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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Improved genome editing by an engineered CRISPR-Cas12a

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis - and trans -DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2–18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

IBM Open Science Price - SWAP Gate Challenge

On November 30, 2020, IBM announced an open science price competition aimed at improving the fidelity of a SWAP gate on their 7 qubit Quantum system named ”Casablanca”. The details of the SWAP gate problem was outlined in a Jupyter notebook, which utilizes the IBM developed open source package Qiskit. The participants were allowed to work in teams with up to five people and restricted to only use open source software in solving the problem. Their results were due on April 16, 2021. Our approach to solving the SWAP gate challenge is based on the quantum optimal control techniques implemented in our open source packages Juqbox.jl and Quandary. The results from the optimal control approach is only as good as the accuracy in the description of the quantum system dynamics, characterized by a Hamiltonian model that was provided by IBM. Based on the calibrated control pulses IBM provide for the standard gate set, we developed a reverse engineering approach to calibrate our computational model. Techniques were developed to translate between Qiskit’s pulse representation and the B-spline formulation used in Juqbox and Quandary. The fidelity of the optimized pulse sequences were estimated using Qiskit’s randomized bench marking techniques.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1985

Mutant Peas as Probes in the Understanding of Growth and Gravitropism

One mutant of Pism sativum CREEP grows normally up to the first internode stage, and then begins to grow plagiotropically. The upper internodes bend slowly downward according to a programmed sequence which follows circumnutation of the previous internode and opening of the previous leaves, but preceeds expansion of the previous leaves. The bending is partially inhibited by excission of the opposing stipules. The second mutant, AGEOTROPUM is gravitropically incompetant when grown etiolated, in the dark. When etiolated plants are illuminated with white light, the stems become gravitropically competant, but the roots do not. If the plants are grown in the light in particulate medium, some secondary roots, growing randomly, emerge into the air, and turn and grow downward toward moist soil. When etiolated AGEOTROPUM plants are illuminated, the shoots then become able to respond to gravity in a normal, negatively orthogravitropic manner. The response is to red light and is reversed by far red light. The mutation may involve one or more of the following: (1) release of sequestered calcium for redistribution; (2) radial transport of released calcium; or (3) net calcium flux in the upward direction.

Jaffe, M. J.↗
NASA NTRS2011

Unsupervised Detection of Planetary Craters by a Marked Point Process

With the launch of several planetary missions in the last decade, a large amount of planetary images is being acquired. Preferably, automatic and robust processing techniques need to be used for data analysis because of the huge amount of the acquired data. Here, the aim is to achieve a robust and general methodology for crater detection. A novel technique based on a marked point process is proposed. First, the contours in the image are extracted. The object boundaries are modeled as a configuration of an unknown number of random ellipses, i.e., the contour image is considered as a realization of a marked point process. Then, an energy function is defined, containing both an a priori energy and a likelihood term. The global minimum of this function is estimated by using reversible jump Monte-Carlo Markov chain dynamics and a simulated annealing scheme. The main idea behind marked point processes is to model objects within a stochastic framework: Marked point processes represent a very promising current approach in the stochastic image modeling and provide a powerful and methodologically rigorous framework to efficiently map and detect objects and structures in an image with an excellent robustness to noise. The proposed method for crater detection has several feasible applications. One such application area is image registration by matching the extracted features.

Troglio, G.↗
DOE OSTI2025

Machine learning enhanced predictions of ICRF heating: Overcoming numerical limitations via data curation

In this work, we present the development of robust surrogate models for Ion Cyclotron Range of Frequencies (ICRF) and High-Harmonic Fast Wave (HHFW) heating predictions in fusion plasmas. Building upon our previous efforts to achieve real-time capable models, we identify the cause of the outliers found using TORIC in certain HHFW heating scenarios. The outliers are observed to be spurious ion Bernstein wave (IBW)-like modes caused by a wavelength control algorithm designed to address challenging scenarios with high perpendicular wavenumbers. The effect arises from the modulation in the perpendicular susceptibility, which can induce sign reversal and IBW-like propagation for scenarios featuring normalized ion Larmor radius λ i ≫ 1. We use TORIC with this algorithm disabled to generate a novel HHFW-NSTX database that is free of outliers. Surrogate models trained on this database, including Random Forest Regressor (RFR), Multi-Layer Perceptrons, and Gaussian Process Regressors (GPR), demonstrate the ability to accurately predict HHFW heating profiles, with regression scores of R 2 ∈[0.93−0.99]. Additionally we demonstrate that it is possible to generalize predictions beyond training data by the use of both RFR and GPR models, enabling the prediction of scenarios previously limited to the original model. GPR models also provide uncertainty quantification, offering insights into model confidence. This work introduces a comprehensive Verification, Validation, and Uncertainty Quantification methodology for surrogate modeling, applicable not only to ICRF heating but also to other RF heating challenges and fusion physics problems. Beyond accelerated inference, these models show effective extrapolation capabilities, providing an alternative for addressing numerical challenges.

Artificial neural networks↗
DOE OSTI2024

Circulating levels of micronutrients and risk of osteomyelitis: a Mendelian randomization study

Background Few observational studies have investigated the effect of micronutrients on osteomyelitis, and these findings are limited by confounding and conflicting results. Therefore, we conducted Mendelian randomization (MR) analyses to evaluate the association between blood levels of eight micronutrients (copper, selenium, zinc, vitamin B12, vitamin C, and vitamin D, vitamin B6, vitamin E) and the risk of osteomyelitis. Methods We performed the two-sample and multivariable Mendelian randomization (MVMR) to investigate causation, where instrument variables for the predictor (micronutrients) were derived from the summary data of micronutrients from independent cohorts of European ancestry. The outcome instrumental variables were used from the summary data of European-ancestry individuals ( n = 486,484). The threshold of statistical significance was set at p < 0.00625. Results We found a significant causal association that elevated zinc heightens the risk of developing osteomyelitis in European ancestry individuals OR = 1.23 [95% confidence interval (CI) [1.07, 1.43]; p = 4.26E-03]. Similarly, vitamin B6 showed a similar significant causal effect on osteomyelitis as a risk factor OR = 2.78 (95% CI [1.34, 5.76]; p = 6.04E-03; in the secondary analysis). Post-hoc analysis suggested this result (vitamin B6). However, the multivariable Mendelian randomization (MVMR) provides evidence against the causal association between zinc and osteomyelitis OR = 0.98(95% CI [−0.11, 0.07]; p = 7.20E-1). After searching in PhenoScanner, no SNP with confounding factors was found in the analysis of vitamin B6. There was no evidence of a reverse causal impact of osteomyelitis on zinc and vitamin B6. Conclusion This study supported a strong causal association between vitamin B6 and osteomyelitis while reporting a dubious causal association between zinc and osteomyelitis.

Zhang, Xu↗
DOE OSTI2021

Nanocomposites Based on Coil-Comb Diblock Copolymers

The polymer chain architecture is an important factor determining the phase behavior of nanoparticle (NP) assembly in polymer matrices. Block copolymers (BCPs) containing a random copolymer (RCP) block present a convenient variation on traditional BCPs to tune the interaction parameters between the polymer blocks and the nanofillers as well as to evaluate the effect of the chain architecture on the NP arrangements within BCP microdomains. Here, we synthesized BCPs with a coil polystyrene (PS) block and a comb RCP block through reversible addition-fragmentation chain transfer polymerization. The RCP block consists of methyl- and lauryl acrylates, the latter of which confers a long-chain alkyl moiety to favorably interact with alkyl-passivated NPs. BCPs showing lamellar, cylindrical, and mixed morphologies were obtained by varying the volume fractions of the RCP block (f RCP ). In comparison to coil-coil BCP, the coil-comb BCPs show highly asymmetric phase behavior with respect to fRCP, where lamellar morphologies were observed at fRCP from 0.31 to 0.51. NPs in the size of 4-5 nm were successfully incorporated in the RCP block of the BCPs with periodicities of 30-60 nm. An order-to-order phase transition from lamellae to PS cylinders was observed after the addition of only 1-2 vol % 5 nm NPs into the BCP with a periodicity of 25 nm and f RCP of 0.51. Self-consistent field theory-density functional theory simulations qualitatively described the observed morphologies and phase transitions in the nanocomposites. Here, the current study presents a platform to fabricate nanocomposites with NP assemblies in coil-comb BCPs that contain a random copolymer block and provides insight into how polymer chain architectures can affect the phase behavior of BCPs and nanocomposites.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗
NASA NTRS1978

Simplified data compressor

Image data are compressed for transmission by simple, economical circuitry. Compressor handles data in blocks of 64 samples. Mean from previous line is subtracted, and pseudo-random sequence of positive and negative 1's multiplies samples of each block. Hadamard transform applied to blocks yields 64 transform coefficients. Each coefficient is compared with approximation to corresponding coefficient of previous line, and difference is quantized. Values are transmitted or stored. Procedure is reversed to reproduce image.

Rice, R. F.↗
DOE OSTI2026

Nanoionics Drastically Accelerating Mass Transfer at Elevated Temperatures over 750 °C

Nanoionics were previously considered thermally unstable and infeasible for devices operating above 500 °C. Here, we elucidate the design principle for establishing stable nanoionics from various oxides. We utilized reversible solid oxide cells (SOCs) as the test bed and implemented nanoionics using atomic layer deposition (ALD). We demonstrate a straightforward, interface-controlled, practical approach to render a conformal, ∼15 nm thick ALD film, which initially thermodynamically favors the formation of a solid solution with the substrate into surface nanoionics with single or double layers of nanograins with random crystal orientations. The nanoionics exhibited conductivity estimated to be 7 orders of magnitude higher than that of their bulk-scale counterpart. They demonstrated conformability with uniform grain sizes of ∼15 nm, even after electrochemical operation for ∼500 h at 750 °C and 1000 h at 850 °C. The thermal stability and conductivity of such nanoionics represent a conceptual and technological framework in nanoionics.

atomic layer deposition↗
DOE OSTI2023

Study of beyond nearest-neighbor environment and intermediate-range order in a sodium aluminosilicate geopolymer using Reverse Monte Carlo modeling

A large scale three-dimensional structural model of a geopolymer with an approximate composition of NaAlSi 2 O 6 .5.5H 2 O obtained by Reverse Monte Carlo (RMC) modeling based on experimental high-energy x-ray diffraction is presented for the first time in order to obtain information regarding beyond nearest-neighbor environment and intermediate-range order (IRO). RMC model exhibits a three-dimensional network consisting of randomly cross-linked AlO 4 and SiO 4 tetrahedral units with uniformly distributed Na atoms and H 2 O molecules. The bond angle distributions, i.e. T-O-T, O-T-O and Na-O-Na angles, are somewhat distorted with lower values compared to analogous crystal systems. The origin of the first peak in the structure factor indicating IRO is investigated using the partial structure factors; Na-Na, Si-Na, Al-Si, O-H, and H-H atom pairs are found to be the main contributors. Ring size distribution analysis demonstrates that the structure mainly involves 6-, 7- and 8-membered rings. Finally, the coherence length of these IRO characteristics is ~10.3 Å.

36 MATERIALS SCIENCE↗
NASA NTRS1973

On the question of adequate hingeless rotor modeling in flight dynamics.

The somewhat controversial question of which elastic blade modes are essential in the flight mechanics of hingeless rotorcraft is studied on the basis of quasi-steady linear aerodynamics including reversed flow effects and uniform inflow. The modes are for the rotating blade, and intermode aerodynamic coupling terms are retained. The criteria for judging elastic mode effects include 19 hub moment and force derivatives, rotor trim data, rotor stability charts for lagged hub moment feedback, step gust and random gust responses. Fixed hub and constant chord blades with widely differing elasticity and inertia and with moderate twist are assumed.

Hohenemser, K. H.↗
NASA NTRS1988

Impact and extinction signatures in complete Cretaceous-Tertiary (K-T) boundary sections

The Zumaya, Caravaca and Agost sections in Spain, the El Kef section in Tunisia and the Negev (Nahal Avdat) sections in Israel are among the most continuous, expanded and complete K-T boundary sections. The distribution patterns of the planktic faunas were quantitatively analyzed in closely spaced samples across the K-T boundary in these sections, in conjuction with the geochemistry, stable isotopes, mineralogy and magnetostratigraphy. Three hundred foraminiferal specimens were randomly selected and determined. Reliable estimates for the foraminiferal productivity changes across the K-T boundary and for the 1 to 2 Ma interval preceding the K-T boundary were made from the numbers of individuals/gram of sediment corrected for the sedimentation rates (calculated from magnetic reversals and lithology). No gradual or stepwise extinction is seen below the K-T boundary nor any productivity decrease. Stable isotope analyses show a warming just after deposition of the ejecta layer, not cooling as predicted by nuclear winter scenarios, although the duration of such cooling may be too short to be observed even in these complete sections. Low REE values and cpx spherules with quench textures idential to quench-textures in diagenetically altered spherules, strongly indicate an oceanic site of (one of) the impactor(s).

Smit, J.↗
DOE OSTI2024

Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model

HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Here using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Atomic arrangements in an amorphous CoFeB ribbon extracted via an analysis of radial distribution functions

Here we discuss the atomic structure of amorphous ferromagnetic FeCoB alloys, which are used widely in spintronics applications. Specifically, we obtain the pair-distribution functions for various atomic pairs based on high-energy x-ray diffraction data taken from an amorphous Co 20 Fe 61 B 19 specimen. We start our reverse Monte Carlo cycles to determine the disordered structure with a two-phase model in which a small amount of cobalt is mixed with Fe 23 B 6 as a second phase. The structure of the alloy is found to be heterogeneous, where the boron atoms drive disorder through the random occupation of the atomic network. Our analysis also indicates the presence of small cobalt clusters that are embedded in the iron matrix and percolating the latter throughout the structure. This morphology can explain the enhanced spin polarization observed in amorphous magnetic materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Microstructural and rheological training and memory of nanocolloidal soft glasses under cyclic shear

An intrinsic feature of disordered and out-of-equilibrium materials, such as glasses, is the dependence of their properties on their history. An important example is rheological memory, in which disordered solids obtain properties based on their deformation history. Here, in this study, we employ x-ray photon correlation spectroscopy with in situ rheometry to characterize memory formation in a nanocolloidal soft glass due to cyclic shear. During a cycle, particles undergo irreversible displacements composed of a combination of shear-induced diffusion and heterogeneous, residual strain fields. At lower shear amplitudes, the displacements resemble a random walk in which the directions in each cycle are independent of those in preceding cycles, while at high amplitude, the irreversible displacements in consecutive cycles become correlated. The magnitudes of the displacements decrease with each cycle before reaching a steady state where the microstructure has been trained to achieve enhanced reversibility even at shear amplitudes well above yielding and despite the presence of thermal fluctuations. At amplitudes below and near yielding, these decreases are monotonic, while well above yielding, they are nonmonotonic, suggesting evidence of shear banding. Accompanying this microstructural training are corresponding decreases in the dissipation during each cycle and the magnitude of the residual stress toward steady-state values. Memory of the training is revealed by measurements in which the amplitude of the shear is changed after steady state is reached. The magnitude of the particle displacements, as well as the dissipation and the change in residual stress, vary nonmonotonically with the new shear amplitude, having minima near the training amplitude, thereby revealing correlated microscopic and macroscopic signatures of memory.

Chen, Yihao [Johns Hopkins Univ., Baltimore, MD (U↗
NASA NTRS1994

Continuous in vitro evolution of bacteriophage RNA polymerase promoters

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.

Non-NASA Center↗
NASA NTRS2004

Microsystem Cooler Development

A patented microsystem Stirling cooler is under development with potential application to electronics, sensors, optical and radio frequency (RF) systems, microarrays, and other microsystems. The microsystem Stirling cooler is most suited to volume-limited applications that require cooling below the ambient or sink temperature. Primary components of the planar device include: two diaphragm actuators that replace the pistons found in traditional-scale Stirling machines; and a micro-regenerator that stores and releases thermal energy to the working gas during the Stirling cycle. The use of diaphragms eliminates frictional losses and bypass leakage concerns associated with pistons, while permitting reversal of the hot and cold sides of the device during operation to allow precise temperature control. Three candidate microregenerators were custom fabricated for initial evaluation: two constructed of porous ceramic, and one made of multiple layers of nickel and photoresist in an offset grating pattern. An additional regenerator was prepared with a random stainless steel fiber matrix commonly used in existing Stirling machines for comparison to the custom fabricated regenerators. The candidate regenerators were tested in a piezoelectric-actuated test apparatus designed to simulate the Stirling refrigeration cycle. In parallel with the regenerator testing, electrostatically-driven comb-drive diaphragm actuators for the prototype device have been designed for deep reactive ion etching (DRIE) fabrication.

Moran, Matthew E.↗