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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 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Multiple CaMKII Binding Modes to the Actin Cytoskeleton Revealed by Single-Molecule Imaging

Localization of the Ca2þ/calmodulin-dependent protein kinase II (CaMKII) to dendritic spine synapses is determined in part by the actin cytoskeleton. We determined binding of GFP-tagged CaMKII to tag-RFP-labeled actin cytoskeleton within live cells using total internal reflection fluorescence microscopy and single-molecule tracking. Stepwise photobleaching showed that CaMKII formed oligomeric complexes. Photoactivation experiments demonstrated that diffusion out of the evanescent field determined the track lifetimes. Latrunculin treatment triggered a coupled loss of actin stress fibers and the colocalized, long-lived CaMKII tracks. The CaMKIIa (a) isoform, which was previously thought to lack F-actin interactions, also showed binding, but this was threefold weaker than that observed for CaMKIIb (b). The bE0 splice variant bound more weakly than a, showing that binding by b depends critically on the interdomain linker. The mutations bT287D and aT286D, which mimic autophosphorylation states, also abolished F-actin binding. Autophosphorylation triggers autonomous CaMKII activity, but does not impair GluN2B binding, another important synaptic protein interaction of CaMKII. The CaMKII inhibitor tatCN21 or CaMKII mutations that inhibit GluN2B association by blocking binding of ATP (bK43R and aK42M) or Ca2þ/calmodulin (bA303R) had no effect on the interaction with F-actin. These results provide the first rationale for the reduced synaptic spine localization of the aT286D mutant, indicating that transient F-actin binding contributes to the synaptic localization of the CaMKIIa isoform. The track lifetime distributions had a stretched exponential form consistent with a heterogeneously diffusing population. This heterogeneity suggests that CaMKII adopts different F-actin binding modes, which is most easily rationalized by multiple subunit contacts between the CaMKII dodecamer and the F-actin cytoskeleton that stabilize the initial weak (micromolar) monovalent interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems

Single-cell multi-omics and spatial technology have been widely applied to biomedical studies and recently to environmental studies. Here, the cell size detected by single-cell omics ranges from ~2 µm (e.g., Bacillus subtilis) to ~120 µm (e.g., human oocytes). Simultaneous detection of single-cell multi-omics is available to human and plant tissues while limited to microbial samples. Spatial technology enables mapping the detected biomolecules in situ. The recent advances in MALDI-MSI and micro/nanoPOTS for the first time allow the application of spatial multi-omics in highly heterogeneous environmental samples composed of plants, fungi, and bacteria. We envision that these technologies will continue to advance our understanding of unique cell types, their developmental trajectory, and the intercellular signaling and interaction within biological samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Atomic-scale mechanisms of helium bubble hardening in iron

Generation of helium due to (n,α) transmutation reactions changes the response of structural materials to neutron irradiation. The whole process of radiation damage evolution is affected by He accumulation and leads to significant changes in the material s properties. A population of nanometric He-filled bubbles affects mechanical properties and the impact can be quite significant because of their high density. Understanding how these basic mechanisms affect mechanical properties is necessary for predicting radiation effects. In this paper we present an extensive study of the interactions between a moving edge dislocation and bubbles using atomic-scale modeling. We focus on the effect of He bubble size and He concentration inside bubbles. Thus, we found that ability of bubbles to act as an obstacle to dislocation motion is close to that of voids when the He-to-vacancy ratio is in the range from 0 to 1. A few simulations made at higher He contents demonstrated that the interaction mechanism is changed for over-pressurized bubbles and they become weaker obstacles. The results are discussed in light of post-irradiation materials testing.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Iron(III)–Oxo Cluster Chemistry with Dimethylarsinate Ligands: Structures, Magnetic Properties, and Computational Studies

A program has been initiated to develop Fe III /oxo cluster chemistry with the ‘pseudo-carboxylate’ ligand dimethylarsinate (Me 2 AsO 2 - ) for comparison with the well investigated Fe III /oxo/carboxylate cluster area. The synthesis and characterization of three polynuclear Fe III complexes are reported, [Fe 12 O 4 (O 2 C t Bu) 8 (O 2 AsMe 2 ) 17 (H 2 O) 3 ]Cl 3 (1), Na 2 [Fe 12 Na 2 O 4 (O 2 AsMe 2 ) 20 (NO 3 ) 6 (Me 2 AsO 2 H) 2 (H 2 O) 4 ](NO 3 ) 6 (2) and [Fe 3 (O 2 AsMe 2 ) 6 (Me 2 AsO 2 H) 2 (hqn) 2 ](NO 3 ) (3), where hqn is 8-hydroxyquinoline. The Fe 12 core of 1 is a type never previously encountered in Fe III carboxylate chemistry, consisting of two Fe 6 units each of which comprises two {Fe 3 (μ 3 -O 2- )} units bridged by three Me 2 AsO 2 - groups and linked into an Fe 12 loop structure by two anti-anti η 1 :η 1 :μ Me 2 AsO 2 - groups, a bridging mode extremely rare with carboxylates. 2 also consists of two Fe 6 units, differing in their ligation from those in 1, and this time linked together into a linear structure by a central {Na 2 (NO 3 ) 2 } bridging unit. 3 is a linear Fe 3 complex with no monoatomic bridges between Fe III ions, a very rare situation in Fe III chemistry with any ligands, and unprecedented in Fe carboxylate chemistry. The distinct differences observed in arsinate vs carboxylate ligation modes are rationalized largely based on the greater basicity of the former vs the latter. Variable-temperature dc and ac magnetic susceptibility data reveal all Fe 2 pairwise interactions to be antiferromagnetic. For 1 and 2, the different J ij couplings were estimated by use of a magnetostructural correlation for high nuclearity Fe III -oxo clusters and by density functional theory calculations using broken symmetry methods, allowing identification of their relative spin vector alignments and thus rationalization of their S = 0 ground states. The J ij values were then used as input values to give excellent fits of the experimental χM T vs T data. For 3, the fits of the experimental χM T vs T data to the Van Vleck equation or with PHI gave a very weak J 12 = -0.8(1) cm -1 (H = –2JŠ i ·Š j convention) between adjacent Fe III ions, and an S = 5/2 ground state. Furthermore, these initial Fe III arsinate complexes also provide structural parameters that help validate literature assignments of arsinate binding modes to iron oxide/hydroxide minerals as part of environmental concerns of using arsenic-containing herbicides in agriculture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B

Ras protein colocalization at the plasma membrane is implicated in the activation of signaling cascades that promote cell growth, survival, and motility. However, the mechanisms that underpin Ras self-association remain unclear. We use molecular dynamics simulations to show how basic and hydrophobic components of the disordered C-terminal membrane tether of K-Ras4B combine to regulate its membrane interactions. Specifically, anionic lipids attract lysine residues to the membrane surface, thereby splitting the peptide population into two states that exchange on the microsecond time scale. These states differ in the membrane insertion of a methionine residue, which is influenced by local membrane composition. As a result, these states may impose context-dependent biases on the disposition of Ras’ signaling domain, with possible implications for the accessibility of its effector binding surfaces. Furthermore, we investigate Ras’ ability to nanocluster by fly-casting for patches of anionic lipids and find that while anionic lipids promote the intermolecular association of K-Ras4B membrane tethers, at short range this appears to be a passive process in which anionic lipids electrostatically screen these cationic peptides to mitigate their natural repulsion. Together with the sub-microsecond stability of interpeptide contacts, this result suggests that experimentally observed K-Ras4B nanoclustering is not driven by direct intermolecular contact of its membrane tethers.

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

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

RCNP E398 {sup 16}O,{sup 12}C(p,p’) experiment: Measurement of the γ-ray emission probability from giant resonances in relation to {sup 16}O,{sup 12}C(ν,ν’) reactions

We propose to measure the γ-ray emission probability from excited states above 5 MeV including giant resonance of {sup 16}O and {sup 12}C as a function of excitation energy in 1-MeV step. Here, we measure both the excitation energy (E{sub x}=5-30MeV) at the forward scattering angles (0°-3°) of the {sup 16}O, {sup 12}C (p, p’) reaction using Grand-Raiden Spectrometer and the energy of γ-rays (E{sub γ}) using an array of NaI(Tl) counters. The purpose of the experiment is to provide the basic and important information not only for the γ-ray production from primary neutral-current neutrino-oxygen (-carbon) interactions but also for that from the secondary hadronic (neutron-oxygen and -carbon) interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Protein–protein binding is key in cellular signaling processes. Molecular dynamics (MD) simulations of protein–protein binding, however, are challenging due to limited timescales. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. Here, we report a successful simulation of the binding of a G-protein mimetic nanobody to the M 2 muscarinic GPCR using the robust Gaussian accelerated MD (GaMD) method. Through long-timescale GaMD simulations over 4,500 ns, the nanobody was observed to bind the receptor intracellular G-protein-coupling site, with a minimum rmsd of 2.48 Å in the nanobody core domain compared with the X-ray structure. Binding of the nanobody allosterically closed the orthosteric ligand-binding pocket, being consistent with the recent experimental finding. In the absence of nanobody binding, the receptor orthosteric pocket sampled open and fully open conformations. The GaMD simulations revealed two low-energy intermediate states during nanobody binding to the M 2 receptor. The flexible receptor intracellular loops contribute remarkable electrostatic, polar, and hydrophobic residue interactions in recognition and binding of the nanobody. As a result, these simulations provided important insights into the mechanism of GPCR–nanobody binding and demonstrated the applicability of GaMD in modeling dynamic protein–protein interactions.

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

The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications

Sucrose transport is the central system for the allocation of carbon resources in vascular plants. During growth and development, plants control carbon distribution by coordinating sites of sucrose synthesis and cleavage in different plant organs and different cellular locations. Sucrose synthase, which reversibly catalyzes sucrose synthesis and cleavage, provides a direct and reversible means to regulate sucrose flux. Depending on the metabolic environment, sucrose synthase alters its cellular location to participate in cellulose, callose, and starch biosynthesis through its interactions with membranes, organelles, and cytoskeletal actin. The x-ray crystal structure of sucrose synthase isoform 1 from Arabidopsis thaliana (AtSus1) has been determined as a complex with UDP-glucose and as a complex with UDP and fructose, at 2.8- and 2.85-{angstrom} resolutions, respectively. The AtSus1 structure provides insights into sucrose catalysis and cleavage, as well as the regulation of sucrose synthase and its interactions with cellular targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Building an extensible cell wall

Abstract This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model’s mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose–cellulose interactions in forming a strong yet extensible network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

First High-Throughput Evaluation of Dark Matter Detector Materials

In this work we perform the first high-throughput search and evaluation of materials that can serve as excellent low-mass dark matter detectors. Using properties of close to 1000 materials from the Materials Project database, we project the sensitivity in dark matter parameter space for experiments constructed from each material, including both absorption and scattering processes between dark matter and electrons. Using the anisotropic materials in the dataset, we further compute the level of daily modulation in interaction rates and the resulting directional sensitivities, highlighting materials with prospects to detect the dark matter wind. Our methods provide the basic tools for the data-driven design of dark matter detectors, and our findings lay the groundwork for the next generation of highly optimized direct searches for dark matter as light as the keV scale. This represents a major step in the application of results from condensed matter physics to dark matter search design.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Windowed multipole representation of R -matrix cross sections

Nuclear cross sections are basic inputs to any nuclear computation. Campaigns of experiments are fitted with the parametric R-matrix model of quantum nuclear interactions, and the resulting cross sections are documented—both pointwise and as resonance parameters (with uncertainties)—in standard evaluated nuclear data libraries (ENDF, JEFF, BROND, JENDL, CENDL, TENDL): these constitute our common knowledge of fundamental low-energy nuclear cross sections. In the past decade, a collaborative effort has been deployed to establish a new nuclear cross-section library format—the Windowed Multipole Library—with the goal of considerably reducing the computational cost of cross-section calculations in nuclear transport simulations. This work lays the theoretical foundations underpinning these efforts. From general R-matrix scattering theory, we derive the windowed multipole representation of nuclear cross sections. Though physically and mathematically equivalent to R-matrix cross sections, the windowed multipole representation is particularly well suited for subsequent temperature treatment of angle-integrated cross sections, in particular Doppler broadening, which is the averaging of cross sections over the thermal motion of the target atoms. Doppler broadening is of critical importance in neutron transport applications, as it ensures the stability of many nuclear reactors (negative thermal reactivity). Yet, Doppler broadening of nuclear cross sections has been a considerable bottleneck for nuclear transport computations, often requiring memory-costly pretabulations. We show that the windowed multipole representation can perform accurate Doppler broadening analytically (up to the first reaction threshold), from which we derive cross-section temperature derivatives to any order—all computable on the fly (without precalculations stored in memory). Furthermore, we here establish a way of converting the R-matrix resonance parameters uncertainty (covariance matrices) into windowed multipole parameters uncertainty. We show that generating stochastic nuclear cross sections by sampling from the resulting windowed multipole covariance matrix can reproduce the cross-section uncertainty in the original nuclear data file. The windowed multipole representation is therefore a novel nuclear physics formalism able to generate Doppler broadened stochastic nuclear cross sections on the fly, unlocking breakthrough computational gains for nuclear computations. Through this foundational paper, we hope to make the windowed multipole representation accessible, reproducible, and usable for the nuclear physics community, as well as provide the theoretical basis for future research on expanding its capabilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

ARC3 Activation by PARC6 Promotes FtsZ-Ring Remodeling at the Chloroplast Division Site

Chloroplast division is initiated by assembly of the stromal Z ring, composed of cytoskeletal Filamenting temperature-sensitive Z (FtsZ) proteins. Midplastid Z-ring positioning is governed by the chloroplast Min (Minicell) system, which inhibits Z-ring assembly everywhere except the division site. The central Min-system player is the FtsZ-assembly inhibitor ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3). Here, we report Arabidopsis (Arabidopsis thaliana) chloroplasts contain two pools of ARC3: one distributed throughout the stroma, which presumably fully inhibits Z-ring assembly at nondivision sites, and the other localized to a midplastid ring-like structure. We show that ARC3 is recruited to the middle of the plastid by the inner envelope membrane protein PARALOG OF ARC6 (PARC6). ARC3 bears a C-terminal Membrane Occupation and Recognition Nexus (MORN) domain; previous yeast two-hybrid experiments with full-length and MORN-truncated ARC3 showed the MORN domain mediates ARC3-PARC6 interaction but prevents ARC3-FtsZ interaction. Using yeast three-hybrid experiments, we demonstrate that the MORN-dependent ARC3-PARC6 interaction enables full-length ARC3 to bind FtsZ. The resulting PARC6/ARC3/FtsZ complex enhances the dynamics of Z rings reconstituted in a heterologous system. In conclusion, our findings lead to a model whereby activation of midplastid-localized ARC3 by PARC6 facilitates Z-ring remodeling during chloroplast division by promoting Z-ring dynamics and reveal a novel function for MORN domains in regulating protein–protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Continuous cultivation of the lithoautotrophic nitrate‐reducing Fe( II )‐oxidizing culture KS in a chemostat bioreactor

Abstract Laboratory‐based studies on microbial Fe(II) oxidation are commonly performed for 5–10 days in small volumes with high substrate concentrations, resulting in geochemical gradients and volumetric effects caused by sampling. We used a chemostat to enable uninterrupted supply of medium and investigated autotrophic nitrate‐reducing Fe(II)‐oxidizing culture KS for 24 days. We analysed Fe‐ and N‐speciation, cell‐mineral associations, and the identity of minerals. Results were compared to batch systems (50 and 700 mL—static/shaken). The Fe(II) oxidation rate was highest in the chemostat with 7.57 mM Fe(II) d −1 , while the extent of oxidation was similar to the other experimental setups (average oxidation of 92% of all Fe(II)). Short‐range ordered Fe(III) phases, presumably ferrihydrite, precipitated and later goethite was detected in the chemostat. The 1 mM solid phase Fe(II) remained in the chemostat, up to 15 μM of reactive nitrite was measured, and 42% of visualized cells were partially or completely mineral‐encrusted, likely caused by abiotic oxidation of Fe(II) by nitrite. Despite (partial) encrustation, cells were still viable. Our results show that even with similar oxidation rates as in batch cultures, cultivating Fe(II)‐oxidizing microorganisms under continuous conditions reveals the importance of reactive nitrogen intermediates on Fe(II) oxidation, mineral formation and cell–mineral interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Light-induced magnetization from magnonic rectification

Rectification describes the conversion of an oscillating field or current into a quasi-static one and the most basic example of a rectifier is an AC/DC converter in electronics. This principle can be translated to nonlinear light-matter interactions, where optical rectification converts the oscillating electric field component of light into a quasi-static polarization and phononic rectification converts a lattice vibration into a quasi-static structural distortion. Here, we present a rectification mechanism for magnetism that we call magnonic rectification, where a spin precession is converted into a quasi-static magnetization through the force exerted by a coupled chiral phonon mode. The transiently induced magnetic state resembles that of a canted antiferromagnet, opening an avenue toward creating dynamical spin configurations that are not accessible in equilibrium.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Considering the Lives of Microbes in Microbial Communities

ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Yet, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

LOKI

LOKI is a simulation code that models weakly-coupled plasma evolution using Eulerian kinetic models in four phase space dimensions. The code is useful to understand basic plasma nonlinear plasma physics phenomena - in particular, wave-particle and wave-wave resonances that occur in laser plasma interactions. LOKI can simulate fundamental physical process in low-density plasmas on a scale of hundreds of light wavelengths. It does so by solving the relativistic Vlasov and Valsov-Fokker-Planck differential transport equations describing the collision less and low-collisionality evolution of charged particles in electromagnetic fields in two configuration space and two velocity space dimensions. Two principle electromagnetic models are provided: electrostatic (Poisson's Equation) and electromagnetic (Maxwell's equations).

DIMITS, ANDRIS↗