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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

Presentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide–MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.

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

Peptoid-directed assembly of CdSe nanoparticles

The high information content of proteins drives their hierarchical assembly and complex function, including the organization of inorganic nanomaterials. Peptoids offer an organic scaffold very similar to proteins, but with a wider solubility range and easily tunable side chains and functional groups to create a variety of self-assembling architectures with atomic precision. If we could harness this paradigm and understand the factors that govern how they direct nucleation and assembly of inorganic materials to design order within such materials, new dimensions of function and fundamental science would emerge. In this work, peptoid tubes and sheets were explored as platforms to assemble colloidal quantum dots (QDs) and clusters. We have successfully synthesized CdSe QDs with difunctionalized capping ligands containing both carboxylic acid and thiol groups and mixed them with maleimide containing peptoids, to create an assembly of the QDs on the peptoid surface via a covalent linkage. This conjugation was seen to be successful with peptoid tubes, sheets and CdSe QDs and clusters. The particles were seen to have a high preference for the peptoid surface but non-specific interactions with carboxylic acid groups on the peptoids limited control over QD density via maleimide conjugation. Replacing the carboxylic acid groups with methoxy ethers, however, allowed for control over QD density as a function of maleimide concentration. 1 H NMR analysis demonstrated that binding of QDs to peptoids involved a subset of surface ligands bound through the carboxylate functional group, allowing the distal thiol to engage in a covalent linkage to the maleimide. Overall, we have shown the compatibility and control of CdSe-peptoid interactions via a covalent linkage with varying peptoid structures and CdSe particles to create complex hybrid structures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Regioselective Hydrosilylation Catalysis with Supported Well-Defined Pt(0) Complexes: Effects of Surface Anions and Phosphenium Ligands

Achieving stable, selective single-atom catalysts is challenging because localsurface-site structures are difficult to control. Surface organometallic chemistry and organic−inorganic hybrid materials offer partial solutions, but applications to supporting zero-valent metals are limited. We demonstrate that well-defined, ionically bound N-heterocyclic phosphenium ([NHP] + ) ligands can be generated on silylium-functionalized sulfated zirconia ([ i Pr 3 Si][SZO]). These surface-bound [NHP][SZO] ligands coordinate Pt(0) centers, forming [(NHP)Pt(0)L][SZO] precatalysts that are highly active for alkyne hydrosilylation. Systematic studies reveal that sterically bulky aromatic ligands enhance regioselectivity, achieving performances comparable to molecular Pt catalysts. Further, more-coordinating anions support more-regioselective precatalysts; therefore, SZO supports more-selective species than weaker-coordinating Al(OC(CF 3 ) 3 ) 3 - functionalized silica, a trend confirmed by molecular analogues. These results demonstrate that both the ligand and support control catalytic behavior and enable solid-state structure− activity relationships.

Catalysts↗
DOE OSTI2021

Unimolecular and bimolecular formic acid decomposition routes on dispersed Cu nanoparticles

The elementary steps and site requirements in formic acid (HCOOH) dehydrogenation on Cu surfaces remain of keen interest because formate species act as intermediates or spectators in methanol synthesis and water–gas shift reactions. Steady-state and transient kinetic data, isotopic effects, infrared spectra during catalytic and stoichiometric reactions, and theoretical treatments based on density functional theory (DFT) provide evidence for bimolecular reactions, in which saturated bidentate formate (*HCOO*) adlayers, present at 0.25 ML (0.25 *HCOO* per surface Cu atom), react with undissociated species (HCOOH$^\square$) bound at interstices within formate adlayers ($^\square$) to form H-bonded bimolecular HCOOH$^\square$-*HCOO* adducts. The co-existence of vicinal HCOOH$^\square$ and *HCOO* moieties is evident from antisymmetric infrared bands for *HCOO* that become stronger as a result of their H-bonding that perturbs the induced dipole moment of *HCOO* upon vibration, consistent with DFT-derived vibrational frequencies and intensities for such perturbed species. The *HCOO* moiety in this complex undergoes C-H activation via a transition state that is preferentially stabilized through H-bonding with the vicinal HCOOH$^\square$ relative to its *HCOO* precursor. DFT-derived HCOOH dehydrogenation activation barriers and those determined from the evolution of CO 2 from pre-adsorbed *HCOO* species are about 10 kJ mol -1 smaller in the presence of gaseous HCOOH reactants (because of HCOOH$^\square$-*HCOO* interactions) than those for the unimolecular decomposition of bound *HCOO* species. Such bimolecular routes are consistent with measured effects of HCOOH, H 2 , and CO pressures and of H/D isotopic substitution on dehydrogenation turnover rates and represent the predominant channel for the formation of CO 2 and H 2 during catalytic HCOOH dehydrogenation on Cu nanoparticles. A saturated *HCOO* adlayer that retains binding interstices and the presence of HCOOH(g) enable a sequence of elementary steps unavailable for *HCOO* species, thus circumventing unassisted unimolecular routes that exhibit higher activation barriers.

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

Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli

In E. coli, editing efficiency with Cas9-mediated recombineering varies across targets due to differences in the level of Cas9:gRNA-mediated DNA double-strand break (DSB)-induced cell death. We found that editing efficiency with the same gRNA and repair template can also change with target position, cas9 promoter strength, and growth conditions. Incomplete editing, off-target activity, nontargeted mutations, and failure to cleave target DNA even if Cas9 is bound also compromise editing efficiency. These effects on editing efficiency were gRNA-specific. We propose that differences in the efficiency of Cas9:gRNA-mediated DNA DSBs, as well as possible differences in binding of Cas9:gRNA complexes to their target sites, account for the observed variations in editing efficiency between gRNAs. We show that editing behavior using the same gRNA can be modified by mutating the gRNA spacer, which changes the DNA DSB activity. Finally, we discuss how variable editing with different gRNAs could limit high-throughput applications and provide strategies to overcome these limitations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

IR side of bounds on theories with spontaneously broken Lorentz symmetry

In nature, some UV features of dynamics are reflected in IR quantities. In fully relativistic theories, this connection can be probed through the analyticity properties of scattering amplitudes, allowing one to understand which IR theories respect the UV assumptions of quantum field theory. The ensuing analyticity bounds can usually be rephrased as the absence of faster-than-light propagation for low-energy excitations. While it is interesting to understand these relations and their IR characterization for theories that have less idealized properties, it is also more difficult to derive analyticity bounds in these cases. For theories that spontaneously break Lorentz symmetry, recent progress was made by considering correlators of conserved currents and their analyticity properties. In this work, we focus on such theories and work to close the gap from the IR side, finding a natural way to express the known analyticity bounds purely in terms of low-energy kinematical quantities. Our analysis shows that the bounds require gapped excitations to have a slower speed than the gapless ones, at least for momenta that are low with respect to the mass gap. These results suggest a way to interpret the UV/IR connection in more complex theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Crossing Symmetric Dispersion Relations in Quantum Field Theories

For 2-2 scattering in quantum field theories, the usual fixed t dispersion relation exhibits only two-channel symmetry. This Letter considers a crossing symmetric dispersion relation, reviving certain old ideas from the 1970s. Rather than the fixed t dispersion relation, this needs a dispersion relation in a different variable z, which is related to the Mandelstam invariants s, t, u via a parametric cubic relation making the crossing symmetry in the complex z plane a geometric rotation. The resulting dispersion is manifestly three-channel crossing symmetric. We give simple derivations of certain known positivity conditions for effective field theories, including the null constraints, which lead to two sided bounds and derive a general set of new nonperturbative inequalities. We show how these inequalities enable us to locate the first massive string state from a low energy expansion of the four dilaton amplitude in type II string theory. We also show how a generalized (numerical) Froissart bound, valid for all energies, is obtained from this approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Compositions and methods for regulating proteins and nucleic acids activities

Compositions and methods for conditionally regulating activities of CRISPR-Cas systems. In some embodiments, the methods comprise providing an inactive guide RNA comprising a regulatory domain bound by a lock nucleic acid different from the guide RNA; and displacing the lock nuclei acid from the regulatory domain by a trigger nucleic acid, thereby activating the guide RNA, wherein the activated guide RNA forms a complex with a Cas enzyme.

Choudhary, Amit↗
DOE OSTI2022

The Kinetics of Electron Transfer from CdS Nanorods to the MoFe Protein of Nitrogenase

Combining the remarkable catalytic properties of redox enzymes with highly tunable light absorbing properties of semiconductor nanocrystals enables the light-driven catalysis of complex, multielectron redox reactions. This work focuses on systems that combine CdS nanorods (NRs) with the MoFe protein of nitrogenase to drive photochemical N 2 reduction. We used transient absorption spectroscopy (TAS) to examine the kinetics of electron transfer (ET) from CdS NRs to the MoFe protein. For CdS NRs with dimensions similar to those previously used for photochemical N 2 reduction, the rate constant for ET from CdS NRs competes with other electron relaxation processes, such that when a MoFe protein is bound to a NR, about one-half of the photoexcited electrons are delivered to the enzyme. The NR-MoFe protein binding is incomplete with more than one-half of the NRs in solution not having a MoFe protein bound to accept electrons. The quantum efficiency of ET (QE ET ) in these ensemble samples is similar to previously reported efficiencies of product (NH 3 and H 2 ) formation, suggesting that the enzyme utilizes the delivered electrons without major loss pathways. Our analysis suggests that QE ET , and therefore the photochemical product formation, is limited at the ensemble level by the NR-MoFe protein binding and at the single-complex level by the competitiveness of ET. We characterized ET kinetics for several CdS NRs samples with varying dimensions and found that for CdS NRs with an average diameter of 4.2 nm the ET efficiency dropped to undetectable levels, defining a maximum NR diameter that should be used to photochemically drive the MoFe protein. The work described here provides insights into the design of systems with increased control of photochemical N 2 reduction catalyzed by the MoFe protein of nitrogenase.

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

Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected the lives and livelihood of millions of individuals around the world. It has mutated several times after its first inception, with an estimated two mutations occurring every month. Although we have been successful in developing vaccines against the virus, the emergence of variants has enabled it to escape therapy. Few of the generated variants are also reported to be more infectious than the wild-type (WT). In this study, we analyze the attributes of all RBD/ACE2 complexes for the reported VOCs, namely, Alpha, Beta, Gamma, and Delta through computer simulations. Results indicate differences in orientation and binding energies of the VOCs from the WT. Overall, it was observed that electrostatic interactions play a major role in the binding of the complexes. Detailed residue level energetics revealed that the most prominent changes in interaction energies were seen particularly at the mutated residues which were present at RBD/ACE2 interface. We found that the Delta variant is one of the most tightly bound variants of SARS-CoV-2 with dynamics similar to WT. The high binding affinity of RBD towards ACE2 is indicative of an increase in viral transmission and infectivity. The details presented in our study provide additional information for the design and development of effective therapeutic strategies for the emerging variants of the virus in the future.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Picoseconds-Limited Exciton Recombination in Metal–Organic Chalcogenides Hybrid Quantum Wells

Metal-organic species can be designed to self-assemble in large-scale, atomically defined, supramolecular architectures. Hybrid quantum wells, where inorganic two-dimensional (2D) planes are separated by organic ligands, are a particular example. The ligands effectively provide an intralayer confinement for charge carriers resulting in a 2D electronic structure, even in multilayered assemblies. Air-stable metal organic chalcogenides hybrid quantum wells have recently been found to host tightly bound 2D excitons with strong optical anisotropy in a bulk matrix. Here, we investigate the excited carrier dynamics in the prototypical metal organic chalcogenide [AgSePh] ∞ , disentangling three excitonic resonances by low temperature transient absorption spectroscopy. Our analysis suggests a complex relaxation cascade comprising ultrafast screening and renormalization, inter-exciton relaxation, and self-trapping of excitons within few picoseconds. Finally, the ps-decay provided by the self-trapping mechanism may be leveraged to unlock the material's potential for ultrafast optoelectronic applications.

2D excitons↗
DOE OSTI2021

High-precision quantum algorithms for partial differential equations

Quantum computers can produce a quantum encoding of the solution of a system of differential equations exponentially faster than a classical algorithm can produce an explicit description. However, while high-precision quantum algorithms for linear ordinary differential equations are well established, the best previous quantum algorithms for linear partial differential equations (PDEs) have complexity poly(1/ϵ), where ϵ is the error tolerance. By developing quantum algorithms based on adaptive-order finite difference methods and spectral methods, we improve the complexity of quantum algorithms for linear PDEs to be poly(d,log(1/ϵ)), where d is the spatial dimension. Our algorithms apply high-precision quantum linear system algorithms to systems whose condition numbers and approximation errors we bound. We develop a finite difference algorithm for the Poisson equation and a spectral algorithm for more general second-order elliptic equations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Comparative Assessment of Pose Prediction Accuracy in RNA–Ligand Docking

Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein–ligand complexes have evolved to improve the accuracy in the computation of binding strengths and poses. In the past decade, RNA has also emerged as a target class for new small-molecule drugs. However, most ligand docking programs have been validated and tested for proteins and not RNA. Here, we test the docking power (pose prediction accuracy) of three state-of-the-art docking protocols on 173 RNA–small molecule crystal structures. The programs are AutoDock4 (AD4) and AutoDock Vina (Vina), which were designed for protein targets, and rDock, which was designed for both protein and nucleic acid targets. AD4 performed relatively poorly. For RNA targets for which a crystal structure of a bound ligand used to limit the docking search space is available and for which the goal is to identify new molecules for the same pocket, rDock performs slightly better than Vina, with success rates of 48% and 63%, respectively. However, in the more common type of early-stage drug discovery setting, in which no structure of a ligand–target complex is known and for which a larger search space is defined, rDock performed similarly to Vina, with a low success rate of ~27%. Further, Vina was found to have bias for ligands with certain physicochemical properties, whereas rDock performs similarly for all ligand properties. Thus, for projects where no ligand–protein structure already exists, Vina and rDock are both applicable. However, the relatively poor performance of all methods relative to protein–target docking illustrates a need for further methods refinement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evaluating Lyman- α constraints for general dark-matter velocity distributions: Multiple scales and cautionary tales

One of the most important observational constraints on possible models of dark-matter physics exploits the Lyman-α absorption spectrum associated with photons traversing the intergalactic medium. Because these data allow us to probe the linear matter power spectrum with great accuracy down to relatively small distance scales, finding ways of accurately evaluating such Lyman-α constraints across large classes of candidate models of dark-matter physics is of paramount importance. While such Lyman-α constraints have been evaluated for dark-matter models that give rise to relatively simple dark-matter velocity distributions, more complex models—particularly those whose dark-matter velocity distributions stretch across multiple scales—have recently been receiving increasing attention. In this paper, we undertake a study of the Lyman-α constraints associated with general dark-matter velocity distributions. Although such Lyman-α constraints are difficult to evaluate in principle, in practice there currently exist two classes of methods in the literature through which such constraints can be recast into forms which are easier to evaluate and which therefore allow a more rapid determination of whether a given dark-matter model is ruled in or out. Accordingly, we utilize both of these recasts in order to determine the Lyman-α bounds on different classes of dark-matter velocity distributions. Here we also develop a general method by which the results of these different recasts can be compared. For relatively simple dark-matter velocity distributions, we demonstrate that these two classes of recasts tend to align and give similar results. However, we find that the situation is far more complex for distributions involving multiple velocity scales: while these two classes of recasts continue to yield similar results within certain regions of parameter space, they nevertheless yield dramatically different results within precisely those regions of parameter space which are likely to be phenomenologically relevant. This, then, serves as a cautionary tale regarding the use of such recasts for complex dark-matter velocity distributions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Modified Eigen-Decomposition-based Interval Analysis (MEDIA) for Power System Dynamic State Estimation

The Bayesian approach has been used for the dynamic state estimation (DSE) of a power system. However, due to the complexity of noise resources, it is difficult to quantify measurement and process noise using probability density functions (PDFs). To overcome the difficulty, the authors of this paper propose a modified eigen-decomposition-based interval analysis (MEDIA) method, which employs bounds instead of PDFs to quantify the noise, and uses the eigen decomposition method to reduce the negative impact of the overestimation problem. Using the simulation data generated from IEEE 16-machine and IEEE 10-machine systems, it is shown that the proposed MEDIA method can estimate the hard boundaries of dynamic states in real time. Furthermore, comparison with the forward-backward propagation method and the extended set-membership filter also shows that the proposed MEDIA method performs better by providing narrower boundaries in the DSE.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Electrically controlled interlayer trion fluid in electron-hole bilayers

Here, the combination of repulsive and attractive Coulomb interactions in a quantum electron-hole (e-h) fluid can produce correlated phases of multiparticle charge complexes, such as excitons, trions, and biexcitons. We report an experimental realization of an electrically controlled interlayer trion fluid in van der Waals heterostructures. In strongly coupled e-h bilayers, electrons and holes spontaneously form three-particle trion bound states. The interlayer trions can assume 1e-2h and 2e-1h configurations. We show that the two holes in 1e-2h trions form a spin-singlet with a spin gap of approximately one milli–electron volt. By electrostatic gating, the equilibrium state can be continuously tuned into an exciton fluid, a trion fluid, an exciton-trion mixture, or a trion-charge mixture. Our work demonstrates a platform to study correlated phases of tunable Bose-Fermi mixtures.

Qi, Ruishi [University of California, Berkeley, CA↗
DOE OSTI2021

Island for gravitationally prepared state and pseudo entanglement wedge

We consider spacetime initiated by a finite-sized initial boundary as a generalization of the Hartle-Hawking no-boundary state. We study entanglement entropy of matter state prepared by such spacetime. We find that the entanglement entropy for large subregion is given either by the initial state entanglement or the entanglement island, preventing the entropy to grow arbitrarily large. Consequently, the entanglement entropy is always bounded from above by the boundary area of the island, leading to an entropy bound in terms of the island. The island I is located in the analytically continued spacetime, either at the bra or the ket part of the spacetime in Schwinger-Keldysh formalism. The entanglement entropy is given by an average of complex pseudo generalized entropy for each entanglement island. We find a necessary condition of the initial state to be consistent with the strong sub-additivity, which requires that any probe degrees of freedom are thermally entangled with the rest of the system. We then find a large parameter region where the spacetime with finite-sized initial boundary, which does not have the factorization puzzle at leading order, dominates over the Hartle-Hawking no-boundary state or the bra ket wormhole. Due to the absence of a moment of time reflection symmetry, the island in our setup is a generalization of the entanglement wedge, called pseudo entanglement wedge. In pseudo entanglement wedge reconstruction, we consider reconstructing the bulk matter transition matrix on A ∪ I, from a fine-grained state on A. The bulk transition matrix is given by a thermofield double state with a projection by the initial state. We also provide an AdS/BCFT model by considering EOW branes with corners. We also find the exponential hardness of such reconstruction task using a generalization of Python’s lunch conjecture to pseudo generalized entropy.

2D gravity↗