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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Tumorigenic p53 mutants undergo common structural disruptions including conversion to α‐sheet structure

Abstract The p53 protein is a commonly studied cancer target because of its role in tumor suppression. Unfortunately, it is susceptible to mutation‐associated loss of function; approximately 50% of cancers are associated with mutations to p53, the majority of which are located in the central DNA‐binding domain. Here, we report molecular dynamics simulations of wild‐type (WT) p53 and 20 different mutants, including a stabilized pseudo‐WT mutant. Our findings indicate that p53 mutants tend to exacerbate latent structural‐disruption tendencies, or vulnerabilities, already present in the WT protein, suggesting that it may be possible to develop cancer therapies by targeting a relatively small set of structural‐disruption motifs rather than a multitude of effects specific to each mutant. In addition, α‐sheet secondary structure formed in almost all of the proteins. α‐Sheet has been hypothesized and recently demonstrated to play a role in amyloidogenesis, and its presence in the reported p53 simulations coincides with the recent re‐consideration of cancer as an amyloid disease.

Bromley, Dennis↗
DOE OSTI2021

Computational study of the effect of core–skin structure on the mechanical properties of carbon nanofibers

The effect of the core–skin structure on the mechanical properties of carbon nanofibers is investigated in large-scale molecular dynamics simulations of tensile deformation of carbon nanofibers with the core–skin and homogeneous structures. Contrary to an established notion of the deleterious effect of the skin layer on the strength of carbon fibers, the presence of a high-quality skin layer is found to increase both the Young’s modulus and tensile strength of the nanofiber. A detailed analysis of the fracture process indicates that the nanofiber strengthening is related to the ability of skin layer to suppress crack nucleation at the core–skin interface. Furthermore, the computational predictions suggest that the design of new approaches to carbon fiber manufacturing and processing leading to the generation of a high-quality skin layer while avoiding the introduction of structural defects at the core–skin interface may yield a significant enhancement of the mechanical properties of carbon fibers.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures

Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Mapping structural heterogeneity at the nanoscale with scanning nano-structure electron microscopy (SNEM)

Here, in this work, we explore the use of scanning electron diffraction (also known as 4D-STEM) coupled with electron atomic pair distribution function analysis (ePDF) to understand the local order (structure and chemistry) as a function of position in a complex multicomponent system, a hot rolled, Ni-encapsulated, Zr 65 Cu 17.5 Ni 10 Al 7.5 bulk metallic glass (BMG), with a spatial resolution of 3 nm. We show that it is possible to gain insight into the chemistry and chemical clustering/ordering tendency in different regions of the sample, including in the vicinity of nano-scale crystallites that are identified from virtual dark field images and in heavily deformed regions at the edge of the BMG. In addition to simpler analysis, unsupervised machine learning was used to extract partial PDFs from the material, modeled as a quasi-binary alloy, and map them in space. These maps allowed key insights not only into the local average composition, as validated by EELS, but also a unique insight into chemical short-range ordering tendencies in different regions of the sample during formation. The experiments are straightforward and rapid and, unlike spectroscopic measurements, don’t require energy filters on the instrument. We spatially map different quantities of interest (QoI’s), defined as scalars that can be computed directly from positions and widths of ePDF peaks or parameters refined from fits to the patterns. We developed a flexible and rapid data reduction and analysis software framework that allows experimenters to rapidly explore images of the sample on the basis of different QoI’s. The power and flexibility of this approach are explored and described in detail. Because of the fact that we are getting spatially resolved images of the nanoscale structure obtained from ePDFs we call this approach scanning nano-structure electron microscopy (SNEM), and we believe that it will be powerful and useful extension of current 4D-STEM methods.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features

Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.

Bio-based polymer↗
DOE OSTI2018

Investigation of structural and magnetic properties of rapidly-solidified iron-silicon alloys at ambient and elevated temperatures

In this work, we investigated the ambient temperature structural properties (~300 K) and the ambient and high temperature (up to 900 K) direct current (DC) magnetic properties of melt-spun Fe-x wt.% Si (x = 3, 5, & 8) alloys. The wheel surface speeds selected for the study were 30 m/s and 40 m/s. The thickness, width, lattice parameter, saturation magnetization (MS), and intrinsic coercivity (HCI) of the melt spun ribbons are presented and compared with data in the literature. The ribbons produced at the lower wheel surface speed (30 m/s) were continuous having relatively uniform edges compared to the ribbons produced at the higher wheel surface speed. The thickness and the width of the melt-spun ribbons ranged between ~15-60 μm and 500-800 μm, respectively. The x-ray diffraction spectra of the melt-spun ribbons indicated the presence of disordered α-phase, irrespective of the composition, and the wheel-surface speed. The lattice parameter decreased gradually as a function of increasing silicon content from ~0.2862 nm (Fe-3 wt.% Si) to ~0.2847 nm (Fe-8 wt.% Si). Wheel surface speed was not shown to have a significant effect on the magnetization, but primarily impacted the ribbon structure. A decreasing trend in the saturation magnetization was observed as a function of increased silicon content. The intrinsic coercivity of the melt-spun alloys ranged between ~50 to 200 A/m. Elevated temperature evaluation of the magnetization in the case of Fe-3 & 5 wt.% Si alloy ribbons was distinctly different from the Fe-8 wt.% Si alloy ribbons. The curves of the as-prepared Fe-3 wt.% Si and Fe-5 wt.% Si alloy ribbons were irreversible while that of Fe-8 wt.% Si was reversible. The MS for any of the combinations of wheel surface speed and composition decreased monotonically with the increase in temperature (from 300 – 900 K). The percentage decrease in MS from 300 K to 900 K for the Fe-3 wt.% Si and Fe-5 wt.% Si alloys was ~19-22 %, while the percentage decrease in the same temperature range for Fe-8 wt.% Si alloy was ~26-30 %. It appears that Fe-3 wt.% Si and Fe-5 wt.% Si alloys ribbons are primarily comprised of the α phase (disordered phase) with any minor constituents being beyond the detection limits of the studies performed, while the Fe-8 wt.% Si alloy ribbons are comprised of disordered and regions of short-range ordering.

Elevated Temperature↗
DOE OSTI2018

Effects of citrate on hexavalent chromium reduction by structural Fe(II) in nontronite

Iron-bearing clay minerals and organic matter are two important components in natural environments that influence hexavalent chromium (Cr(VI)) reduction. Previous studies have shown that organic ligands could influence Cr(VI) reduction by aqueous Fe2+ and pyrite. However, the effects of organic ligands on Cr(VI) reduction by structural Fe(II) in clays are not well understood. In this study, the effects of citrate on Cr(VI) reduction by nontronite (NAu-2) were investigated under near neutral pH condition (pH=6). Our results showed that the presence of citrate decreased the rate but increased the amount of Cr(VI) reduction by structural Fe(II) in NAu-2. The decreased reaction rate was likely due to competitive sorption of citrate and polyanionic dichromate (Cr2O7- ), because sorption of dichromate appeared to be the first step for subsequent Cr(VI) reduction. The increased amount of Cr(VI) reduction in the presence of citrate was likely because citrate provided additional reducing power through ligand-metal electron transfer in the presence of soluble Fe 3+ derived from dissolution of reduced NAu-2. Soluble Cr(III)-citrate complex was the possible form of reduced chromium when citrate was present. In contrast, nanometer-sized Cr2O3 particles were the product of Cr(VI) reduction by reduced NAu-2 without citrate. Our study highlights the importance of organic ligands on Cr(VI) reduction and immobilization when iron-bearing clay minerals are applied to treat Cr(VI) contaminant in organic matter rich environments.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Structural and Biophysical Properties of a [4Fe-4S] Ferredoxin-Like Protein from Synechocystis sp. PCC 6803 with a Unique Two Domain Structure

Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron-sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe-2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2x[4Fe-4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 +/- 9 mV and -516 +/- 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe-4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.

cyanobacteria↗