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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

3DRISM↗
NASA NTRS1992

Application of narrow band control to reduce vibrations in magnetic bearing systems

The benefits of narrowband control theory for simple, open-loop stable systems are illustrated, and how the approach changes for magnetic bearing systems, which are open-loop unstable, is discussed. Magnetic bearing systems are good applications for narrowband control theory. Two sources of synchronous forces, the measurement error and the magnetic unbalance, are discussed. Both the measurement error and the magnetic unbalance manifest themselves as synchronous disturbances. It is shown that narrowband control theory for simple, open-loop stable systems provides excellent performance and good stability robustness. Because magnetic bearing systems are open-loop stable, the narrowband control approach becomes more complex. Disturbance accommodating control (DAC) theory is introduced as an effective approach to reduce vibrations in magnetic bearing systems. It is used to develop a control/estimation scheme that enables the rotor to spin about its center of mass in the presence of the measurement error disturbances.

Gaffney, Monique S.↗
DOE OSTI2025

Hydrogenation of ethylene over molybdenum–sulfur complexes supported on UiO-66

Development of supported single-site catalysts using small metal sulfide complexes could significantly help in the development of cost-effective catalytic materials to drive selective hydrogenation and hydrogenolysis. The goal of this study is to contribute to the development of metal sulfide catalysts by calculating the thermodynamics of a catalytic cyclic involving a metal organic framework functionalized by insertion of metal sulfide. Anchored metal sulfide complexes can potentially be designed with ligands with distinctly different electronic and catalytic properties for specific catalytic applications. Here we examine the hydrogenation of ethylene as a model. We use density functional theory to investigate molybdenum–sulfur complexes as active catalysts anchored on the metal–organic framework UiO-66 as a stable support. Our calculations show that the anchored complexes with more than two sulfur ligands are unfavorable for ethylene adsorption, so we study complexes with one or two sulfur ligands. Hydrogenation of the unsaturated carbon double bond requires the transfer of two hydrogen atoms, which can occur via heterolytic activation of hydrogen to form a Mo-hydride and a protonated sulfur – either by hydride transfer followed by proton transfer or via proton transfer followed by hydride transfer, and we find that both mechanisms proceed via two-state reactivity involving two spin states along the reaction path. Of the two catalysts studied in gas the phase, the MoS single-sulfur–ligand complex with lower oxidation states produces thermodynamically more favorable intermediates along the pathway for the first hydrogen transfer for both the hydride-first mechanism and the proton-first mechanism. As a result, the quantum mechanical calculations provide experimentally inaccessible partial atomic charges and geometries of the various intermediates encountered along the steps of the reaction mechanisms.

Kermani, Maryam Mansoori [University of Minnesota,↗
NASA NTRS2004

Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

Park, Jin-Young↗
NASA NTRS2003

The Development of the Ducted Fan Noise Propagation and Radiation Code CDUCT-LaRC

The development of the ducted fan noise propagation and radiation code CDUCT-LaRC at NASA Langley Research Center is described. This code calculates the propagation and radiation of given acoustic modes ahead of the fan face or aft of the exhaust guide vanes in the inlet or exhaust ducts, respectively. This paper gives a description of the modules comprising CDUCT-LaRC. The grid generation module provides automatic creation of numerical grids for complex (non-axisymmetric) geometries that include single or multiple pylons. Files for performing automatic inviscid mean flow calculations are also generated within this module. The duct propagation is based on the parabolic approximation theory of R. P. Dougherty. This theory allows the handling of complex internal geometries and the ability to study the effect of non-uniform (i.e. circumferentially and axially segmented) liners. Finally, the duct radiation module is based on the Ffowcs Williams-Hawkings (FW-H) equation with a penetrable data surface. Refraction of sound through the shear layer between the external flow and bypass duct flow is included. Results for benchmark annular ducts, as well as other geometries with pylons, are presented and compared with available analytical data.

Nark, Douglas M.↗
DOE OSTI2025

Gating Single Molecules with Counterions

We report atomic-scale gating and visualization of local charge distribution within individual rare-earth-based molecular complexes on a metallic surface. The complexes are formed by a positively charged lanthanum ion coordinated to a (pcam)3 molecule and a negatively charged counterion trapped underneath via electrostatic interactions on a Au(111) surface. Local gating is performed by adding an additional negatively charged counterion to one side of the complex, which results in the redistribution of charges within the complex and a positive shift of the frontier orbitals. This is caused by the internal Stark effect induced by the added counterion. This effect is directly captured using tunneling spectroscopy and spectroscopic mapping at 5 K substrate temperature. The polarizability of the complex is corroborated by density functional theory and analytical calculations based on experimental findings. Furthermore, the influence of charge polarization on nearby complexes is investigated in a cluster purposely assembled using three complexes, which reveals maintaining the charge states as in single complexes. These findings will enable the design of robust charged rare-earth complexes to be tailored for potential solid-state applications.

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

Reducing Operator Complexity of Galerkin Coarse-grid Operators with Machine Learning

Here, we propose a data-driven and machine-learning-based approach to compute non-Galerkin coarse-grid operators in multigrid (MG) methods, addressing the well-known issue of increasing operator complexity. Guided by the MG theory on spectrally equivalent coarse-grid operators, we have developed novel machine learning algorithms that utilize neural networks combined with smooth test vectors from multigrid eigenvalue problems. The proposed method demonstrates promise in reducing the complexity of coarse-grid operators while maintaining overall MG convergence for solving parametric partial differential equation problems. Numerical experiments on anisotropic rotated Laplacian and linear elasticity problems are provided to showcase the performance and comparison with existing methods for computing non-Galerkin coarse-grid operators.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Efficient Unitary Designs from Random Sums and Permutations

A unitary k-design is an ensemble of unitaries that matches the first k moments of the Haar measure. In this work, we provide two efficient constructions of k-designs on n-qubits using new random matrix theory techniques. Our first construction is based on exponentiating sums of random i.i.d. Hermitian matrices and uses O(k2n2)-many gates. In the spirit of central limit theorems, we show that this random sum approximates the Gaussian Unitary Ensemble (GUE). We then show that the product of just two exponentiated GUE matrices is already approximately Haar random. Our second construction is based on products of exponentiated sums of random permutations and uses Õ(k poly (n)) many gates. The k dependence is optimal (up to polylogarithmic factors) and is inherited from the efficiency of existing k-wise independent permutations. Furthermore, replacing random permutations with quantum-secure pseudorandom permutations (PRPs), we also obtain a pseudorandom unitary (PRU) ensemble that is secure under nonadaptive queries. A central feature of both proofs is a new connection between the polynomial method in quantum query complexity and the large-dimension (N) expansion in random matrix theory. In particular, the first construction uses the polynomial method to control high moments of certain random matrix ensembles without requiring delicate Weingarten calculations. In doing so, we define and solve a moment problem on the unit circle, asking whether a finite number of equally weighted points can reproduce a given set of moments. In our second construction, the key step is to exhibit an orthonormal basis for irreducible representations of the partition algebra that has a low-degree large-N expansion. This allows us to show that the distinguishing probability is a low-degree rational polynomial of the dimension N.

algebra↗
DOE OSTI2022

Probing the Critical Nucleus Size in the Metal-Insulator Phase Transition of VO 2

In a first-order phase transition, critical nucleus size governs nucleation kinetics, but the direct experimental test of the theory and determination of the critical nucleation size have been achieved only recently in the case of ice formation in supercooled water. The widely known metal-insulator phase transition (MIT) in strongly correlated VO 2 is a first-order electronic phase transition coupled with a solid-solid structural transformation. It is unclear whether classical nucleation theory applies in such a complex case. Here we directly measure the critical nucleus size of the MIT by introducing size-controlled nanoscale nucleation seeds with focused ion irradiation at the surface of a deeply supercooled metal phase of VO 2 . The results compare favorably with classical nucleation theory and are further explained by phase-field modeling. This Letter validates the application of classical nucleation theory as a parametrizable model to describe phase transitions of strongly correlated electron materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Framework for predicting the fractionation of complex liquid feeds via polymer membranes

The separation of complex liquid hydrocarbon mixtures was recently demonstrated using the glassy polymer SBAD-1, showing that small molecule fractionation is possible by such organic membrane materials. Here, in this work, we develop a framework that will enable workable predictions of permeate flux and composition in complex hydrocarbon liquids through intrinsically porous glassy polymers. The predictions are made by incorporating experimentally-derived unary sorption and diffusion parameters in a Maxwell-Stefan framework coupled with multicomponent sorption models and various distinct diffusion phenomena. Across the range of sorption and diffusion phenomena considered, both the conventional Flory-Huggins model and the proposed Langmuir + Flory-Huggins sorption model combined with a simple average guest diffusivity or a more complex free-volume theory-based transport resulted in the lowest prediction error for three chosen multicomponent separations. The proposed Maxwell-Stefan framework simply requires pure component transport parameters to allow a fast approximation of the separation of multicomponent liquid hydrocarbon feeds that can potentially be extended to more complex feeds such as crude oil fractions.

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

Antimony stable isotope fractionation during adsorption onto birnessite: A molecular perspective from X-ray absorption spectroscopy and density functional theory

Sorption of antimony (Sb) onto birnessite significantly influences the fate of Sb in oceanic and terrestrial environments and fractionates Sb isotopes. Nevertheless, little is known about Sb isotopic fractionation during its adsorption on birnessite. Here, in this study, we show the value of Δ 123 Sb adsorbed-aqueous increases from −0.398 to −0.332 ‰ in 1 h and then decreases and stabilizes at −0.384 ‰ in 72 h. The enrichment of the light Sb isotope is predominantly due to the distortion of the octahedral symmetry. X-ray absorption spectroscopy results indicate Sb first forms a double-corner-sharing complex on birnessite and then transforms to a double-edge-sharing complex during adsorption. The optimized bond distances for double-corner-sharing (3.37 Å) and double-edge-sharing (2.90 Å) complexes calculated using density functional theory (DFT) fits well with the structure (3.41 and 3.00 Å) revealed by X-ray absorption spectroscopy, respectively. The fractionation derived from reduced partition function ratios calculated using DFT aligns well with the experimental results. Therefore, the variation in Sb isotopic fractionation during adsorption is attributed to the evolving structure of Sb complexes on birnessite. Our results demonstrate the isotopic fractionation of Sb during adsorption on birnessite and provide a molecular-scale understanding of Sb behavior, contributing to the correct reconstruction of the Sb isotope composition of ancient seawater using ferromanganese crusts and nodules, and efforts to trace Sb migration in epigenetic mining environments.

Adsorption↗
NASA NTRS1988

The critical complex in nucleation is not the nucleus

A theory of nucleation is presented which combines features of classical nucleation. In this theory, the nucleus is a cluster of finite size with a sharp interface and spinodal decomposition, in which a fluctuation in density or composition generates the critical complex and nucleus. Thus, the nucleus is a product of nucleation. Schematic models for the classical and the proposed routes to nucleation are compared, focusing on the relation between pressure and volume in the models. In the proposed model, the critical complex, or critical state, is between the parent state and the nucleus.

Rasmussen, Don H.↗
DOE OSTI2024

Moduli axions, stabilizing moduli, and the large field swampland conjecture in heterotic M-theory

We compute the F- and D-term potential energy for the dilaton, complex structure, and Kähler moduli of realistic vacua of heterotic M-theory compactified on Calabi-Yau threefolds where, for simplicity, we choose ℎ 1,1 = ℎ 2,1 = 1. However, the formalism is immediately applicable to the “universal” moduli of Calabi-Yau threefolds with ℎ 1,1 = ℎ 1,2 > 1 as well. The F-term potential is computed using the nonperturbative complex structure, gaugino condensate and “world sheet instanton” superpotentials in theories in which the hidden sector contains an anomalous U⁡(1) structure group. The Green-Schwarz anomaly cancellation induces inhomogeneous “axion” transformations for the imaginary components of the dilaton and Kähler modulus—which then produce a D-term potential. V D is a function of the real components of the dilaton and Kähler modulus (s and t) that is minimized and precisely vanishes along a unique line in the s–t plane. Excitations transverse to this line have a mass m anom which is an explicit function of t. The F-term potential energy is then evaluated along the V D = 0 line. For values of t small enough that m anom ≳ M U —where M U is the compactification scale—we plot V F for a realistic choice of coefficients as a function of the Pfaffian parameter p. We find values of p for which V F has a global minimum at negative or zero vacuum density or a metastable minimum with positive vacuum density. In all three cases, the s, t, and associated “axion” moduli are completely stabilized. Finally, we show that, for any of these vacua, the large t behavior of the potential energy satisfies the “large scalar field” Swampland conjecture.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Magnetic exchange interactions in binuclear and tetranuclear iron(III) complexes described by spin‐flip DFT and Heisenberg effective Hamiltonians

Abstract Low‐energy spectra of single‐molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground‐state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants ( J ) for a set of iron (III) binuclear and tetranuclear complexes from all‐electron calculations using non‐collinear spin‐flip time‐dependent density functional theory (NC‐SF‐TDDFT). For 12 binuclear complexes with J ‐values ranging from −6 to −132 cm −1 , our benchmark calculations using the short‐range hybrid ω PBEh functional and 6‐31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm −1 ). For the tetranuclear SMMs, the computed J constants are within 6 cm −1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin‐flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.

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

Binding of Sulfates and Water to Monovalent Cations

The binding of the sulfate ligand group to monovalent cations in the presence of water is important for many systems. To understand the structure and energetics of sulfate complexes, we use density functional theory to study ethyl sulfate binding to the monovalent cations Li + , Na + , and K + , and to water. The free energies of binding and optimal structures are calculated for a range of the number of ethyl sulfates and waters. Without water, the most optimal structure for all the cations is bidentate binding by two ethyl sulfates, yielding a 4-fold coordination. With water, the lowest free energy structures also have two ethyl sulfates, but the coordination varies with cations. For complexes with water, the four oxygen atoms in the sulfate group enable multiple binding geometries for the cations and for hydrogen bonding with water. Many of these geometries differ in free energy by only a small amount (1–2 kcal/mol), meaning there will be multiple binding configurations in bulk solution. In comparison to the optimal structures for binding to the carboxylate group, there is more variation for binding to the sulfate group as a function of cation type and the number of waters. Further, the polarization of the atoms is significant and varies among the sulfate oxygen atoms. The water oxygen charge is often larger than that of sulfate oxygen, which plays a role in the preference for monodentate ligand binding to cations in the presence of water.

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

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin

The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

Measurement of cavity perturbation to determine the microwave absorption of a sphere in a single mode resonator

Experiments have been conducted on materials in a single mode microwave resonator to test predictions of a new theory of microwave absorption by a lossy dielectric sphere. An analysis of cavity perturbation for verifying the new absorption model revealed a limitation of a standard form of cavity perturbation theory and led to a modification which generalized its application. The cavity perturbations of a nylon sphere were used to calculate the complex permittivity using the standard perturbation theory and the modified form. These permittivity values were compared to that determined from cavity perturbation using a thin nylon rod where the standard and modified forms agree. The results show that the modification is necessary to correctly apply perturbation theory to spherical samples. A second experiment confirmed the theoretical prediction that under certain sample conditions the power absorbed by a sphere in a resonant cavity can be maximum at a location in the cavity where the empty cavity electric field intensity is a minimum.

Watkins, J. L.↗