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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 sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Correlations for the specific heat capacity of ( U x Pu 1 - x ) 1 - y Gd y O 2 - z derived from molecular dynamics

We report UO 2 is the primary conventional fuel used in most nuclear reactors with Gd 2 O 3 commonly added as a burnable absorber to produce a more level power distribution in the reactor core at the beginning of operation. It can also be mixed with other actinide oxides to produce mixed oxide (MOx) fuel. In this study, molecular dynamics simulations were used to predict the specific heat capacity of Gd-doped PuO 2 , UO 2 and (U, Pu)O 2 MOx accommodating Gd 3+ substituted at cation sites via two charge compensation mechanisms - oxygen vacancy formation and the oxidation of U 4+ to U 5+ . The specific heat capacity values for PuO 2 and UO 2 are in good agreement with other studies showing a distinct peak at high temperatures - above 1800 K. As Gd 3+ is added, the peak height reduces for each composition considered. An analytical fit was applied to the data where Gd 3+ was fully charge compensated by either oxygen vacancies or U 5+ . The expression was then validated by predicting the specific heat capacity for three compositions of (Ux Pu 1-x ) 1-y Gd y O 2-z containing both oxygen vacancies and U 5+ , and compared to molecular dynamics data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Prediction of nonlinear specific heat during single crystal HMX phase transition

Here, we develop a thermodynamically consistent chemo-thermo-mechanical model for the β → δ phase transition of energetic HMX crystals. In contrast to previous models, which either considered specific heat to be a constant or utilized a calibrated function, this model provides novel expressions for the specific heats at constant volume and constant elastic strains derived directly from continuum mechanics. In addition, the model provides a novel prediction for the critical temperature at which the chemical heating rate achieves its extremum for Arrhenius kinetics. The numerical solution predicts highly nonlinear specific heat behavior including order of magnitude changes.

42 ENGINEERING↗
DOE OSTI2014

Autocatalytic activity and substrate specificity of the pestivirus N-terminal protease N{sup pro}

Pestivirus N{sup pro} is the first protein translated in the viral polypeptide, and cleaves itself off co-translationally generating the N-terminus of the core protein. Once released, N{sup pro} blocks the host's interferon response by inducing degradation of interferon regulatory factor-3. N{sup pro'}s intracellular autocatalytic activity and lack of trans-activity have hampered in vitro cleavage studies to establish its substrate specificity and the roles of individual residues. We constructed N{sup pro}-GFP fusion proteins that carry the authentic cleavage site and determined the autoproteolytic activities of N{sup pro} proteins containing substitutions at the predicted catalytic sites Glu22 and Cys69, at Arg100 that forms a salt bridge with Glu22, and at the cleavage site Cys168. Contrary to previous reports, we show that N{sup pro'}s catalytic activity does not involve Glu22, which may instead be involved in protein stability. Furthermore, N{sup pro} does not have specificity for Cys168 at the cleavage site even though this residue is conserved throughout the pestivirus genus. - Highlights: • N{sup pro'}s autoproteolysis is studied using N{sup pro}-GFP fusion proteins. • N-terminal 17 amino acids are dispensable without loss of protease activity. • The putative catalytic residue Glu22 is not involved in protease catalysis. • No specificity for Cys168 at the cleavage site despite evolutionary conservation. • N{sup pro} prefers small amino acids with non-branched beta carbons at the P1 position.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes). Gene targets can be specifically labelled with at least about 20 PNA-probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3D-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. - Highlights: • Denaturation free protocols preserve 3D architecture of chromosomes and nuclei. • Labelling sets are determined in silico for duplex and triplex binding. • Probes are produced chemically with freely chosen backbones and base variants. • Peptide nucleic acid backbones reduce hindering charge interactions. • Intercalating side chains stabilize binding of short oligonucleotides.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Ecological Traits of Fish for Mercury Biomonitoring: Insights from Compound-Specific Nitrogen and Stable Mercury Isotopes

Here we coupled compound-specific isotopic analyses of nitrogen (N) in amino acids (δ 15 N Glu , δ 15 N Phe ) and mercury stable isotopes (δ 202 Hg, Δ 199 Hg) to quantify ecological traits governing the concentration, variability, and source of Hg in largemouth bass (LB) and pike gudgeon (PG) across four rivers, South Korea. PG displayed uniform Hg concentration (56–137 ng/g), trophic position (TP corrected ; 2.6–3.0, n = 9), and N isotopes in the source amino acid (δ 15 N Phe ; 7–13‰), consistent with their specialist feeding on benthic insects. LB showed wide ranges in Hg concentration (45–693 ng/g), TP corrected (2.8–3.8, n = 14), and δ 15 N Phe (1.3–16‰), reflecting their opportunistic feeding behavior. Hg sources assessed using Hg isotopes reveal low and uniform Δ 199 Hg in PG (0.20–0.49‰), similar to Δ 199 Hg reported in sediments. LB displayed site-specific δ 202 Hg (-0.61 to -0.04‰) and Δ 199 Hg (0.53–1.09‰). At the Yeongsan River, LB displayed elevated Δ 199 Hg and low δ 15 N Phe , consistent with Hg and N sourced from the atmosphere. LB at the Geum River displayed low Δ 199 Hg and high δ 15 N Phe , both similar to the isotope values of anthropogenic sources. Our results suggest that a specialist fish (PG) with consistent ecological traits and Hg concentration is an effective bioindicator species for Hg. When accounting for Hg sources, however, LB better captures site-specific Hg sources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Design of Specific Serine Protease Inhibitors Based on a Versatile Peptide Scaffold: Conversion of a Urokinase Inhibitor to a Plasma Kallikrein Inhibitor

All serine proteases hydrolyze peptide bonds by the same basic mechanism and have very similar active sites, in spite of the fact that individual proteases have different physiological functions. We here report a strategy for designing high-affinity and high-specificity serine protease inhibitors using a versatile peptide scaffold, a 10-mer peptide, mupain-1 (CPAYSRYLDC). Mupain-1 was previously reported as a specific inhibitor of murine urokinase-type plasminogen activator (K i = 0.55 μM) without measurable affinity to plasma kallikrein (K i > 1000 μM). On the basis of a structure-based rational design, we substituted five residues of mupain-1 and converted it to a potent plasma kallikrein inhibitor (K i = 0.014 μM). X-ray crystal structure analysis showed that the new peptide was able to adapt a new set of enzyme surface interactions by a slightly changed backbone conformation. Furthermore, with an appropriate re-engineering, mupain-1 can be redesigned to specific inhibitors of other serine proteases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Prediction of Specificity of α-Conotoxins to Subtypes of Human Nicotinic Acetylcholine Receptors with Semi-supervised Machine Learning

Conotoxins are a family of highly toxic neurotoxins composed of cysteine-rich peptides produced by marine cone snails. The most lethal cone snail species to humans is Conus geographus, with fatality rates of up to ∼65% from a single sting, which is caused mostly by the activity of α-conotoxins against human nicotinic acetylcholine receptors (nAChRs). While sequence-based machine learning (ML) classifiers have been trained to identify targets of conotoxins binding voltage-gated ion channels, no ML model has been built to predict the subtype-specific nAChR targets of α-conotoxins. Here, we trained an ML model in a semi-supervised manner to predict the specificity of α-conotoxin binding toward different human nAChR subtypes to overcome the challenge of limited data in subtype-specific nAChR targets of α-conotoxins and the issue that one α-conotoxin can bind multiple nAChR subtypes with high selectivity. We considered additional features of sequences of α-conotoxins in training our ML model, including the secondary structure propensities and electrostatic properties, which resulted in better prediction capability for the ML model. Notably, we identify that most α-conotoxins bind to α3β2, α1γδ, and α7 subtypes of human nAChRs. Our findings from this study provide a framework for predicting targets of various kinds of toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases

Mutation at a single amino acid alters the isoprene donor specificity of prenyltransferases involved in the modification of ribosomally synthesized and post-translationally modified peptides (RiPPs). Though most characterized RiPP prenyltransferases carry out the regiospecific transfer of C 5 dimethylallyl donor to the side chain atoms on macrocyclic acceptor substrates, the elucidation of the cyanobactin natural product piricyclamide 70005E1 identifies an O-geranyl modification on Tyr, a reaction with little prior biochemical precedence. Reconstitution and kinetic studies of the presumptive geranyltransferase PirF shows that the enzyme utilizes a C 10 donor, with no C 5 transferase activity. The crystal structure of PirF reveals a single amino acid difference in the vicinity of the isoprene-binding pocket, relative to the C 5 utilizing enzymes. Remarkably, only a single amino acid mutation is necessary to completely switch the donor specificity from a C 5 to a C 10 prenyltransferase, and vice versa. Lastly, we demonstrate that these enzymes may be used for the chemospecific attachment of C 5 or C 10 lipid groups on lanthipeptides, an unrelated class of RiPP natural products. Overall, these studies represent a rare example where prenyl donor specificity can be discretely altered, which expands the arsenal of synthetic biology tools for tuning biological activities of peptide natural products.

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

Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase

DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N{sup 6}-ethenoadenine ({var_epsilon}A) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their {var_epsilon}A activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Specific heat of twisted bilayer graphene: Engineering phonons by atomic plane rotations

We have studied the phonon specific heat in single-layer, bilayer, and twisted bilayer graphene. The calculations were performed using the Born-von Karman model of lattice dynamics for intralayer atomic interactions and spherically symmetric interatomic potential for interlayer interactions. We found that at temperature T < 15 K, specific heat varies with temperature as T{sup n}, where n = 1 for graphene, n = 1.6 for bilayer graphene, and n = 1.3 for the twisted bilayer graphene. The phonon specific heat reveals an intriguing dependence on the twist angle in bilayer graphene, which is particularly pronounced at low temperature. The results suggest a possibility of phonon engineering of thermal properties of layered materials by twisting the atomic planes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Reconstruction of the “phase separation – ordering” type and specific heat in carbon nanotubes

The low-temperature behavior of the specific heat in disordered nanotubes strongly depends on structure changes and was not explained by the phonon contribution. Expression for electronic specific heat was carried out taking into account the multiple elastic scattering of electrons on impurities and structural inhomogeneities of short-range order type, it includes dependence on diameter of nanotube, concentration of impurities, parameters of short-range order (structural heterogeneity) and temperature. Anomalous low-temperature behavior of the specific heat of disordered CNT is shown to have electronic nature and may be associated with the electrons that are involved in restructuring.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Element specificity of ortho-positronium annihilation for alkali-metal loaded SiO{sub 2} glasses

Momentum distributions associated with ortho-positronium (o-Ps) pick-off annihilation photon are often influenced by light elements, as, e.g., carbon, oxygen, and fluorine. This phenomenon, so-called element specificity of o-Ps pick-off annihilation, has been utilized for studying the elemental environment around the open spaces. To gain an insight into the element specificity of o-Ps pick-off annihilation, the chemical shift of oxygen 1s binding energy and the momentum distributions associated with o-Ps pick-off annihilation were systematically investigated for alkali-metal loaded SiO{sub 2} glasses by means of X-ray photoelectron spectroscopy and positron-age-momentum correlation spectroscopy, respectively. Alkali metals introduced into the open spaces surrounded by oxygen atoms cause charge transfer from alkali metals to oxygen atoms, leading to the lower chemical shift for the oxygen 1s binding energy. The momentum distribution of o-Ps localized into the open spaces is found to be closely correlated with the oxygen 1s chemical shift. This correlation with the deepest 1s energy level evidences that the element specificity of o-Ps originates from pick-off annihilation with orbital electrons, i.e., dominantly with oxygen 2p valence electrons and s electrons with lower probability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Neutron diffraction, specific heat and magnetization studies on Nd{sub 2}CuTiO{sub 6}

Structural and physical properties of a double-perovskite compound, Nd{sub 2}CuTiO{sub 6} have been studied using neutron diffraction, magnetization and specific heat measurements. The compound crystallizes in an orthorhombic structure in space group Pnma. The interesting observation we make here is that, though no long range magnetic order is observed between 2 and 300 K, the low temperature specific heat and magnetic susceptibility behavior exhibits non-Fermi liquid like behavior in this insulating compound. The magnetization and specific heat data are presented and discussed in light of these observations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Crystallization of glass-forming liquids: Specific surface energy

A generalization of the Stefan-Skapski-Turnbull relation for the melt-crystal specific interfacial energy is developed in terms of the generalized Gibbs approach extending its standard formulation to thermodynamic non-equilibrium states. With respect to crystal nucleation, this relation is required in order to determine the parameters of the critical crystal clusters being a prerequisite for the computation of the work of critical cluster formation. As one of its consequences, a relation for the dependence of the specific surface energy of critical clusters on temperature and pressure is derived applicable for small and moderate deviations from liquid-crystal macroscopic equilibrium states. Employing the Stefan-Skapski-Turnbull relation, general expressions for the size and the work of formation of critical crystal clusters are formulated. The resulting expressions are much more complex as compared to the respective relations obtained via the classical Gibbs theory. Latter relations are retained as limiting cases of these more general expressions for moderate undercoolings. By this reason, the formulated, here, general relations for the specification of the critical cluster size and the work of critical cluster formation give a key for an appropriate interpretation of a variety of crystallization phenomena occurring at large undercoolings which cannot be understood in terms of the Gibbs’ classical treatment.

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

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Development and Study of Nb 3 Sn Wires With High Specific Heat

Recently, a new type of Nb 3 Sn conductors were developed, which, by incorporating substances with high specific heat at 2-8 K in a proper design, have demonstrated significant improvement of minimum quench energy (MQE). This method to improving energy margins of conductors is promising to reduce Nb 3 Sn magnet training. Here, we continue studying this type of conductors. Voltage-current (V-I) measurements from 15 T to 0 T and voltage-field (V-B) sweeps at various currents were conducted to investigate the influence of increased specific heat on the intrinsic stability of Nb 3 Sn conductors. Normal zone propagation velocity (NZPV) was also studied. Lastly, a new scheme was put forward to introduce a new type of substances with not only high specific heat but also high thermal diffusivity to Nb 3 Sn conductors, which is expected to work more effectively.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Mitigation of Motor Stalling and FIDVR via Energy Storage Systems with Temporal Logic Specifications

The fault-induced delayed voltage recovery (FIDVR) phenomenon has been very common from the distribution system through the transmission system. It causes a delay on recovering significantly depressed local voltage after the fault is cleared, and it can also lead to more widespread cascading system failures. Mitigating this event with current control approaches is challenging and becoming a crucial issue. Here, a model predictive control-based strategy employing signal temporal logic specifications is proposed to help mitigate FIDVR. To this end, it investigates and extends a dynamic performance model allowing analytic insights into the system-wide impact of motor stalling and FIDVR. The proposed controller provides richer descriptions of voltage specifications addressing both magnitude and time simultaneously. We consider different control specifications with reactive power support from energy storage systems to prevent the voltage during/after the fault from dropping too low, and reduce the delay time of voltage recovery. The simulation results conducted with the IEEE 57 bus test network validate the proposed method and demonstrate the effectiveness of the mitigation strategy on FIDVR.

25 ENERGY STORAGE↗
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗