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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Sequence-based analysis of the Vitis vinifera L. cv Cabernet Sauvignon grape must mycobiome in three South African vineyards employing distinct agronomic systems

Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. In addition, data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Metastatic castration resistant prostate cancer with squamous cell, small cell, and sarcomatoid elements—a clinicopathologic and genomic sequencing-based discussion

Histologic variants are uncommon but well reported amongst cases of prostatic adenocarcinoma, including those in the setting of hormonal and/or chemoradiation therapy and castration resistance. However, the spectrum of morphologic phenotypes and molecular alterations present in such histologic variants are still incompletely understood. Herein, we describe a case of metastatic prostatic adenocarcinoma with hormonal and chemoradiation therapy-associated differentiation, displaying a combination of squamous cell, small cell, and sarcomatoid elements. The morphologic, immunohistochemical, and molecular observations are discussed with attention given to the gene alterations present, including in TP53, NF1, AR, PTEN, and RB1. Finally, we will compare our findings with those observed in uncommonly reported similar cases so as to detail the molecular underpinnings of such processes which may carry therapeutic implications.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Sequence-based generative AI design of versatile tryptophan synthases

Enzymes are powerful and sustainable catalysts, but their widespread application is limited by the difficulty of identifying functional starting points for optimization, creating a major bottleneck in early- stage biocatalyst discovery. Designing libraries of such starting enzymes remains particularly challenging. Here, we use the GenSLM protein language model to generate novel β-subunit of tryptophan synthase (TrpB) enzymes that express in Escherichia coli and are both stable and catalytically active. Many generated TrpBs also display significant substrate promiscuity, outperforming their natural counterparts on non-native substrates. Some even surpass laboratory-evolved TrpBs. Comparison of the most-active and most-promiscuous generated TrpB to its closest natural homolog confirms that the enhanced versatility is absent from the natural enzyme, highlighting the creative potential of generative models. These results demonstrate that the generated TrpBs not only preserve natural structure and function but also acquire non-natural properties, establishing generative models as powerful tools for biocatalyst discovery and engineering.

biocatalysis↗
DOE OSTI2014

Chip-based sequencing nucleic acids

A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sequence-Based Anomaly Detection in Critical Infrastructure Networks

United States critical infrastructure faces new cyber threats from adversarial nation-state actors in the form of malware-free attacks. Traditional cybersecurity techniques use rules-based methods to identify indicators of compromise on networks, often missing these sophisticated attacks. Our approach leverages multiple state of the art machine learning models in a pipeline to identify abnormal network events through sequential analysis. We combine both device and packet-level information into individual events to characterize anomalous network actions. The model is trained and tested on real network traffic from the Idaho National Lab High Performance Computing (HPC) with greater than 98% precision. It is capable of flagging malicious tactics used by adversaries in malware-free attacks, severe changes to the network, and abnormal user activity by network devices.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2019

Light-Driven Charge Transfer in Face-to-Face Donor-Spacer-Acceptor Supramolecular Systems

The efficient conversion of sunlight to a useful form of energy both in green plants and in manmade dye-sensitized solar cells requires the efficient separation of a positive and negative charge. The charge separation process begins with the absorption of visible or ultraviolet light by a pigment such as chlorophyll or a dye such as a transition metal complex followed by fast electron transfer to a neighboring molecule to form a pair of ionized molecules with opposite charges. At that point, one of the two opposite charges must rapidly move away from the other one by the process of charge separation. Once the migrating charge reaches its destination, it can be converted to electrical or chemical energy. The overall efficiency of charge separation in these systems is determined by the competition between charge separation and charge recombination at each stage in the process. Whereas most investigations of photoinduced charge separation have employed synthetic polymers or covalent linkages to separate the photoactive molecular and charge acceptor, we have employed the natural biopolymer DNA for this purpose. DNA possesses a unique structure consisting of a hydrophobic core of hydrogen-bonded base pairs which form a one-dimensional π-stacked array. The possibility that the π-stacked base pairs of DNA might function as a one-dimensional conductor or molecular wire was first advanced over 50 years ago. However, systematic measurements of the dynamics and efficiency of charge separation in DNA-based systems were not undertaken prior to the initiation of our studies 22 years ago. A variety of organic chromophores can be attached to one or both ends of the base pair domain of DNA or at any location within the domain. The length and base sequence of the base pair domain can also be varied. The structures of these synthetic derivatives of DNA have been determined using a combination of X-ray diffraction, NMR spectroscopy, and molecular modeling. Selective excitation with UV or visible light of the appropriate chromophore can effect injection of either positive charge (holes) or negative charge (electrons) into the base pair domain. The dynamics of hole or electron injection can be studied by a combination of fluorescence quenching and transient absorption measurements. Moreover, the simple design of our systems is amenable to theoretical modeling, allowing the development and testing of models which may prove applicable to more complex systems. Our initial studies of hole transport in short synthetic DNA with either repeating or alternating base sequences showed it to be strongly distance dependent, seemingly contradicting claims that DNA might serve as a wire in molecular electron devices. Further research on the base-sequence dependence of hole transport dynamics showed that significant enhancement in hole transport dynamics could be achieved by the used of special sequences designed to prevent the photo-generated charges from recombining. More recent experimental research and theoretical modelling has served to define each stage of the charge-separation process: electronic excitation, hole injection, hole transport, hole transport, and charge recombination. DNA is less effective as a carrier for electron transport; however, many of these details have also been determined for this process. In summary, a combination of molecular design and synthesis, spectroscopy, and theory have made possible the most complete study of photoinduced charge separation on any complex donor-bridge-acceptor system studied to date. These results serve as a benchmark to which related studies can be compared.

14 SOLAR ENERGY↗
NASA NTRS1993

Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

Non-NASA Center↗
DOE OSTI2016

Extracting flat-field images from scene-based image sequences using phase correlation

Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1993

Telerobot control system

This invention relates to an operator interface for controlling a telerobot to perform tasks in a poorly modeled environment and/or within unplanned scenarios. The telerobot control system includes a remote robot manipulator linked to an operator interface. The operator interface includes a setup terminal, simulation terminal, and execution terminal for the control of the graphics simulator and local robot actuator as well as the remote robot actuator. These terminals may be combined in a single terminal. Complex tasks are developed from sequential combinations of parameterized task primitives and recorded teleoperations, and are tested by execution on a graphics simulator and/or local robot actuator, together with adjustable time delays. The novel features of this invention include the shared and supervisory control of the remote robot manipulator via operator interface by pretested complex tasks sequences based on sequences of parameterized task primitives combined with further teleoperation and run-time binding of parameters based on task context.

Backes, Paul G.↗
DOE OSTI2019

Foldamer architectures of triazine-based sequence-defined polymers investigated with molecular dynamics simulations and enhanced sampling methods

Triazine-based sequence-defined polymers have recently been developed that are biomimetic and robust (Grate \latin{et al.} Angewandte Chemie 2016). In molecular dynamics (MD) simulations, the triazine polymers were shown to form linear nanorod foldamers through hydrogen bonding and $\pi$-$\pi$ interactions. The nanorod foldamers have motifs resembling those of DNA, $\alpha$-helices, and $\beta$-sheets, and have potential to be useful building blocks for new macromolecules and materials. To understand the formation of nanorod foldamers, we investigate how linker structures in the middle of the triazine polymers lead to folding using MD simulations. We found that a variety of linkers can participate in folding, but that specific linker structures are more favorable than others, depending on the polymer length. Folding of hexamers into well-defined nanorod foldamers was most favorable with pentanediamine and \emph{ortho}-xylenediamine linkers in the center of the polymers. Foldamers with \emph{ortho}-xylenediamine linkers in the center were investigated for longer polymers, i.e., octamers and decamers, using two different enhanced sampling methods, since regular MD simulations had failed to show any folding for these longer polymers. In particular, the recently developed concurrent adaptive sampling (CAS) algorithm (Ahn \latin{et al.} J. Chem. Phys. 2017) and replica exchange molecular dynamics (REMD) were used. We found that the two enhanced sampling methods did lead to the observation of foldamers, and that REMD revealed new foldamer architectures where \emph{cis}-\emph{trans} isomerizations had occurred. Foldamer formation, diversity, and the strengths and limitations of simulation techniques are discussed. These findings provide new insights into the diversity of foldamer architectures for a new type of biomimetic synthetic polymer.

Foldamers, Nanorods, Free energy landscapes, Molec↗
DOE OSTI2018

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and π–π interactions, and conserve their cis/trans conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated with the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimers of triazine trimers. Here, we found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.

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

Robust deep learning–based protein sequence design using ProteinMPNN

Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning–based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo–electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

PLAN-IT - Knowledge-based mission sequencing

PLAN-IT (Plan-Integrated Timelines), a knowledge-based approach to assist in mission sequencing, is discussed. PLAN-IT uses a large set of scheduling techniques known as strategies to develop and maintain a mission sequence. The approach implemented by PLAN-IT and the current applications of PLAN-IT for sequencing at NASA are reported.

Biefeld, Eric W.↗
DOE OSTI2024

Structure-aware annotation of leucine-rich repeat domains

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Xu, Boyan↗