocity width associated with the excited molecules depends only on the QCL linewidth. We demonstrate a velocity distribution limited by the effective linewidth of our free-running QCL (Γ = 3.2 MHz). Our development provides a cost-effective, flexible approach to resolve quantum-state selective chemical dynamics with excellent velocity resolution in a wide variety of molecules with infrared-active transitions. This technique has been formulated to provide ultrahigh collisional energy resolution in molecular beams to delineate final quantum-state product pairs in studies of molecular collisions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Superhydrophilicity of $α$-alumina surfaces results from tight binding of interfacial waters to specific aluminols

Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Here, contact angles at the alumina (0001) and ($11\bar{2}0$) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

On the performance of composite schemes in determining equilibrium molecular structures

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

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

How Rh surface breaks CO 2 molecules under ambient pressure

Utilization of carbon dioxide (CO 2 ) molecules leads to increased interest in the sustainable synthesis of methane (CH 4 ) or methanol (CH 3 OH). The representative reaction intermediate consisting of a carbonyl or formate group determines yields of the fuel source during catalytic reactions. However, their selective initial surface reaction processes have been assumed without a fundamental understanding at the molecular level. Here, we report direct observations of spontaneous CO 2 dissociation over the model rhodium (Rh) catalyst at 0.1 mbar CO 2 . The linear geometry of CO 2 gas molecules turns into a chemically active bent-structure at the interface, which allows non-uniform charge transfers between chemisorbed CO 2 and surface Rh atoms. By combining scanning tunneling microscopy, X-ray photoelectron spectroscopy at near-ambient pressure, and computational calculations, we reveal strong evidence for chemical bond cleavage of O-CO* with ordered intermediates structure formation of (2 × 2)-CO on an atomically flat Rh(111) surface at room temperature.

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

Cooperative effect of local active stresses on the macroscopic contractility of elastic fiber networks

The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, in this study, we investigate how the macroscopic boundary stress in model elastic fiber networks depends on the number and nature of embedded contractile units, each exerting an isotropic force dipole, as well as on the bending stiffness of fibers. We find that the macroscopic stress increases nonlinearly with the number of dipoles due to mutual stiffening of initially soft, bending-dominated networks. Using effective medium theory, we relate this enhanced contractility to an increase in the effective average network coordination number due to constraints imposed by the force dipoles. By comparing three distinct force dipole models that differ in their local structures, we demonstrate that the specific manner in which an active unit constrains the network strongly influences the onset and nature of the stiffening transition. Our results highlight that not only the quantity but also the local geometry of force-generating units critically determines the macroscopic mechanical behavior. This framework provides a physical basis for understanding how biological systems—such as molecular motors in the cytoskeleton, or adherent cells in the extracellular matrix—can modulate network-scale nonlinear elastic properties through local tuning of active force-generating units.

Biological and medical sciences↗
DOE OSTI2020

Polymorphous nature of cubic halide perovskites

Many common crystal structures can be described by a single (or very few) repeated structural motif (“monomorphous structures”) such as octahedron in cubic halide perovskites. Interestingly, recent accumulated evidence suggests that electronic structure calculations based on such macroscopically averaged monomorphous cubic ($\textit{Pm} – 3m$) halide perovskites obtained from x-ray diffraction, show intriguing deviations from experiment. These include systematically too small band gaps, dielectric constants dominated by the electronic, negative mixing enthalpy of alloys, and significant deviations from the measured pair distribution function. We show here that a minimization of the systems $\textit{T}$ = 0 internal energy via density functional theory reveals a distribution of different low-symmetry local motifs, including tilting, rotations, and B-atom displacements (“polymorphous networks”). This is found only if one allows for larger-than-minimal cell size that does not geometrically exclude low symmetry motifs. As the (super) cell size increases, the energy is lowered relative to the monomorphous cell, and stabilizes after ~32 formula units (≥160 atoms) are included. Being a result of nonthermal energy minimization in the internal energy without entropy, this correlated set of displacements must represent the intrinsic geometry preferred by the underlying chemical bonding (lone pair bonding), and as such has a different origin than the normal, dynamic thermal disorder modeled by molecular dynamics. Indeed, the polymorphous network, not the monomorphous ansatz, is the kernel structure from which high temperature thermal agitation develops. The emerging physical picture is that the polymorphous network has an average structure with high symmetry, yet the local structural motifs have low symmetries. In this work we find that, compared with monomorphous counterparts, the polymorphous networks have significantly lower predicted total energies, larger band gaps, and ionic dominated dielectric constants, and agree much more closely with the observed pair distribution functions. An analogous polymorphous situation is found in the paraelectric phase of a few cubic oxide perovskites where local polarization takes the role of local displacements in halide perovskites, and in the paramagnetic phases of a few 3 d oxides where the local spin configuration takes that role.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Materials Data on H9Au(ClO)4 by Materials Project

AuCl4(H2O)2H5O2 crystallizes in the triclinic P1 space group. The structure is zero-dimensional and consists of one molecular hydrogen;dihydrate molecule, two water molecules, and one AuCl4 cluster. In the AuCl4 cluster, Au3+ is bonded in a rectangular see-saw-like geometry to four Cl1- atoms. There are one shorter (2.31 Å) and three longer (2.32 Å) Au–Cl bond lengths. There are four inequivalent Cl1- sites. In the first Cl1- site, Cl1- is bonded in a single-bond geometry to one Au3+ atom. In the second Cl1- site, Cl1- is bonded in a single-bond geometry to one Au3+ atom. In the third Cl1- site, Cl1- is bonded in a single-bond geometry to one Au3+ atom. In the fourth Cl1- site, Cl1- is bonded in a single-bond geometry to one Au3+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Fe2S3O23 by Materials Project

FeSO7Fe(SO6)2(O2)2 crystallizes in the triclinic P-1 space group. The structure is zero-dimensional and consists of four molecular oxygen molecules, two Fe(SO6)2 clusters, and two FeSO7 clusters. In each Fe(SO6)2 cluster, Fe is bonded in a 5-coordinate geometry to five O atoms. There are a spread of Fe–O bond distances ranging from 1.86–2.41 Å. There are two inequivalent S sites. In the first S site, S is bonded in a tetrahedral geometry to four O atoms. There is three shorter (1.47 Å) and one longer (1.54 Å) S–O bond length. In the second S site, S is bonded in a tetrahedral geometry to four O atoms. There are a spread of S–O bond distances ranging from 1.46–1.54 Å. There are twelve inequivalent O sites. In the first O site, O is bonded in a single-bond geometry to one S atom. In the second O site, O is bonded in a 2-coordinate geometry to one Fe and one O atom. The O–O bond length is 1.30 Å. In the third O site, O is bonded in a single-bond geometry to one S atom. In the fourth O site, O is bonded in a single-bond geometry to one O atom. The O–O bond length is 1.24 Å. In the fifth O site, O is bonded in a single-bond geometry to one S atom. In the sixth O site, O is bonded in a bent 120 degrees geometry to one Fe and one S atom. In the seventh O site, O is bonded in a water-like geometry to one Fe and one O atom. In the eighth O site, O is bonded in a 2-coordinate geometry to one Fe and one O atom. In the ninth O site, O is bonded in a single-bond geometry to one S atom. In the tenth O site, O is bonded in a single-bond geometry to one S atom. In the eleventh O site, O is bonded in a single-bond geometry to one S atom. In the twelfth O site, O is bonded in a bent 150 degrees geometry to one Fe and one S atom. In each FeSO7 cluster, Fe is bonded in a see-saw-like geometry to four O atoms. There are a spread of Fe–O bond distances ranging from 1.66–1.84 Å. S is bonded in a tetrahedral geometry to four O atoms. There are a spread of S–O bond distances ranging from 1.46–1.56 Å. There are seven inequivalent O sites. In the first O site, O is bonded in a bent 150 degrees geometry to one Fe and one S atom. In the second O site, O is bonded in a single-bond geometry to one Fe atom. In the third O site, O is bonded in a single-bond geometry to one Fe atom. In the fourth O site, O is bonded in a single-bond geometry to one Fe atom. In the fifth O site, O is bonded in a single-bond geometry to one S atom. In the sixth O site, O is bonded in a single-bond geometry to one S atom. In the seventh O site, O is bonded in a single-bond geometry to one S atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on CaB5H4O9 by Materials Project

(CaB5HO9)2(H2)3 crystallizes in the monoclinic P2_1/c space group. The structure is two-dimensional and consists of four molecular hydrogen molecules and two CaB5HO9 sheets oriented in the (0, 1, 0) direction. In each CaB5HO9 sheet, Ca is bonded in a 8-coordinate geometry to eight O atoms. There are a spread of Ca–O bond distances ranging from 2.50–2.79 Å. There are five inequivalent B sites. In the first B site, B is bonded to four O atoms to form corner-sharing BO4 tetrahedra. There are a spread of B–O bond distances ranging from 1.44–1.53 Å. In the second B site, B is bonded in a trigonal planar geometry to three O atoms. There is one shorter (1.35 Å) and two longer (1.39 Å) B–O bond length. In the third B site, B is bonded in a trigonal planar geometry to three O atoms. There is two shorter (1.37 Å) and one longer (1.40 Å) B–O bond length. In the fourth B site, B is bonded to four O atoms to form corner-sharing BO4 tetrahedra. There are a spread of B–O bond distances ranging from 1.44–1.51 Å. In the fifth B site, B is bonded in a trigonal planar geometry to three O atoms. There are a spread of B–O bond distances ranging from 1.35–1.42 Å. H is bonded in a single-bond geometry to one O atom. The H–O bond length is 0.98 Å. There are nine inequivalent O sites. In the first O site, O is bonded in a bent 120 degrees geometry to one B and one H atom. In the second O site, O is bonded in a distorted bent 120 degrees geometry to one Ca and two B atoms. In the third O site, O is bonded in a distorted water-like geometry to two equivalent Ca and two B atoms. In the fourth O site, O is bonded in a bent 120 degrees geometry to one Ca and two B atoms. In the fifth O site, O is bonded in a bent 120 degrees geometry to two B atoms. In the sixth O site, O is bonded in a bent 120 degrees geometry to one Ca and two B atoms. In the seventh O site, O is bonded in a distorted bent 120 degrees geometry to two equivalent Ca and two B atoms. In the eighth O site, O is bonded in a bent 120 degrees geometry to two B atoms. In the ninth O site, O is bonded in a distorted bent 120 degrees geometry to one Ca and two B atoms.

36 MATERIALS SCIENCE↗
NASA NTRS2001

Ranges of Applicability for the Continuum-beam Model in the Constitutive Analysis of Carbon Nanotubes: Nanotubes or Nano-beams?

Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.

Harik, Vasyl Michael↗
NASA NTRS1999

Demonstration of Imaging Flow Diagnostics Using Rayleigh Scattering in Langley 0.3-Meter Transonic Cryogenic Tunnel

The feasibility of using the Rayleigh scattering technique for molecular density imaging of the free-stream flow field in the Langley 0.3-Meter Transonic Cryogenic Tunnel has been experimentally demonstrated. The Rayleigh scattering was viewed with a near-backward geometry with a frequency-doubled output from a diode-pumped CW Nd:YAG laser and an intensified charge-coupled device camera. Measurements performed in the range of free-stream densities from 3 x 10(exp 25) to 24 x 10(exp 25) molecules/cu m indicate that the observed relative Rayleigh signal levels are approximately linear with flow field density. The absolute signal levels agree (within approx. 30 percent) with the expected signal levels computed based on the well-known quantities of flow field density, Rayleigh scattering cross section for N2, solid angle of collection, transmission of the optics, and the independently calibrated camera sensitivity. These results show that the flow field in this facility is primarily molecular (i.e., not contaminated by clusters) and that Rayleigh scattering is a viable technique for quantitative nonintrusive diagnostics in this facility.

Shirinzadeh, B.↗
DOE OSTI2025

An Accurate, Affordable Density Functional Tight-Binding Model for Excited State Hydrocarbon Polymer Molecular Dynamics

We have developed a density functional tight-binding model for hydrocarbon excited state dynamics by referencing to high-level electronic structure theory and incorporating a many-body repulsive energy. We then validate our model against n-octane geometry optimizations, bond dissociation scans, and vibrational frequencies. Our model is approximately 10 3 times more efficient than hybrid time-dependent density functional theory calculations with comparable accuracy. In conclusion, our efforts enable longer timescale excited state simulations of photochemistry and scattering of incident radiation.

Chemical calculations↗
NASA NTRS1993

Comprehensive investigation of HgCdTe metalorganic chemical vapor deposition

The principal objective of this experimental and theoretical research program was to explore the possibility of depositing high quality epitaxial CdTe and HgCdTe at very low pressures through metalorganic chemical vapor deposition (MOCVD). We explored two important aspects of this potential process: (1) the interaction of molecular flow transport and deposition in an MOCVD reactor with a commercial configuration, and (2) the kinetics of metal alkyl source gas adsorption, decomposition and desorption from the growing film surface using ultra high vacuum surface science reaction techniques. To explore the transport-reaction issue, we have developed a reaction engineering analysis of a multiple wafer-in-tube ultrahigh vacuum chemical vapor deposition (UHV/CVD) reactor which allows an estimate of wafer or substrate throughput for a reactor of fixed geometry and a given deposition chemistry with specified film thickness uniformity constraints. The model employs a description of ballistic transport and reaction based on the pseudo-steady approximation to the Boltzmann equation in the limit of pure molecular flow. The model representation takes the form of an integral equation for the flux of each reactant or intermediate species to the wafer surfaces. Expressions for the reactive sticking coefficients (RSC) for each species must be incorporated in the term which represents reemission from a wafer surface. The interactions of MOCVD precursors with Si and CdTe were investigated using temperature programmed desorption (TPD) in ultra high vacuum combined with Auger electron spectroscopy (AES). These studies revealed that diethyltellurium (DETe) and dimethylcadmium (DMCd) adsorb weakly on clean Si(100) and desorb upon heating without decomposing. These precursors adsorb both weakly and strongly on CdTe(111)A, with DMCd exhibiting the stronger interaction with the surface than DETe.

Raupp, Gregory B.↗
DOE OSTI2021

Substituent Effects on Transient, Carbodiimide-Induced Geometry Changes in Diphenic Acids

Nucleotide-induced conformational changes in motor proteins are key to many important cell functions. Inspired by this biological behavior, we report a simple chemically fueled system that exhibits carbodiimide-induced geometry changes. Bridging via transient anhydride formation leads to a significant reduction of the twist about the biaryl bond of substituted diphenic acids, giving a simple molecular clamp. The kinetics are well-described by a simple mechanism, allowing structure–property effects to be determined. The kinetic parameters can be used to derive important characteristics of the system such as the efficiencies (anhydride yields), maximum anhydride concentrations, and overall lifetimes. Transient diphenic anhydrides tolerate steric hindrance ortho to the biaryl bond but are significantly affected by electronic effects, with electron-deficient substituents giving lower yields, peak conversions, and lifetimes. Furthermore, the results provide useful guidelines for the design of functional systems incorporating diphenic acid units.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗