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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 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

One dimensional full wave analysis of slow-to-fast mode conversion in lower hybrid frequencies

The linear conversion from the slow wave to the fast wave in the lower hybrid range of frequencies is analyzed numerically by using the set of field equations describing waves in a cold plane-stratified plasma. The equations are solved as a two-point boundary value problem, where the polarizations of each mode are set consistently in the boundary conditions. The scattering coefficients and the field patterns are obtained for various density profiles. It is shown that, for large density scale length, the results agree well with the traditional cognitions. In contrast, the reflected component and the probable transmitted-converted component from the conversion region, which are neglected in the usual calculations, become significant when the scale length is smaller than the wavelength of the mode. The inclusion of these new components will improve the accuracy of the simulated propagation and deposition for the injected rf power when the conversion process is involved within a sharp-varying density profile. Meanwhile, the accessibility of the incident slow wave for the low frequency case is also affected by the scale length of the density profile.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗
DOE OSTI2024

Sentinel

Network intrusion detection systems (NIDS) are commonplace in network security but they frequently employ algorithms that are computational demanding requiring hardware and software with significant power requirements. Two examples of such resource-intensive algorithms used for network security are regular expression matching and broader signature pattern matching which are commonly used in deep packet inspection (DPI). Network security algorithms that have large power requirements may be a challenge for low-power internet-of-things (IoT) environments, which generally lack the power resources to implement complex security measures like computationally expensive DPI at the edge. Furthermore, IoT environments incorporating 5G standalone networks have network latency constraints beyond just power that make DPI at the edge even more difficult. Programmable logic is ideally suited for machine learning inference for DPI because of its deep instruction level parallelism and single-cycle memory access. Machine learning approaches for DPI have been explored before using the programmable logic of field programmable gate arrays (FPGA) as a potential solution for NIDS approaches that would be power-suitable for IoT. However, those previous programmable logic NIDS approaches utilize either a supervised or unsupervised learning model. Sentinel utilizes the ensemble of these two machine learning approaches known as a semi-supervised approach which has shown promise in NIDS implementations. Sentinel provides a programmable logic implementation of a semi-supervised approach for DPI which operates at much lower power and latency than a GPU implementation with negligible loss of accuracy due to quantization through a logistic regressor.

Anderson, MatthewW [Idaho National Laboratory (INL↗
DOE OSTI2025

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗
DOE OSTI2022

Quantitative measurements of density in shock-compressed silver up to 330 GPa using x-ray diffraction

This work presents a structural study of shock-compressed states in Ag to 331 GPa, accessed via laser shock compression. Structures of the resulting crystalline phases and the average atomic distribution of the liquid state are determined using in situ x-ray diffraction. We employ structure factor analysis, adapted for a non-monochromatic x-ray source, to determine the density of the liquid phase from analysis of x-ray diffraction data for the first time in shock compressed Ag. We also present a detailed analysis of the crystalline phases, which shows good agreement with the phase boundaries reported in previous experimental and theoretical works. We utilize the whole powder pattern fitting approach implemented in the MAUD package to constrain stacking faults in the face centered cubic structure. We observe the ambient fcc structure up to a stress of 146 GPa before a transition to a body-centered cubic structure and liquid phase at 179 GPa, with full melting above 212 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Inferring UAV Position Relative to Smartphone Sensor Based on Acoustic Characteristics

As commercial and non-commercial unmanned aerial vehicles (UAVs) improve technologically and increase in accessibility, their potential for use in actions antithetical to nuclear non-proliferation efforts increases as well. The ability to identify and locate UAVs using ubiquitous, inexpensive hardware and software would be advantageous as both a deterrent and an initial warning system. Our team looks to utilize smartphones as acoustic sensors to record and characterize UAV movement based on the sound produced while in flight. Multi-rotor UAVs produce identifiable acoustic spectral characteristics with frequencies and harmonics corresponding to motor revolutions per minute and the propeller characteristics. As the source moves closer to the receiver these spectral patterns remain relatively stable (at slow speeds), while the energy observed from the waves increases. The goal of this work is to utilize a small network of smartphone sensors with known, fixed positions to infer the relative position of an in-flight UAV with respect to the position of the smartphones through the variation in acoustic energy.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
DOE OSTI2019

On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, `naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Synthesis and Exploratory Catalysis of 3d Metals: Group-Transfer Reactions, and the Activation and Functionalization of Small Molecules Including Greenhouse Gases

Our work over the past three years has resulted in the development of electron rich and low-coordinate vanadium fragments, molecular nitrides of vanadium and parent imide systems of titanium, and the synthesis of phosphorus containing molecules of the 3d transition metal series. Likewise, with financial support from BES Division in DOE (DE-FG02-07ER15893), we now completed the full characterization of the first single molecular magnet (SMM) of Fe(III). We demonstrated that this monomeric form of Fe(III) has an unusual slow relaxation of the magnetization under zero applied field. To make matters more interesting, this system also undergoes a rare example of an intermediate to high-spin transition (an S = 3/2 to S = 5/2 transition). In 2010 we reported the synthesis of the first neutral and low-coordinate vanadium complexes having the terminal nitride functionality. We have now completed a full study to understand formation of the nitride ligand from the metastable azide precursor, and have also explored the reactivity of the nitride ligand in the context of incomplete and complete N-atom transfer. During the 2010-2013 period we also discovered a facile approach to assemble low-coordinate and low-valent vanadium(II) complexes and exploit their multielectron chemistry ranging from 1-3 electrons. Consequently, we can now access 3d ligand frameworks such as cyclo-P3 (and its corresponding radical anion), nitride radical anions and cations, low-coordinate vanadium oxo’s, and the first example of a vanadium thionitrosyl complex. A cis-divacant iron(IV) imido having some ligand centered radical has been also discovered, and we are in the process of elucidating its electronic structure (in particular the sign of zero field splitting and the origin of its magnitude), bonding and reactivity. We have also revisited some paramagnetic and classic metallocene compounds with S >1/2 ground states in order to understand their reactivity patterns and electronic structure. Lastly, we are completing the synthesis and characterization of a titanium nitride anion and formation of the first example of boryl and aluminyl imido titanium complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

TEMPI: An Interposed MPI Library with Canonical Representation of MPI Datatypes [Poster]

TEMPI provides a transparent non-contiguous data-handling layer compatible with various MPIs. MPI Datatypes are a powerful abstraction for allowing an MPI implementation to operate on non-contiguous data. CUDA-aware MPI implementations must also manage transfer of such data between the host system and GPU. The non-unique and recursive nature of MPI datatypes mean that providing fast GPU handling is a challenge. The same noncontiguous pattern may be described in a variety of ways, all of which should be treated equivalently by an implementation. This work introduces a novel technique to do this for strided datatypes. Methods for transferring non-contiguous data between the CPU and GPU depends on the properties of the data layout. This work shows that a simple performance model can accurately select the fastest method. Unfortunately, the combination of MPI software and system hardware available may not provide sufficient performance. The contributions of this work are deployed on OLCF Summit through an interposer library which does not require privileged access to the system to use

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes

Abstract Combining surface‐initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI‐TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush‐functionalized DNA nanostructures. We demonstrate that SI‐TcEP can site‐specifically pattern DONs with brushes containing both natural and non‐natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse‐grained simulations predict the conformation of the brush‐functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush‐functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site‐specific growth of polynucleotide brushes. The ability to site‐specifically decorate DONs with brushes of natural and non‐natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

Yang, Yunqi↗
DOE OSTI2020

Design of functional composite and all-inorganic nanostructured materials via infiltration of polymer templates with inorganic precursors

Robust and efficient approaches for the synthesis of materials with structure, porosity, and composition controlled at the nanoscale are highly important for a wide range of applications. Polymer templates are promising platforms to achieve such control. The self-assembly process of polymers provides access to diverse structures that can serve as templates for the deposition of inorganic materials. By infiltrating metal precursors from gas or liquid phases, using sequential infiltration synthesis (SIS) or swelling-based infiltration (SBI), respectively, into the polymer templates, one can create finely-tuned texturing of the surface films and bulk materials. In this review, we outline the specifics and dynamics of the polymer infiltration process and characterize the structure and properties of the synthesized materials. Finally, we highlight recent progress in implementing polymer infiltration-based nanoporous ceramics for many applications, including sensors, antireflective coatings, oil-absorbing foams, nanolithographic patterns, and catalytic materials.

Berman, Diana↗
DOE OSTI2026

Modelling belowground plant acclimation to low soil nitrogen – a heuristic optimality-based approach

Increased root growth to access greater soil mineral nitrogen resources and increased root exudation to stimulate microbial mineralization of soil organic nitrogen are widely observed plant acclimations to nitrogen limitation. However, their quantitative contribution to plant growth and ecosystem productivity remains largely elusive. Here, we present a novel optimality-based eco-evolutionary model in which plants dynamically regulate carbon partitioning between root growth and exudation to maximize their aboveground growth. Our simulations indicated that the availability of soil mineral and organic nitrogen as well as plant nitrogen demand and nitrogen uptake capacity shape optimal carbon partitioning between root growth and exudation. The simulated carbon allocation patterns aligned with empirical studies on belowground plant responses to varying soil nitrogen resources. Our eco-evolutionary approach represents a paradigmatic change in modelling plant nitrogen foraging, which is essential to generate hypotheses on optimal plant acclimation in future soil environments characterized by more erratic nitrogen availability.

Chakrawal, Arjun (ORCID:0000000345724347)↗
DOE OSTI2020

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

p -Azaquinodimethane: A Versatile Quinoidal Moiety for Functional Materials Discovery

The past 50 years of discovery in organic electronics have been driven in large part by the donor–acceptor design principle, wherein electron-rich and electron-poor units are assembled in conjugation with each other to produce small band gap materials. While the utility of this design strategy is undoubtable, it has been largely exhausted as a frontier of new avenues to produce and tune novel functional materials to meet the needs of the ever-increasing world of organic electronics applications. Its sister strategy of joining quinoidal and aromatic groups in conjugation has, by comparison, received much less attention, to a great extent due to the categorically poor stability of quinoidal conjugated motifs. In 2017 though, the p-azaquinodimethane (AQM) motif was first unveiled, which showed a remarkable level of stability despite being a close structural analogue to p-quinodimethane, a notably reactive compound. In contrast, dialkoxy AQM small molecules and polymers are stable even under harsh conditions and could thus be incorporated into conjugated polymers. When polymerized with aromatic subunits, these AQM-based polymers show notably reduced band gaps that follow reversed structure–property trends to some of their donor–acceptor polymer counterparts and yield organic field-effect transistor (OFET) hole mobilities above 5 cm 2 V –1 s –1 . Additionally, in an ongoing study, these AQM-based compounds are also showing promise as singlet fission (SF) active materials due to their mild diradicaloid character. An expanded world of AQMs was accessed through their ditriflate derivatives, which were first used to produce ionic AQMs (iAQMs) sporting two directly attached cationic groups that significantly affect the AQM motif’s electronics, producing strongly electron-withdrawing quinoidal building blocks. Conjugated polyelectrolytes (CPEs) created with these iAQM building blocks exhibit optical band gaps stretching into the near-infrared I (NIR-I) region and showed exemplary behavior as photothermal therapy agents. In contrast to these stable AQM examples, the synthetic exploration of AQMs also produced examples of more typical diradicaloid reactivity but in forms that were controllable and produced intriguing and high-value products. With certain substitution patterns, AQMs were found to dimerize to form highly substituted [2.2]paracyclophanes in distinctly more appreciable yields than typical cyclophane formation reactions. Certain AQM ditriflates, when crystallized, undergo light-induced topochemical polymerization to form ultrahigh molecular weight (>10 6 Da) polymers that showed excellent performances as dielectric energy storage materials. These same AQM ditriflates could be used to produce the strongly electron-donating redox-active pentacyclic structure: pyrazino[2,3-b:5,6-b']diindolizine (PDIz). Importantly, the PDIz motif allowed for the synthesis of exceedingly small band gap (0.7 eV) polymers with absorbances reaching all the way into the NIR-II region that were also found to produce strong photothermal effects. Both as stable quinoidal building blocks and through their controllable diradicaloid reactivity, AQMs have already proven to be versatile and effective as functional organic electronics materials.

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

Direct Correlation of Charge Carrier Transport to Local Crystal Quality in Lead Halide Perovskites

Although solution processing methods provide an attractive route toward development of low-cost functional materials, these accessible fabrication approaches can engender high concentrations of microscopic structural defects that are detrimental to performance. In lead halide perovskites, structural disorder derived from solution processing has been implicated as an important determiner of photophysical properties. However, a direct correlation between the functional properties of these materials and the local crystal structure in which non-equilibrium states evolve has remained elusive, in part because structural heterogeneities occur on length scales that defy conventional characterization techniques. To address this knowledge gap, in this work we have combined ultrafast pump–probe microscopy and electron backscattering diffraction to directly correlate charge carrier transport with the local diffraction pattern contrast, an indicator of crystal quality. Spatial correlation of these measurements strongly suggests that even on individual single crystal CsPbBr3 domains, microscopic variability in the crystal quality profoundly impacts the efficiency of charge carrier transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

β-Functionalized trans -A2B2 push–pull tetrabenzoporphyrins

A series of β-functionalized trans-A2B2 tetrabenzoporphyrins have been successfully designed and synthesized through newly developed regioselective bromination chemistry of porphyrins and a Pd(0) catalyzed three-step-one pot reaction. These benzoporphyrins exhibit unique patterns of UV-Vis absorptions and emissions. Tetrabenzoporphyrins possess a unique combination of photophysical, optoelectronic, and physicochemical properties due to their largely extended π-conjugation and associated dynamics of ring deformation which make them distinctive from their parent porphyrins. As compared with their parent porphyrins, tetrabenzoporphyrins often display significantly red-shifted absorption bands, a much-desired feature for various applications ranging from biomedicine to organic electronics. However, due to limited synthetic methods, only a small number of simple symmetrical tetrabenzoporphyrins have been available for study. Unsymmetrical tetrabenzoporphyrins, in particular those functionalized at the porphyrin β-positions, are very difficult to access. A2B2 porphyrins, on the other hand, represent an attractive class of materials for non-linear optical applications as well as for other applications such as those involving dye-sensitized solar cells. meso-Functionalized push–pull trans-A2B2 porphyrins have previously been made available through the Suzuki coupling reaction, the Heck reaction and the Sonogashira coupling reaction of 5,10-dibromoporphyrin with the corresponding alkyl boronic acids, olefins and alkynes, respectively and have demonstrated interesting non-linear optical properties. In contrast, β-functionalized push–pull A2B2 porphyrins of the type shown in Fig. 1 have until now remained unknown. Furthermore, we present the synthesis and characterization for the first examples of β-functionalized A2B2 push–pull tetrabenzoporphyrins.

Kumar, Siddhartha↗
DOE OSTI2019

Cold plasma finite element wave model for helicon waves

Helicon waves have been recently proposed as an off-axis current drive actuator due to their expected high current drive efficiency in the mid-radius region in high beta tokamaks. This current drive efficiency has mostly been calculated ignoring the effects of the plasma in the scrape-off-layer (SOL) in the modeling. The net core current drive efficiency will decrease if helicon power is lost to the SOL. Previous efforts to estimate the loss of helicon power in the SOL have used the hot plasma code AORSA. The large computational cost of AORSA prevents large parametric scans, so to further the understanding of helicon power loss in the SOL, a reduced finite element, full wave plasma model with effective collision frequency for collisional and Landau damping has been developed to study the helicon wave power lost to the SOL. It will be shown that the reduced finite element model (FEM) can reproduce the magnitude and trends of helicon |E| field patterns and power loss in the SOL of the hot plasma AORSA model. The reduced FEM provides significant advantages over AORSA in reducing the computational time and memory requirements, and in simulating arbitrary tokamak vessel geometry. Parametric scans of antenna parallel refractive index, antenna location, minimum SOL density, SOL density gradient, and vacuum vessel geometry will be carried out to determine the dependencies of the helicon power lost to the SOL as a function of important parameters. Subsequently, the helicon cutoff density is shown to be an important quantity in determining helicon power lost to the SOL. Furthermore, losses due to antenna loading and wave accessibility are also observed at different antenna and plasma parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗