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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Mitigating Damage to Hybrid Perovskites Using Pulsed-Beam TEM

Using a pulsed-beam transmission electron microscope, we discover a reduction in damage to methylammonium lead iodide (MAPbI3) as compared to conventional beams delivered at the same dose rates. For rates as low as 0.001 e·Å –2 ·s –1 , we find up to a 17% reduction in damage at a total dose of 10 e·Å –2 . We systematically study the effects of number of electrons in each pulse and the duration between pulse arrival. Damage increases for both, though the number of electrons per pulse has a larger effect. A crossover is identified, where a pulsed beam causes more damage than a conventional one. Although qualitatively similar to previous findings, the degree to which damage is reduced in MAPbI3 is less than that observed for other materials (e.g., C36H74), supporting the hypothesis that the effects are material- and damage-mechanism-dependent. Despite this, the observation here of damage reduction for relatively large electron packets (up to 200 electrons per pulse) suggests that MAPbI3 is in fact less susceptible to irradiation than C36H74, which may be related to reported self-healing effects. This work provides insights into damage processes and durability in hybrid perovskites and also illustrates the viability of using pulsed-beam TEM to explore the associated molecular-level routes to degradation, analogous to laser-accelerated energetic pulsed electron beams and the study of damage to biomolecules, cells, and tissues in radiobiology.

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

Nicotine Monitoring with a Wearable Sweat Band

The tobacco epidemic is a public health threat that has taken a heavy toll of lives around the globe each year. Smoking affects both the smokers and those who are exposed to secondhand smoke, and careful tracking of exposure can be key to mitigating the potential hazards. For smokers, the variation of chemical compositions between commercial cigarettes has led to ambiguity in estimating the health risks, both for active smokers and others involuntarily exposed to tobacco smoke and byproducts. In this regard, sweat possesses an attractive opportunity to monitor smoke exposure due to sweat's abundance in biomolecules and its great accessibility. In this paper, we present a wearable sweat band to monitor nicotine, a prominent ingredient in cigarettes, as a viable way to quantitatively assess a wearer's exposure to smoking. Both smokers and normal subjects are tested to demonstrate the use of this device for smoke-related health monitoring. Our results exhibit confirmable and elevated nicotine levels in sweat for subjects inhaling cigarette smoke. This continuous and personalized sweat sensing device is leverage to monitor smoke pollution for a potentially broad population.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Computational and Experimental Study for the Denitrification of Biomass-Derived Hydrothermal Liquefaction Oil

Hydrothermal liquefaction (HTL) is a promising method for processing wet biomass and waste feedstock to produce biofuels. During the HTL process, proteins and other biomolecules in certain feedstock get converted into nitrogenous compounds in produced biocrude, which represents a major challenge to further upgrading them into fuels. One promising approach is to separate nitrogenous compounds from the biocrude using polymeric resins. In this study, experiments were conducted to down-select sorbent and resin systems using a nitrogen-compound-containing surrogate biocrude. We model the binding interactions between an Amberlyst polymeric resin with various compounds present in the biocrude mixture such as nitrogenous compounds like pyrrole, pyridine, hexanamide, and representative co-existing compounds like phenol and dodecanoic acid. To ascertain the efficiency of various resins in the denitrogenation process, we have developed a quantitative structure–function model for the interacting components in the mixture. Our results suggest that the Amberlyst resin is a viable candidate for efficient removal of target nitrogen-containing compounds (such as pyridine) from the biocrude as a result of favorable interactions. The computational studies provide some insight into how and why the identified resin (Amberlyst) works in selective extraction of nitrogenous compound(s).

09 BIOMASS FUELS↗
DOE OSTI2024

Advances in Engineering Nucleotide Sugar Metabolism for Natural Product Glycosylation in Saccharomyces cerevisiae

Glycosylation is a ubiquitous modification present across all of biology, affecting many things such as physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Nucleotide sugars are important precursors needed to study glycosylation and produce glycosylated products. Saccharomyces cerevisiae is a potentially powerful platform for producing glycosylated biomolecules, but it lacks nucleotide sugar diversity. Nucleotide sugar metabolism is complex, and understanding how to engineer it will be necessary to both access and study heterologous glycosylations found across biology. This review overviews the potential challenges with engineering nucleotide sugar metabolism in yeast from the salvage pathways that convert free sugars to their associated UDP-sugars to de novo synthesis where nucleotide sugars are interconverted through a complex metabolic network with governing feedback mechanisms. Finally, recent examples of engineering complex glycosylation of small molecules in S. cerevisiae are explored and assessed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineered Membrane Vesicle Production via oprF or oprI Deletion Has Distinct Phenotypic Effects in Pseudomonas putida

Membrane vesicle (MV) production is a natural phenomenon in Gram-negative bacteria and represents an emerging synthetic biology tool for the secretion of biomolecules or bioproducts. Manipulation of membrane components has proven successful in enhancing MV production. However, the impact of membrane disruptions on strain fitness and protein composition warrants further investigation for the use of MVs in industrial bioprocesses. Here, we identify and characterize two genetic engineering strategies for inducing hypervesiculation-deletion of genes for the outer membrane porin OprF or the lipoprotein OprI-in the commonly used platform Pseudomonas putida KT2440. Deletion of oprI generated up to a 1.5-fold increase in MVs, larger MVs with a greater proportion of outer membrane proteins, and no significant impact on strain fitness compared to wild type. In contrast, deletion of oprF, relative to wild type, generated up to a 4-fold increase in MVs but diminished growth, permeabilized membranes, and increased cytosolic protein packaging. Both hypervesiculation phenotypes increased nontargeted and MV-targeted mNeonGreen extracellular signal by up to 6-fold, demonstrating vesiculation as a mechanism for protein secretion. Despite increased blebbing of MVs from gene deletions, proteins involved in membrane biosynthesis were not elevated relative to wild type. Overexpression of gpsA, which initiates glycerophospholipid biosynthesis, in the ΔoprF background improved the membrane integrity by 37% and maintained MV formation, highlighting the importance of membrane biosynthesis in restoring the membrane in hypervesiculating strains. Together, this study provides genetic engineering strategies with corresponding phenotypic outcomes toward providing a synthetic biology toolset for MV deployment in P. putida.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

13 C Radiofrequency Amplification by Stimulated Emission of Radiation Threshold Sensing of Chemical Reactions

Conventional nuclear magnetic resonance (NMR) enables detection of chemicals and their transformations by exciting nuclear spin ensembles with a radio-frequency pulse followed by detection of the precessing spins at their characteristic frequencies. The detected frequencies report on chemical reactions in real time and the signal amplitudes scale with concentrations of products and reactants. Here, we employ Radiofrequency Amplification by Stimulated Emission of Radiation (RASER), a quantum phenomenon producing coherent emission of 13 C signals, to detect chemical transformations. The 13 C signals are emitted by the negatively hyperpolarized biomolecules without external radio frequency pulses and without any background signal from other, nonhyperpolarized spins in the ensemble. Here, we studied the hydrolysis of hyperpolarized ethyl-[1- 13 C]acetate to hyperpolarized [1- 13 C]acetate, which was analyzed as a model system by conventional NMR and 13 C RASER. The chemical transformation of 13 C RASER-active species leads to complete and abrupt disappearance of reactant signals and delayed, abrupt reappearance of a frequency-shifted RASER signal without destroying 13 C polarization. Further, the experimentally observed “quantum” RASER threshold is supported by simulations.

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

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Matter-wave interference of a native polypeptide

The de Broglie wave nature of matter is a paradigmatic example of quantum physics and it has been exploited in precision measurements of forces and fundamental constants. However, matter-wave interferometry has remained an outstanding challenge for natural polypeptides, building blocks of life, which are fragile and difficult to handle. Here, we demonstrate the wave nature of gramicidin, a natural antibiotic composed of 15 amino acids. Its center of mass is delocalized over more than 20 times the molecular size in our timedomain Talbot-Lau interferometer. We compare the observed interference fringes with a model that includes both a rigorous treatment of the peptide’s quantum wave nature as well as a quantum chemical assessment of its optical properties to distinguish our result from classical predictions. The realization of quantum optics with this prototypical biomolecule paves the way for quantum-assisted measurements on a large class of biologically relevant molecules.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding

Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone–sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone–sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg 2+ and the key tertiary interactions. The absence of Mg 2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue

Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin’s nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method’s sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microsecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learning

Label-free vibrational imaging by stimulated Raman scattering (SRS) provides unprecedented insight into real-time chemical distributions. Specifically, SRS in the fingerprint region (400–1800 cm -1 ) can resolve multiple chemicals in a complex bio-environment. However, due to the intrinsic weak Raman cross-sections and the lack of ultrafast spectral acquisition schemes with high spectral fidelity, SRS in the fingerprint region is not viable for studying living cells or large-scale tissue samples. Here, we report a fingerprint spectroscopic SRS platform that acquires a distortion-free SRS spectrum at 10 cm -1 spectral resolution within 20 µs using a polygon scanner. Meanwhile, we significantly improve the signal-to-noise ratio by employing a spatial-spectral residual learning network, reaching a level comparable to that with 100 times integration. Collectively, our system enables high-speed vibrational spectroscopic imaging of multiple biomolecules in samples ranging from a single live microbe to a tissue slice.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

An in silico method to assess antibody fragment polyreactivity

Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models’ performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A unifying Bayesian framework for merging X-ray diffraction data

Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The emergence of three-dimensional chiral domain walls in polar vortices

Abstract Chirality or handedness of a material can be used as an order parameter to uncover the emergent electronic properties for quantum information science. Conventionally, chirality is found in naturally occurring biomolecules and magnetic materials. Chirality can be engineered in a topological polar vortex ferroelectric/dielectric system via atomic-scale symmetry-breaking operations. We use four-dimensional scanning transmission electron microscopy (4D-STEM) to map out the topology-driven three-dimensional domain walls, where the handedness of two neighbor topological domains change or remain the same. The nature of the domain walls is governed by the interplay of the local perpendicular (lateral) and parallel (axial) polarization with respect to the tubular vortex structures. Unique symmetry-breaking operations and the finite nature of domain walls result in a triple point formation at the junction of chiral and achiral domain walls. The unconventional nature of the domain walls with triple point pairs may result in unique electrostatic and magnetic properties potentially useful for quantum sensing applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Directing polymorph specific calcium carbonate formation with de novo protein templates

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-C a2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

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

Engineering self-deliverable ribonucleoproteins for genome editing in the brain

The delivery of CRISPR ribonucleoproteins (RNPs) for genome editing in vitro and in vivo has important advantages over other delivery methods, including reduced off-target and immunogenic effects. However, effective delivery of RNPs remains challenging in certain cell types due to low efficiency and cell toxicity. To address these issues, we engineer self-deliverable RNPs that can promote efficient cellular uptake and carry out robust genome editing without the need for helper materials or biomolecules. Screening of cell-penetrating peptides (CPPs) fused to CRISPR-Cas9 protein identifies potent constructs capable of efficient genome editing of neural progenitor cells. Further engineering of these fusion proteins establishes a C-terminal Cas9 fusion with three copies of A22p, a peptide derived from human semaphorin-3a, that exhibits substantially improved editing efficacy compared to other constructs. We find that self-deliverable Cas9 RNPs generate robust genome edits in clinically relevant genes when injected directly into the mouse striatum. Overall, self-deliverable Cas9 proteins provide a facile and effective platform for genome editing in vitro and in vivo.

59 BASIC BIOLOGICAL SCIENCES↗