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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Three-dimensional dendritic needle network model for alloy solidification

Here, we present a three-dimensional (3D) formulation of the multiscale Dendritic Needle Network (DNN) model for dendritic microstructure growth. This approach is aimed at simulating quantitatively the solidification dynamics of complex hierarchical networks in spatially extended dendritic arrays, hence bridging the scale gap between phase-field simulations at the scale of a few dendrites and coarse-grained simulations on the larger scale of entire polycrystalline structures. In the DNN model, the dendritic network is represented by a network of branches that interact through the solutal diffusion field. The tip velocity V(t) and tip radius ρ(t) of each needle is determined by combining a standard solvability condition that fixes the product ρ 2 V and a solute flux conservation condition that fixes the product ρV 2 in 2D and ρV in 3D as a function of a solutal flux intensity factor ℱ(t). The latter measures the intensity of the solute flux in the dendrite tip region and can be calculated by contour (2D) or surface (3D) integration around the tip of each needle. We first present an extended formulation of the 2D DNN model where needles have a finite thickness and parabolic tips. This formulation remains valid for a larger range of tip Péclet number than the original thin needle formulation and is readily extended to 3D needles with paraboloidal tips. The 3D DNN model based on this thick-needle formulation is developed for both isothermal and directional solidification. Model predictions are validated by comparisons with known analytical solutions that describe the early transient and steady-state growth regimes. We exploit the power of the DNN model to characterize the competitive growth of well-developed secondary branches in 3D on the scale of the diffusion length. The results show that the length of active secondary branches increases as a power law of distance behind the tip with an exponent in good quantitative agreement with experimental measurements. Finally, we apply the model to simulate the three-dimensional directional solidification of an Al-7wt% Si alloy, which we directly compare to observed microstructures from microgravity experiments onboard the International Space Station. The predictions of selected microstructural features, such as dendrite arm spacings, show a good agreement with experiments. The computationally-efficient DNN model opens new avenues for investigating the dynamics of large dendritic arrays at length and time scales relevant to solidification experiments and processes.

36 MATERIALS SCIENCE↗
DOE OSTI2026

A new self-adaptive reconstruction method to identify defects through Wigner–Seitz approach

A new self-adaptive reconstruction method based on local atomic structure at any given molecular dynamics (MD) step has been developed in this article. The method can be used in Wigner–Seitz defect analysis approach to correctly and efficiently explore the information of both point defects and complex defect clusters (e.g. dislocation loops and voids) formed after a displacement cascade where the cascade interacts with grain boundaries and/or dislocations. The algorithm and validation are provided in detail. Results for identification of radiation defects during and after cascades interacting with a dislocation network show that the new method can well recognize all simple and complex defects and defect clusters. Thus, this new method provides a totally new way to explore the density and size of radiation defects at atomic scale after complex MD evolution processes, providing correct information to understand and predict radiation damage in materials through atomic simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Molecular response of poplar to single and combined ozone and drought

High concentration in ground-level ozone (O 3 ) and water deficit affect forest ecosystems service. Earlier we found intercellular CO 2 concentration and isoprene emission were affected by the combination of O 3 and drought, but the molecular mechanisms controlling these phenotypes are still open questions. In this study, we examined the stomatal conductance (g s ) and transcriptome changes in an O 3 -sensitive hybrid poplar exposed to two O 3 levels [charcoal-filtered ambient air (CF) and non-filtered ambient air plus 40 ppb (NF40)] and two water conditions [well-watered (W) and moderate drought (D)]. NF40 reduced the g s more under D than W. We identified the differentially expressed genes (DEGs) from pairwise comparisons and found the poplar's molecular response to drought was counteracted by elevated O 3 . From nine clusters obtained through K-means clustering, 12 core transcription factors were identified. DEGs involved in isoprene biosynthesis and phytohormones signal pathways indicate the molecular response and stomatal closure of poplar under O 3 and/or drought might be through MEP/DOXP and ABA-dependent pathways. In addition, 102 Helitrons capturing DEGs were involved in response to O 3 and/or drought and related with ABA-dependent pathway. This integrated analysis provides multi-dimensional insights to understand the molecular response to the combination of O 3 and drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model

Network and protein–protein interaction analyses of proteins undergoing Hg{sup 2+}-induced phosphorylation and dephosphorylation in Hg{sup 2+}-intoxicated mouse WEHI-231 B cells identified Lyn as the most interconnected node. Lyn is a Src family protein tyrosine kinase known to be intimately involved in the B cell receptor (BCR) signaling pathway. Under normal signaling conditions the tyrosine kinase activity of Lyn is controlled by phosphorylation, primarily of two well known canonical regulatory tyrosine sites, Y-397 and Y-508. However, Lyn has several tyrosine residues that have not yet been determined to play a major role under normal signaling conditions, but are potentially important sites for phosphorylation following mercury exposure. In order to determine how Hg{sup 2+} exposure modulates the phosphorylation of additional residues in Lyn, a targeted MS assay was developed. Initial mass spectrometric surveys of purified Lyn identified 7 phosphorylated tyrosine residues. A quantitative assay was developed from these results using the multiple reaction monitoring (MRM) strategy. WEHI-231 cells were treated with Hg{sup 2+}, pervanadate (a phosphatase inhibitor), or anti-Ig antibody (to stimulate the BCR). Results from these studies showed that the phosphoproteomic profile of Lyn after exposure of the WEHI-231 cells to a low concentration of Hg{sup 2+} closely resembled that of anti-Ig antibody stimulation, whereas exposure to higher concentrations of Hg{sup 2+} led to increases in the phosphorylation of Y-193/Y-194, Y-501 and Y-508 residues. These data indicate that mercury can disrupt a key regulatory signal transduction pathway in B cells and point to phospho-Lyn as a potential biomarker for mercury exposure. - Highlights: • Inorganic mercury (Hg{sup 2+}) induces changes in the WEHI-231 B cell phosphoproteome. • The B cell receptor (BCR) signaling pathway was the pathway most affected by Hg{sup 2+}. • The Src family phosphoprotein kinase Lyn was the most interconnected node. • Lyn is likely central to the immunotoxic potential of Hg{sup 2+}. • Lyn phosphorylation profiles may be biomarkers for Hg{sup 2+} intoxication of B cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Vibrational signatures of HNO 3 acidity when complexed with microhydrated alkali metal ions, M + ∙(HNO 3 )(H 2 O) n =5 (M = Li, K, Na, Rb, Cs), at 20 K

The speciation of strong acids like HNO 3 under conditions of restricted hydration is an important factor in the rates of chemical reactions at the air-water interface. Here we explore the trade-offs in play when HNO 3 is attached to alkali ions (Li + -Cs + ) with four water molecules in their primary hydration shells. This is achieved by analyzing the vibrational spectra of the M + ∙(HNO 3 )(H 2 O) 5 clusters cooled to about 20 K in a cryogenic photofragmentation mass spectrometer. The local acidity of the acidic OH group is estimated by the extent of the red shift in its stretching frequency when attached to a single water molecule. Here, the persistence of this local structural motif (HNO 3 -H 2 O) in all of these alkali metal clusters enables us to determine the competition between the effect of the direct complexation of the acid with the cation, which acts to enhance acidity, and the role of the water network in the first hydration shell around the ions, which acts to counter (screen) the intrinsic effect of the ion. Analysis of the vibrational features associated with the acid molecule as well as those of the water network reveal how cooperative interactions in the micro hydration regime conspire to effectively offset the intrinsic enhancement of HNO 3 acidity afforded by attachment to the smaller cations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2

The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein–protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cage is essential for full catalytic activity, but details of this regulation are not fully understood. EED’s recognition of the product of PRC2 activity, histone H3 lysine 27 trimethylation (H3K27me3), stimulates PRC2 methyltransferase activity at adjacent nucleosomes leading to H3K27me3 propagation and, ultimately, gene repression. By coupling combinatorial chemistry and structure-based design, we optimized a low-affinity methylated jumonji, AT-rich interactive domain 2 (Jarid2) peptide to a smaller, more potent peptidomimetic ligand (K d = 1.14 ± 0.14 μM) of the aromatic cage of EED. Our strategy illustrates the effectiveness of applying combinatorial chemistry to achieve both ligand potency and property optimization. Furthermore, the resulting ligands, UNC5114 and UNC5115, demonstrate that targeted disruption of EED’s reader function can lead to allosteric inhibition of PRC2 catalytic activity.

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

Defect Self-Elimination in Nanocube Superlattices Through the Interplay of Brownian, van der Waals, and Ligand-Based Forces and Torques

Understanding defect healing is necessary for realizing devices based on nanoparticle-superlattices with controlled electronic and optoelectronic performance. However, key questions remain regarding nanoparticle interactions and resulting assembly dynamics and defect self-elimination. In particular, for anisotropic particles, additional degrees of freedom beyond those of spherical particles, such as rotational dynamics and toques, significantly impact phenomena. Here, in this work, we investigate nanocube (NC) superlattices by employing liquid phase transmission electron microscopy, continuum theories and molecular dynamics simulations. Analyzing interparticle forces and torques due to van der Waals, Brownian, and ligand interactions, we find that the latter dominates and that the anisotropic NC morphology introduces significant torques. In imperfect regions, unbalanced forces and torques induce NC translations and rotations that are transmitted to neighboring NCs, prompting “chain interactions” in a 2D network, which lead to defect self-elimination. This fundamental understanding will further enable design and fabrication of defect-free superlattices, as well as those with tailored defects, via assembly of anisotropic particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.

Environmental Sciences & Ecology↗
DOE OSTI2020

CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid

hnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Water properties under nano-scale confinement

Abstract Water is the universal solvent and plays a critical role in all known geological and biological processes. Confining water in nano-scale domains, as encountered in sedimentary rocks, in biological, and in engineered systems, leads to the deviations in water’s physicochemical properties relative to those measured for the non-confined phase. In our comprehensive analysis, we demonstrate that nano-scale confinement leads to the decrease in the melting/freezing point temperature, density, and surface tension of confined water. With increasing degree of spatial confinement the population of networked water, as evidenced by alterations in the O-H stretching modes, increases. These analyses were performed on two groups of mesoporous silica materials, which allows to separate pore size effects from surface chemistry effects. The observed systematic effects of nano-scale confinement on the physical properties of water are driven by alterations to water’s hydrogen-bonding network—influenced by water interactions with the silica surface — and has implications for how we understand the chemical and physical properties of liquids confined in porous materials.

Science & Technology - Other Topics↗
DOE OSTI2020

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

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

Wave function analysis with a maximum flow algorithm

An efficient algorithm for computing the maximum-flow path in a network is applied to the identification of the dominant configuration state functions (CSFs) in a graphically contracted function (GCF), configuration interaction, wave function. The flow network is a space of spin-adapted CSFs represented by a Shavitt graph, wherein the nodes correspond to orbital occupations and spin quantum numbers. The graph nodes are connected by arcs, and an arc density is defined as sums of the associated squared CSF coefficients. A max-min approach determines an upper bound to the maximum possible incoming flow for each graph node. A backtracking step generates a candidate walk and is followed by a limited search of alternative branching paths for the dominant CSF. The arc density contributions are removed from the graph, and the algorithm is reapplied to the updated graph. This list of generated walks can be partitioned in order to guarantee that the dominant CSFs have been identified. All of the steps in this algorithm are computationally efficient and do not depend on the potentially large dimension of the underlying linear CSF expansion space. An analysis of low-lying valence states of C-2 illustrates the method.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2013

A FLUX ROPE NETWORK AND PARTICLE ACCELERATION IN THREE-DIMENSIONAL RELATIVISTIC MAGNETIC RECONNECTION

We investigate magnetic reconnection and particle acceleration in relativistic pair plasmas with three-dimensional particle-in-cell simulations of a kinetic-scale current sheet in a periodic geometry. We include a guide field that introduces an inclination between the reconnecting field lines and explore outside-of-the-current sheet magnetizations that are significantly below those considered by other authors carrying out similar calculations. Thus, our simulations probe the transitional regime in which the magnetic and plasma pressures are of the same order of magnitude. The tearing instability is the dominant mode in the current sheet for all guide field strengths, while the linear kink mode is less important even without the guide field, except in the lower magnetization case. Oblique modes seem to be suppressed entirely. In its nonlinear evolution, the reconnection layer develops a network of interconnected and interacting magnetic flux ropes. As smaller flux ropes merge into larger ones, the reconnection layer evolves toward a three-dimensional, disordered state in which the resulting flux rope segments contain magnetic substructure on plasma skin depth scales. Embedded in the flux ropes, we detect spatially and temporally intermittent sites of dissipation reflected in peaks in the parallel electric field. Magnetic dissipation and particle acceleration persist until the end of the simulations, with simulations with higher magnetization and lower guide field strength exhibiting greater and faster energy conversion and particle energization. At the end of our largest simulation, the particle energy spectrum attains a tail extending to high Lorentz factors that is best modeled with a combination of two additional thermal components. We confirm that the primary energization mechanism is acceleration by the electric field in the X-line region. The highest-energy positrons (electrons) are moderately beamed with median angles {approx}30 Degree-Sign -40 Degree-Sign relative to (the opposite of) the direction of the initial current density, but we speculate that reconnection in more highly magnetized plasmas would give rise to stronger beaming. Finally, we discuss the implications of our results for macroscopic reconnection sites, and which of our results may be expected to hold in systems with higher magnetizations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families inArabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein–protein and co-occurrence interactions, informed by gene network patterns using the STRING database, inArabidopsis thalianaandChlamydomonas reinhardtiiunveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified inArabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue ‘The evolution of plant metabolism’.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2026

Thermal nature of confining strings

We investigate the quantum statistical properties of the confining string connecting a static fermion-antifermion pair in the massive Schwinger model. By analyzing the reduced density matrix of the subsystem located in between the fermion and antifermion, we demonstrate that as the interfermion separation approaches the string-breaking distance, the overlap between the microscopic density matrix and an effective thermal density matrix exhibits a pronounced, narrow peak, approaching unity at the onset of string breaking. This behavior reveals that the confining flux tube evolves toward a genuinely thermal state as the separation between the charges grows, even in the absence of an external heat bath. In other words, one cannot tell whether a reduced state of the subsystem arises from a surrounding heat bath or from entanglement with the rest of the system. The entanglement spectrum near the critical string-breaking distance exhibits a rapid transition from the dominance of a single state describing the confining electric string towards a strongly entangled state containing virtual fermion-antifermion pairs. Our findings establish a quantitative link between confinement, entanglement, and emergent thermality, and suggest that string breaking corresponds to a microscopic thermalization transition within the flux tube.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

On Analytics of File Transfer Rates over Dedicated Wide-Area Connections

File transfers between the decentralized storage sites over dedicated wide-area connections are becoming increasingly important in high-performance computing and big data scenarios. Designing such scientific workflows for large file transfers is extremely challenging as they depend on the file, I/O, host, and local- and wide-area network subsystems, and their interactions. To gain insights into file-transfer rate profiles, we develop polynomial, bagging, and boosting regression models for Lustre and XFS file transfer measurements, which are collected using XDD over a suite of 10 Gbps connections with 0-366 ms round trip times (RTTs). In addition to overall trends and analytics, these regressions also provide file-transfer rate estimates for RTTs and number of parallel flows at which measurements might not have been collected. They show that bagging and boosting techniques provide closer data fits than the polynomial regression. We develop probabilistic bounds on the generalization error of these methods, which combined with the cross-validation error establish that former two are more accurate estimators than the polynomial regression. In addition, we present a method to efficiently determine the number of parallel flows to achieve a peak file-transfer rate using fewer than full sweep measurements; in our measurements, the peak is achieved in 96% of cases with 15-25% of measurements of a full sweep.

Sen, Satyabrata↗