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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS1994

Binding and activation of major histocompatibility complex class II-deficient macrophages by staphylococcal exotoxins

Macrophages from C2D transgenic mice deficient in the expression of major histocompatibility complex (MHC) class II proteins were used to identify binding sites for superantigens distinct from the MHC class II molecule. Iodinated staphylococcal enterotoxins A and B (SEA and SEB) and exfoliative toxins A and B (ETA and ETB) bound to C2D macrophages in a concentration-dependent and competitive manner. All four toxins increased F-actin concentration within 30 s of their addition to C2D macrophages, indicating that signal transduction occurred in response to toxin in the absence of class II MHC. Furthermore, ETA, ETB, SEA, and, to a lesser extent, SEB induced C2D macrophages to produce interleukin 6. Several molecular species on C2D macrophages with molecular masses of 140, 97, 61, 52, 43, and 37 kDa bound SEA in immunoprecipitation experiments. These data indicate the presence of novel, functionally active toxin binding sites on murine macrophages distinct from MHC class II molecules.

Non-NASA Center↗
NASA NTRS2009

Computing Bounds on Resource Levels for Flexible Plans

A new algorithm efficiently computes the tightest exact bound on the levels of resources induced by a flexible activity plan (see figure). Tightness of bounds is extremely important for computations involved in planning because tight bounds can save potentially exponential amounts of search (through early backtracking and detection of solutions), relative to looser bounds. The bound computed by the new algorithm, denoted the resource-level envelope, constitutes the measure of maximum and minimum consumption of resources at any time for all fixed-time schedules in the flexible plan. At each time, the envelope guarantees that there are two fixed-time instantiations one that produces the minimum level and one that produces the maximum level. Therefore, the resource-level envelope is the tightest possible resource-level bound for a flexible plan because any tighter bound would exclude the contribution of at least one fixed-time schedule. If the resource- level envelope can be computed efficiently, one could substitute looser bounds that are currently used in the inner cores of constraint-posting scheduling algorithms, with the potential for great improvements in performance. What is needed to reduce the cost of computation is an algorithm, the measure of complexity of which is no greater than a low-degree polynomial in N (where N is the number of activities). The new algorithm satisfies this need. In this algorithm, the computation of resource-level envelopes is based on a novel combination of (1) the theory of shortest paths in the temporal-constraint network for the flexible plan and (2) the theory of maximum flows for a flow network derived from the temporal and resource constraints. The measure of asymptotic complexity of the algorithm is O(N O(maxflow(N)), where O(x) denotes an amount of computing time or a number of arithmetic operations proportional to a number of the order of x and O(maxflow(N)) is the measure of complexity (and thus of cost) of a maximumflow algorithm applied to an auxiliary flow network of 2N nodes. The algorithm is believed to be efficient in practice; experimental analysis shows the practical cost of maxflow to be as low as O(N1.5). The algorithm could be enhanced following at least two approaches. In the first approach, incremental subalgorithms for the computation of the envelope could be developed. By use of temporal scanning of the events in the temporal network, it may be possible to significantly reduce the size of the networks on which it is necessary to run the maximum-flow subalgorithm, thereby significantly reducing the time required for envelope calculation. In the second approach, the practical effectiveness of resource envelopes in the inner loops of search algorithms could be tested for multi-capacity resource scheduling. This testing would include inner-loop backtracking and termination tests and variable and value-ordering heuristics that exploit the properties of resource envelopes more directly.

Muscvettola, Nicola↗
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↗
NASA NTRS1987

Pattern recognition techniques for failure trend detection in SSME ground tests

The Space Shuttle Main Engine (SSME) is a complex power plant. To evaluate its performance 1200 hot-wire ground tests have been conducted, varying in duration from 0 to 500 secs. During the test some 500 sensors are sampled every 20 ms. The sensors are generally bounded by red lines so that an excursion beyond could lead to premature shutdown. In 27 tests it was not possible to effect an orderly premature shutdown, resulting in major incidents with serious damage to the SSME and test stand. The application of pattern recognition are investigated to detect SSME performance trends that may lead to major incidents. Based on the sensor data a set of (n) features is defined. At any time during the test, the state of the SSME is given by a point in the n-dimensional feature space. The history of a test can now be represented as a trajectory in the n-dimensional feature space. Portions of the normal trajectories and failed test trajectories would lie in different regions of the n-dimensional feature space. The latter can now be partitioned into regions of normal and failed tests. Thus, it is possible to examine the trajectory of a test in progress and predict if it is going into the normal or failure region.

Choudry, A.↗
NASA NTRS1990

Computational efficiency of parallel combinatorial OR-tree searches

The performance of parallel combinatorial OR-tree searches is analytically evaluated. This performance depends on the complexity of the problem to be solved, the error allowance function, the dominance relation, and the search strategies. The exact performance may be difficult to predict due to the nondeterminism and anomalies of parallelism. The authors derive the performance bounds of parallel OR-tree searches with respect to the best-first, depth-first, and breadth-first strategies, and verify these bounds by simulation. They show that a near-linear speedup can be achieved with respect to a large number of processors for parallel OR-tree searches. Using the bounds developed, the authors derive sufficient conditions for assuring that parallelism will not degrade performance and necessary conditions for allowing parallelism to have a speedup greater than the ratio of the numbers of processors. These bounds and conditions provide the theoretical foundation for determining the number of processors required to assure a near-linear speedup.

Li, Guo-Jie↗
NASA NTRS1994

Empirical study of parallel LRU simulation algorithms

This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.

Carr, Eric↗
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↗
NASA NTRS1987

Improvements in the perturbation simulations of the global reference atmospheric model

The Global Reference Atmospheric Model (GRAM) program includes the capability for simulating pseudo-random perturbations in density, temperature, pressure, or wind components along a simulated reentry trajectory or other path through the atmosphere. Some concerns were expressed by GRAM users, however, that the mean-square perturbation gradients may be too large for small values of the vertical separation Delta z. The present GRAM perturbation simulations, based on a one-step autoregressive model, yield a power spectrum versus wavenumber k which is proportional to k sup -2 at high wavenumbers. This feature also produces mean-square perturbation differences which are directly proportional to Delta z, and mean-square perturbation gradients which are inversely proportional to Delta z. Thus, root-mean-square gradients, (Delta f/Delta z) sub rms, increase with decreasing Delta a as Delta z sup -1/2. A simple modification to GRAM is suggested which overcomes this problem, i.e., which produce root-mean-square gradient that remain bound as Delta z approaches zero. Possible applications of more sophisticated simulation approaches, e.g., second order autoregressive models, or fractal model techniques, were also explored briefly but found to yield improvements which appear too small to justify their considerable added complexity for use in the GRAM programs.

Justus, C. G.↗