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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 sources NASA NTRS DOE OSTI

DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Phase evolution and amorphous stability upon solid-state reaction in superlattice like Ge–Sb–Te combinatorial thin-film

In this paper, the superlattice-like (SLL) Ge–Sb–Te combinatorial thin films were prepared by using a high-throughput ion beam sputtering system. The phase evolution and amorphous stability of such films undergoing heat treatment as a function of the coating sequence and modulation period were systematically studied. The composition structure diagram was constructed via an automated process of data obtained by high-throughput synchrotron micro-X-ray diffraction and lab-based micro-X-ray fluorescence. Furthermore, the element distribution and microstructure in the depth direction of the SLL thin films were characterized with time-of-flight secondary ion mass spectrometry and transmission electron microscopy, respectively. These studies demonstrated that the coating sequence has a significant effect on the element distribution in the as-deposited SLL thin films and the structure of the final product upon solid-state reaction. Reducing the modulation period of the SLL thin film improves the stability of the amorphous Ge–Sb–Te phase. This work lays a solid foundation for the rational design of SLL Ge–Sb–Te thin films to improve their performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

Sources, Sinks, and the Distribution of OH in the Lower Stratosphere

Extensive measurement campaigns by the NASA ER-2 research aircraft have obtained a nearly pole-to-pole database of the species that control HOx (OH + HO2) chemistry. The wide dynamic range of these in situ measurements provides an opportunity to demonstrate empirically the mechanisms that control the HOx system. Measurements in the lower stratosphere show a remarkably tight correlation of OH concentration with the solar zenith angle (SZA). This correlation is nearly invariant over latitudes ranging from 70 S to 90 N and all seasons. An analysis of the production and loss of HOx in terms of the rate determining steps of reaction sequences developed by Johnston and Podolske and Johnston and Kinnison is used to clarify the behavior of the system and to directly test our understanding of the system with observations. Calculations using in situ measurements show that the production rate of HOx is proportional to O3 and ultraviolet radiation flux. The loss rate is proportional to the concentration and the partitioning of NOy (reactive nitrogen) and the concentration of HO2. In the absence of heterogeneous reactions, the partitioning of NOy is controlled by O3 and NOx and the concentration of HO2 is controlled by NOy and O3, so that the removal rate of OH is buffered against changes in the correlation of O3 and NOy. The heterogeneous conversion of NO2 to HNO3 is not an important net source of HO, because production and removal sequences are nearly balanced. Changes in NOy partitioning resulting from heterogeneous chemistry have a large effect on the loss rates of HOx, but little or no impact on the measured abundance of OH. The enhanced loss rates at high NO2/HNO3 are offset in the data set examined here by enhanced production rates resulting from increased photolysis rates resulting from the decreased O3 column above the ER-2.

Hanisco, T. F.↗

DOE OSTI2024

scMicrobe PTA: near complete genomes from single bacterial cells

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1987

A study of some approximations in the modeling of a coupled rotor/fuselage aeromechanical system

Equations of motion for a three-bladed hingeless rotor coupled to a gimbal-supported fuselage are developed. A brief derivation of the equations is presented, including the assumptions made, the ordering scheme, and a discussion of both the source of the aerodynamic axial load term and the reason for differences due to hinge sequence. The solution of the equations is discussed, including linearization, the use of multiblade coordinates to eliminate periodic coefficients, and specialization to a root-sprung model. The treatment of the blade root offset by using an ordering scheme to neglect higher-order terms is found to affect results in pitch and roll. A small aerodynamic loading term in the blade axial direction has a significant effect at large collective pitch settings, as does the choice of a flap-lag or a lag-flap transformation sequence for blade motion. The results for a hingeless rotor also differ significantly from those for the root-sprung model when the nonrotating natural frequencies are matched.

Blelloch, P. A.↗

DOE OSTI2026

Impact of control signal phase noise on qubit fidelity

As qubit decoherence times are increased and readout technologies are improved, nonidealities in the drive signals, such as phase noise, are going to represent a growing limitation to the fidelity achievable at the end of complex control pulse sequencies. Here we study the impact on fidelity of phase noise affecting reference oscillators with the help of numerical simulations, which allow us to directly take into account the interaction between the phase fluctuations in the control signals and the evolution of the qubit state. Our method is based on the generation of phase noise realizations consistent with a given power spectral density, that are then applied to the pulse carrier in simulations, with Qiskit-Dynamics, of the qubit temporal evolution. By comparing the final state obtained at the end of a noisy pulse sequence with that in the ideal case and averaging over multiple noise realizations, we estimate the resulting degradation in fidelity, and exploiting an approximate analytical representation of a carrier affected by phase fluctuations, we discuss the contributions of the different spectral components of phase noise.

Barsotti, Agata [Pisa U.]↗

DOE OSTI2026

Methyl formate oxidation kinetics up to 100 atm

Methyl formate (MF, CH3OCHO), the simplest ester, is a representative oxygenated fuel with high oxygen content, and low sooting tendency. However, its oxidation behavior under high-pressure and intermediate-temperature conditions remains insufficiently understood, especially where low-temperature peroxy radical chemistry, methanol chemistry, and pressure-dependent reaction pathways play a critical role. In this study, MF oxidation experiments were conducted in the Princeton supercritical-pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm over the temperature range of 400–950 K under both fuel-lean and fuel-rich conditions. Based on the experimental results, an updated HP-Mech was developed by incorporating previous MF sub-mechanisms, expanded low-temperature peroxy pathways, and evaluated pressure-dependent decomposition kinetics. The newly updated HP-Mech shows greatly improved performance in predicting the onset temperature, the key intermediate species fractions, methanol formation, and the progression of MF oxidation across all the experimental conditions. Path flux analysis indicates that MF consumption at the onset stage is dominated by H-abstraction at the methyl site, forming CH2OCHO radicals that lead to the formation and isomerization of O2CH2OCHO, driving low-temperature chain propagation. Moreover, H-abstraction at the formate site forms CH3OCO radicals that preferentially decompose to CH3, initiating the methanol formation pathway linked to CH3O2 and HO2 chemistry. At the same time, HO2 formation is strongly coupled to MF oxidation through multiple MF-derived radical pathways. HCO originates from MF oxidation and acts as a key coupling species linking fuel consumption to HO2 buildup, especially under high-pressure and intermediate-temperature conditions. In addition to this dominant channel, supplementary HO2 formation pathways involving CH3, CH3O, CH2OH, and CH3O2 reacting with O2 further connect methanol chemistry and oxygenated radical chemistry to the HO2 pool, indicating the central role of HO2 in governing MF oxidation. Sensitivity analysis identifies MF with OH/HO2/CH3O2 reactions and the HO2/H2O2/OH sequence as the key factors controlling reactivity in the high-pressure and intermediate-temperature regime. MF directly reacts with OH/HO2/CH3O2 to consume the fuel and produce reactive radicals like CH2OCHO and CH3OCO that undergo subsequent oxidation pathways. Moreover, HO2 recombination suppresses oxidation at lower temperatures, while thermal decomposition of H2O2 accelerates OH production and promotes fuel consumption as temperature increases. The direct formation of active OH from HO2 radicals further completes the mechanism, improving its prediction especially during the oxidation onset stage.

Low-temperature Chemistry↗

DOE OSTI2023

Gas-phase microactuation using kinetically controlled surface states of ultrathin catalytic sheets

Biological systems convert chemical energy into mechanical work by using protein catalysts that assume kinetically controlled conformational states. Synthetic chemomechanical systems using chemical catalysis have been reported, but they are slow, require high temperatures to operate, or indirectly perform work by harnessing reaction products in liquids (e.g., heat or protons). Here, we introduce a bioinspired chemical strategy for gas-phase chemomechanical transduction that sequences the elementary steps of catalytic reactions on ultrathin (<10 nm) platinum sheets to generate surface stresses that directly drive microactuation (bending radii of 700 nm) at ambient conditions (T = 20 °C; P total = 1 atm). When fueled by hydrogen gas and either oxygen or ozone gas, we show how kinetically controlled surface states of the catalyst can be exploited to achieve fast actuation (600 ms/cycle) at 20 °C. Finally, we also show that the approach can integrate photochemically controlled reactions and can be used to drive the reconfiguration of microhinges and complex origami- and kirigami-based microstructures.

42 ENGINEERING↗

DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Pentose Phosphate Pathway Reactions in Photosynthesizing Cells

The pentose phosphate pathway (PPP) is divided into an oxidative branch that makes pentose phosphates and a non-oxidative branch that consumes pentose phosphates, though the non-oxidative branch is considered reversible. A modified version of the non-oxidative branch is a critical component of the Calvin–Benson cycle that converts CO2 into sugar. The reaction sequence in the Calvin–Benson cycle is from triose phosphates to pentose phosphates, the opposite of the typical direction of the non-oxidative PPP. The photosynthetic direction is favored by replacing the transaldolase step of the normal non-oxidative PPP with a second aldolase reaction plus sedoheptulose-1,7-bisphosphatase. This can be considered an anabolic version of the non-oxidative PPP and is found in a few situations other than photosynthesis. In addition to the strong association of the non-oxidative PPP with photosynthesis metabolism, there is recent evidence that the oxidative PPP reactions are also important in photosynthesizing cells. These reactions can form a shunt around the non-oxidative PPP section of the Calvin–Benson cycle, consuming three ATP per glucose 6-phosphate consumed. A constitutive operation of this shunt occurs in the cytosol and gives rise to an unusual labeling pattern of photosynthetic metabolites while an inducible shunt in the stroma may occur in response to stress.

13C↗

NASA NTRS1970

Apollo 12 photography 70 mm, 16 mm, and 35 mm frame index

For each 70-mm frame, the index presents information on: (1) the focal length of the camera, (2) the photo scale at the principal point of the frame, (3) the selenographic coordinates at the principal point of the frame, (4) the percentage of forward overlap of the frame, (5) the sun angle (medium, low, high), (6) the quality of the photography, (7) the approximate tilt (minimum and maximum) of the camera, and (8) the direction of tilt. A brief description of each frame is also included. The index to the 16-mm sequence photography includes information concerning the approximate surface coverage of the photographic sequence and a brief description of the principal features shown. A column of remarks is included to indicate: (1) if the sequence is plotted on the photographic index map and (2) the quality of the photography. The pictures taken using the lunar surface closeup stereoscopic camera (35 mm) are also described in this same index format.

Source record↗

NASA NTRS1984

Propagation as a mechanism of reorientation of the Juan de Fuca ridge

A revised model is presented of the tectonic evolution of the Juan de Fuca ridge by propagating rifting. The new model has three different relative rotation poles, covering the time intervals 17.0-8.5 Ma, 8.5-5.0 Ma, and 5.0 Ma to the present. The rotation pole shifts at 8.5 and 5.0 Ma imply clockwise shifts in the direction of relative motion of 10 deg to 15 deg. At each of these shifts, the pattern of propagation reorganizes, and the new ridges formed by propagation are at an orientation closer to orthogonal to the new direction of motion than the orientation of the preexisting ridges. The model, containing a total of seven propagation sequences, shows excellent agreement with the isochrons inferred from the magnetic anomaly data, except in areas complicated by the separate Explorer and Gorda plates. The agreement between model and data near the Explorer plate breaks down abruptly at an age of about 5 Ma, indicating that the probable cause of the rotation pole shift at that time was the separation of the Explorer plate from the Juan de Fuca plate.

Wilson, D. S.↗

NASA NTRS1999

A complex ligase ribozyme evolved in vitro from a group I ribozyme domain

Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.

NASA Discipline Exobiology↗

NASA NTRS2007

URANS Application with CFL3D

This case was run using CFL3D, a multi-zone Reynolds-averaged Navier-Stokes code developed at NASA Langley [1]. It solves the thin-layer form of the Navier-Stokes equations in each of the (selected) coordinate directions. It can use 1-to-1, patched, or overset grids, and employs local time step scaling, grid sequencing, and multigrid to accelerate convergence to steady state. In time-accurate mode, CFL3D has the option to employ dual-time stepping with subiterations and multigrid, and it achieves second order temporal accuracy. CFL3D is a finite volume method. It uses third-order upwind-biased spatial differencing on the convective and pressure terms, and second-order differencing on the viscous terms; it is globally second-order spatially accurate. The flux difference-splitting (FDS) method of Roe is employed to obtain fluxes at the cell faces. It is advanced in time with an implicit three-factor approximate factorization method.

Rumsey, C. L.↗

NASA NTRS2007

RANS and URANS Application with CFL3D

Rumsey, C. L.↗

NASA NTRS2014

Spatio-Temporal Video Segmentation with Shape Growth or Shrinkage Constraint

We propose a new method for joint segmentation of monotonously growing or shrinking shapes in a time sequence of noisy images. The task of segmenting the image time series is expressed as an optimization problem using the spatio-temporal graph of pixels, in which we are able to impose the constraint of shape growth or of shrinkage by introducing monodirectional infinite links connecting pixels at the same spatial locations in successive image frames. The globally optimal solution is computed with a graph cut. The performance of the proposed method is validated on three applications: segmentation of melting sea ice floes and of growing burned areas from time series of 2D satellite images, and segmentation of a growing brain tumor from sequences of 3D medical scans. In the latter application, we impose an additional intersequences inclusion constraint by adding directed infinite links between pixels of dependent image structures.

Segmentation↗

NASA NTRS2017

Application of Human-Autonomy Teaming to an Advanced Ground Station for Reduced Crew Operations

Within human factors there is burgeoning interest in the "human-autonomy teaming" (HAT) concept as a way to address the challenges of interacting with complex, increasingly autonomous systems. The HAT concept comes out of an aspiration to interact with increasingly autonomous systems as a team member, rather than simply use automation as a tool. The authors, and others, have proposed core tenets for HAT that include bi-directional communication, automation and system transparency, and advanced coordination between human and automated teammates via predefined, dynamic task sequences known as "plays." It is believed that, with proper implementation, HAT should foster appropriate teamwork, thus increasing trust and reliance on the system, which in turn will reduce workload, increase situation awareness, and improve performance. To this end, HAT has been demonstrated and/or studied in multiple applications including search and rescue operations, healthcare and medicine, autonomous vehicles, photography, and aviation. The current paper presents one such effort to apply HAT. It details the design of a HAT agent, developed by Human Automation Teaming Solutions, Inc., to facilitate teamwork between the automation and the human operator of an advanced ground dispatch station. This dispatch station was developed to support a NASA project investigating a concept called Reduced Crew Operations (RCO); consequently, we have named the agent R-HATS. Part of the RCO concept involves a ground operator providing enhanced support to a large number of aircraft with a single pilot on the flight deck. When assisted by R-HATS, operators can monitor and support or manage a large number of aircraft and use plays to respond in real-time to complicated, workload-intensive events (e.g., an airport closure). A play is a plan that encapsulates goals, tasks, and a task allocation strategy appropriate for a particular situation. In the current implementation, when a play is initiated by a user, R-HATS determines what tasks need to be completed and has the ability to autonomously execute them (e.g., determining diversion options and uplinking new routes to aircraft) when it is safe and appropriate. R-HATS has been designed to both support end users and researchers in RCO and HAT. Additionally, R-HATS and its underlying architecture were developed with generalizability in mind as a modular software applicable outside of RCO/aviation domains. This paper will also discuss future further development and testing of RHATS.

automation↗

NASA NTRS2017

Flight Deck Surface Trajectory-Based Operations (STBO): A Four-Dimensional Trajectory (4DT) Simulation

Within human factors there is burgeoning interest in the Human-Autonomy Teaming (HAT) concept as away to address the challenges of interacting with complex, increasingly autonomous systems. The HAT concept comes out of an aspiration to interact with increasingly autonomous automation as a team member, rather than simply use automation as a tool. The authors, and others, have proposed core tenets for HAT that include bi-directional communication, automation and system transparency, and advanced coordination between human and automated teammates via predefined, dynamic task sequences known as plays (Shively et al., 2017). It is believed that, with proper implementation, HAT should foster appropriate teamwork, thus increasing trust and reliance on the system, which in turn will reduce workload, increase situation awareness, and improve performance. To this end, HAT has been demonstrated and/or studied in multiple applications including search and rescue operations (Nourbakhsh et al., 2005), healthcare and medicine (Tsui Yanco, 2007), autonomous vehicles (Parasuraman, Barnes, Cosenzo, Mulgund, 2007), photography (Lachter, Brandt, Sadler, Shively, in press), and aviation (Shively et al., in press). The current paper presents one such effort to apply HAT. It details the design of a R-HAT Agent developed as part of a NASA Research Agreement awarded to Human-Autonomy Teaming Solutions Inc. (HATS Inc), and developed in collaboration with the Human-Autonomy Teaming Laboratory at NASA Ames Research Center. The role of this Agent is to mediate interaction between the automation and the human operator of an advanced ground dispatch station, with this mediation based upon previously mentioned core tenets for HAT and the many lessons learned from the HAT research literature. This dispatch station was developed to support a NASA project investigating a concept called Reduced Crew Operations (RCO; Lachter, Brandt, Battiste, Matessa, Johnson, in press). Part of the RCO concept involves a ground operator providing enhanced support to a large number of aircraft with a single pilot on the flight deck. When assisted by the Agent, operators can monitor and support or manage a large number of aircraft and use plays to respond in real-time to complicated, workload-intensive events (e.g., an airport closure). A play is a plan that encapsulates goals, tasks, and a task allocation strategy appropriate for a particular situation. In the current implementation, when a play is initiated by a user, the Agent determines what tasks need to be done and has the ability to autonomously execute them (e.g., determining diversion options and uplinking new routes to aircraft) when it is safe and appropriate. The R-HAT Agent has been designed to both support end users and research in RCO and HAT. Additionally, the Agent and its underlying architecture were developed with generalizability in mind as a modular piece of software applicable outside of RCO aviation in domains such as those mentioned above. This paper will also discuss future further development and testing of the R-HAT Agent.

Bakowski, Deborah L.↗