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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 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Surface passivation of (100) GaSb using self-assembled monolayers of long-chain octadecanethiol

The passivation of (100) GaSb surface was investigated by means of the long-chain octadecanethiol (ODT) self-assembled monolayer (SAM). The properties of ODT SAM on (100) GaSb were characterized by the atomic force microscopy using Kelvin probe force microscopy mode and X-ray photoelectron spectroscopy. The chemical treatment of 10 mM ODT-C{sub 2}H{sub 5}OH has been applied to the passivation of a type-II superlattice InAs/GaSb photodetector. The electrical measurements indicate that the current density was reduced by one order of magnitude as compared to an unpassivated photodetector.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach

Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonian method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Impact of charge carrier injection on single-chain photophysics of conjugated polymers

Charges in conjugated polymer materials have a strong impact on the photophysics and their interaction with the primary excited state species has to be taken into account in understanding device properties. Here, we employ single-molecule spectroscopy to unravel the influence of charges on several photoluminescence (PL) observables. The charges are injected either stochastically by a photochemical process or deterministically in a hole-injection sandwich device configuration. We find that upon charge injection, besides a blue-shift of the PL emission and a shortening of the PL lifetime due to quenching and blocking of the lowest-energy chromophores, the non-classical photon arrival time distribution of the multichromophoric chain is modified towards a more classical distribution. Surprisingly, the fidelity of photon antibunching deteriorates upon charging, whereas one would actually expect the opposite: the number of chromophores to be reduced. A qualitative model is presented to explain the observed PL changes. The results are of interest to developing a microscopic understanding of the intrinsic charge-exciton quenching interaction in devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Vapor phase nucleation of the short-chain n -alkanes ( n -pentane, n -hexane and n -heptane): Experiments and Monte Carlo simulations

We measured the nucleation rates of n-pentane through n-heptane in a supersonic nozzle at temperatures ranging from ca. 109 K to 168 K. For n-pentane and n-hexane, these are the first nucleation rate measurements that have been made, and the trends in the current data agree well with those in the earlier work of Ghosh et al. for longer chain alkanes. Complementary Monte Carlo simulations, using the transferable potentials for phase equilibria-united atom potentials, suggest that despite the high degree of supercooling, the critical clusters remain liquid like under experimental conditions for n-pentane through n-heptane, but adopt more ordered structures for n-octane and n-nonane. For all three alkanes, the experimental and simulated nucleation rates are offset by ~3 orders of magnitude when plotted as a function of ln S/(T c /T – 1) 1.5 . Explicitly accounting for the surface tension difference between the real and model substances, or alternatively using the Hale scaling parameter, Ω, consistent with the model potential, increases the offset to ~6 orders of magnitude.

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

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

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

Two-stage laser-induced synthesis of linear carbon chains

A method is proposed for the synthesis of linear carbon chains under irradiation of colloidal systems consisting of schungite nanoparticles by an ytterbium fibre laser with a pulse duration of 100 ns and an energy up to 1 mJ. Colloidal systems have been previously prepared by laser ablation of a schungite target in distilled water using a Nd{sup 3+} : YAG laser with a pulse duration of 1 ms and an energy up to 10 J. (interaction of laser radiation with matter)

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

Spatial order in interference of a chain of Bose condensates with random phases

We have observed the interference of a long chain of Bose condensates prepared at the initial time moment in antinodes of a standing electromagnetic wave. The initial distribution of the condensate density in the system under consideration is periodic while the condensate phases can be different. Then the standing wave is quickly turned off, and the condensates start to expand and interfere. A spatial order of the interference fringes is observed with a period being substantially different from the period arising in the case of the Talbot effect. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Stabilization of amyloidogenic immunoglobulin light chains by small molecules

In Ig light-chain (LC) amyloidosis (AL), the unique antibody LC protein that is secreted by monoclonal plasma cells in each patient misfolds and/or aggregates, a process leading to organ degeneration. As a step toward developing treatments for AL patients with substantial cardiac involvement who have difficulty tolerating existing chemotherapy regimens, we introduce small-molecule kinetic stabilizers of the native dimeric structure of full-length LCs, which can slow or stop the amyloidogenicity cascade at its origin. Specifically, a protease-coupled fluorescence polarization-based high-throughput screen was employed to identify small molecules that kinetically stabilize LCs. NMR and X-ray crystallographic data demonstrate that at least one structural family of hits bind at the LC–LC dimerization interface within full-length LCs, utilizing variable-domain residues that are highly conserved in most AL patients. Stopping the amyloidogenesis cascade at the beginning is a proven strategy to ameliorate postmitotic tissue degeneration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Anomalous relaxation and the high-temperature structure factor of XXZ spin chains

We compute the spin-structure factor of XXZ spin chains in the Heisenberg and gapped (Ising) regimes in the high-temperature limit for nonzero magnetization, within the framework of generalized hydrodynamics, including diffusive corrections. The structure factor shows a hierarchy of timescales in the gapped phase, owing to s-spin magnon bound states (“strings”) of various sizes. Although short strings move ballistically, long strings move primarily diffusively as a result of their collisions with short strings. The interplay between these effects gives rise to anomalous power-law decay of the spin-structure factor, with continuously varying exponents, at any fixed separation in the late-time limit. We elucidate the cross-over to diffusion (in the gapped phase) and to superdiffusion (at the isotropic point) in the half-filling limit. We verify our results via extensive matrix product operator calculations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Scale-free, programmable design of morphable chain loops of kilobots and colloidal motors

Micron-scale robots require systems that can morph into arbitrary target configurations controlled by external agents such as heat, light, electricity, and chemical environment. Achieving this behavior using conventional approaches is challenging because the available materials at these scales are not programmable like their macroscopic counterparts. To overcome this challenge, we propose a design strategy to make a robotic machine that is both programmable and compatible with colloidal-scale physics. Our strategy uses motors in the form of active colloidal particles that constantly propel forward. We sequence these motors end-to-end in a closed chain forming a two-dimensional loop that folds under its mechanical constraints. We encode the target loop shape and its motion by regulating six design parameters, each scale-invariant and achievable at the colloidal scale. We demonstrate the plausibility of our design strategy using centimeter-scale robots called kilobots . We use Brownian dynamics simulation to explore the large design space beyond that possible with kilobots, and present an analytical theory to aid the design process. Multiple loops can also be fused together to achieve several complex shapes and robotic behaviors, demonstrated by folding a letter shape “M,” a dynamic gripper , and a dynamic pacman . The material-agnostic, scale-free, and programmable nature of our design enables building a variety of reconfigurable and autonomous robots at both colloidal scales and macroscales.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases

Biocatalytic C–H activation has the potential to merge enzymatic and synthetic strategies for bond formation. Fe II /αKG-dependent halogenases are particularly distinguished for their ability both to control selective C–H activation as well as to direct group transfer of a bound anion along a reaction axis separate from oxygen rebound, enabling the development of new transformations. In this context, we elucidate the basis for the selectivity of enzymes that perform selective halogenation to yield 4-Cl-lysine (BesD), 5-Cl-lysine (HalB), and 4-Cl-ornithine (HalD), allowing us to probe how site-selectivity and chain length selectivity are achieved. We now report the crystal structure of the HalB and HalD, revealing the key role of the substrate-binding lid in positioning the substrate for C 4 vs C 5 chlorination and recognition of lysine vs ornithine. Targeted engineering of the substrate-binding lid further demonstrates that these selectivities can be altered or switched, showcasing the potential to develop halogenases for biocatalytic applications.

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

Perpendicular crossing chains enable high mobility in a noncrystalline conjugated polymer

The nature of interchain π-system contacts, and their relationship to hole transport, are elucidated for the high-mobility, noncrystalline conjugated polymer C16-IDTBT by the application of scanning tunneling microscopy, molecular dynamics, and quantum chemical calculations. The microstructure is shown to favor an unusual packing motif in which paired chains cross-over one another at near-perpendicular angles. By linking to mesoscale microstructural features, revealed by coarse-grained molecular dynamics and previous studies, and performing simulations of charge transport, it is demonstrated that the high mobility of C16-IDTBT can be explained by the promotion of a highly interconnected transport network, stemming from the adoption of perpendicular contacts at the nanoscale, in combination with fast intrachain transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment

It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 {angstrom} resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complex reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of {beta}-toxins to its Na+ channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)

Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. Here, the causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in V L -CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the V L and the V H , and between the V L and CXCL13. Importantly, a single, germline-encoded V L -CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe–2S cluster

Iron–sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron–sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. In this study we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis ( Mtb ), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 Å resolution, revealing a 2Fe–2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg 2+ ion 6.5 Å from the 2Fe–2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb -DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.

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

The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase

Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. In this work we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD + reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the “aromatic box” that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.

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

Myosin light chain kinase regulates cell polarization independently of membrane tension or Rho kinase

Cells polarize to a single front and rear to achieve rapid actin-based motility, but the mechanisms preventing the formation of multiple fronts are unclear. We developed embryonic zebrafish keratocytes as a model system for investigating establishment of a single axis. We observed that, although keratocytes from 2 d postfertilization (dpf) embryos resembled canonical fan-shaped keratocytes, keratocytes from 4 dpf embryos often formed multiple protrusions despite unchanged membrane tension. Using genomic, genetic, and pharmacological approaches, we determined that the multiple-protrusion phenotype was primarily due to increased myosin light chain kinase (MLCK) expression. MLCK activity influences cell polarity by increasing myosin accumulation in lamellipodia, which locally decreases protrusion lifetime, limiting lamellipodial size and allowing for multiple protrusions to coexist within the context of membrane tension limiting protrusion globally. In contrast, Rho kinase (ROCK) regulates myosin accumulation at the cell rear and does not determine protrusion size. These results suggest a novel MLCK-specific mechanism for controlling cell polarity via regulation of myosin activity in protrusions.

Cell Biology↗
DOE OSTI2011

SPECTRAL ENERGY DISTRIBUTION FITTING WITH MARKOV CHAIN MONTE CARLO: METHODOLOGY AND APPLICATION TO z = 3.1 Ly{alpha}-EMITTING GALAXIES

We present GalMC, a Markov Chain Monte Carlo (MCMC) algorithm designed to fit the spectral energy distributions (SEDs) of galaxies to infer physical properties such as age, stellar mass, dust reddening, metallicity, redshift, and star formation rate. We describe the features of the code and the extensive tests conducted to ensure that our procedure leads to unbiased parameter estimation and accurate evaluation of uncertainties. We compare its performance to grid-based algorithms, showing that the efficiency in CPU time is {approx}100 times better for MCMC for a three-dimensional parameter space and increasing with the number of dimensions. We use GalMC to fit the stacked SEDs of two samples of Lyman alpha emitters (LAEs) at redshift z = 3.1. Our fit reveals that the typical LAE detected in the IRAC 3.6 {mu}m band has age = 0.67 [0.37-1.81] Gyr and stellar mass = 3.2 [2.5-4.2] x 10{sup 9} M{sub sun}, while the typical LAE not detected at 3.6 {mu}m has age = 0.06 [0.01-0.2] Gyr and stellar mass = 2 [1.1-3.4] x 10{sup 8} M{sub sun}. The SEDs of both stacks are consistent with the absence of dust. The data do not significantly prefer exponential with respect to constant star formation history. The stellar populations of these two samples are consistent with the previous study by Lai et al., with some differences due to the improved modeling of the stellar populations. A constraint on the metallicity of z = 3.1 LAEs from broadband photometry, requiring Z < Z{sub sun} at 95% confidence, is found here for the first time.

79 ASTRONOMY AND ASTROPHYSICS↗