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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 361 records · Page 20

Electron-nuclear decoupling at a spin clock transition

The ability to design quantum systems that decouple from environmental noise sources is highly desirable for development of quantum technologies with optimal coherence. The chemical tunability of electronic states in magnetic molecules combined with advanced electron spin resonance techniques provides excellent opportunities to address this problem. Indeed, so-called clock transitions have been shown to protect molecular spin qubits from magnetic noise, giving rise to significantly enhanced coherence. Here we conduct a spectroscopic and computational investigation of this physics, focusing on the role of the nuclear bath. Away from the clock transition, linear coupling to the nuclear degrees of freedom causes a modulation and decay of electronic coherence, as quantified via electron spin echo signals generated experimentally and in silico. Meanwhile, the effective hyperfine interaction vanishes at the clock transition, resulting in electron-nuclear decoupling and an absence of quantum information leakage to the nuclear bath, providing opportunities to characterize other decoherence sources.

74 ATOMIC AND MOLECULAR PHYSICS↗

A chemical approach for the specific generation of cysteine sulfinylation

Oxidative modifications of protein cysteines play a crucial role in regulating redox homeostasis, redox signaling, and protein function. One of the modifications involves the oxidation of a cysteine thiol to a sulfinic acid (R-SO 2 H) which has been considered a marker for oxidative stress and an important activator for certain proteins. Here, in this study, we report a protocol for the selective formation of sulfinic acids on cysteine residues in a simple 3-step operation under mild conditions: thiol-blocking, oxidation, and reduction. The specificity and efficiency of the method were demonstrated by using both small molecule substrates and a protein model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei

Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized. To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose. This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.

59 BASIC BIOLOGICAL SCIENCES↗

Interfacing Atmospheric Flow Tube to Ion Mobility Spectrometry: FY 2021 Final Report

An atmospheric flow tube (AFT) provides extended ion-molecule reaction times of 2-3 seconds compared to milliseconds in typical mass spectrometers. This results in several orders of magnitude enhanced sensitivity allowing for vapor detection at the parts-per-quadrillion levels when an AFT is coupled to a mass spectrometer (MS). The goal of this project was to demonstrate the feasibility of integrating an AFT ionization source to a more portable ion mobility spectrometer (IMS). This project was successful in integrating AFT to IMS, as shown in Figure ES.1. The PNNL team demonstrated measurable ion signal from an AFT-IMS with a Faraday plate detector. Reasonable ion signals were detectable at low flow rates approaching 1 m/s. This is close to the flow rates used with the AFT-MS, which has demonstrated parts-per-quadrillion vapor detection. Vapor detection enables non-contact detection of a variety of illicit substances for various applications including cargo screening, mail sorting facilities, and checkpoints. With further improvements to enhance detection, AFT-IMS has the potential to allow ultra-trace vapor detection in a more portable device.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Artificial Transmembrane Channel Constructed from Shape-Persistent Covalent Organic Molecular Cages Capable of Ion and Small Molecule Transport

Shape-persistent arylene ethynylene molecular cages have been investigated as transmembrane channels for ions and small molecules. The molecular cages were obtained starting from tetrayne monomers through alkyne metathesis cyclooligomerization. We found these porphyrin-based rigid molecular cages can insert into the lipid bilayer and efficiently transport ions and small molecules (e.g., calcein). Our study reveals longer hydrophobic alkyl chains on the cage molecule promote the channeling efficiency, while shorter and/or more polar side chains impair such activity. Kinetic analysis shows linear correlation between the rate of proton transport and the concentration of the cage, suggesting the active species is likely a monomeric cage. We found that C70-encapsulated cages are nearly inactive for transmembrane ion transportation, indicating that ions are likely transported through the internal cavity of the cage. Discrete shape-persistent organic cages represent highly stable synthetic ion channels or pores, which could have interesting applications in biomimetic signaling and drug delivery.

alkyne metathesis↗

Bacteria export alarmone synthetases that produce (p)ppApp and (p)ppGpp

Guanosine penta- and tetraphosphate [(p)ppGpp] and their adenosine analogs [(p)ppApp] are bacterial second messengers known as alarmones. Members of the RelA-SpoT homolog (RSH) family synthesize (p)ppGpp to mediate the stringent response during nutrient starvation, whereas (p)ppApp synthetases have been identified as bactericidal toxins in diverse contexts including type VI secretion systems, toxin-antitoxin modules, and phages. Although alarmone synthesis has traditionally been viewed as a cytoplasmic process, early studies in Streptomyces suggested the existence of secreted alarmone synthetases. Here, we identify SaEAS, an exported alarmone synthetase (EAS) from Streptomyces albidoflavus, as the long-mysterious source of extracellular alarmone synthetase activity in Streptomyces. SaEAS produces both (p)ppGpp and (p)ppApp at rates exceeding 100,000 molecules per minute and has kinetic properties adapted to low substrate environments. A broader bioinformatic survey reveals ~600 EASs linked to a range of specialized bacterial secretion systems. Characterization of two additional EASs, VpEAS from Vibrio parahaemolyticus and AaEAS from Amycolatopsis azurea, shows that both produce (p)ppGpp exclusively and inhibit bacterial growth when localized to the cytoplasm. These findings challenge the longstanding view of (p)ppGpp as strictly pro-survival and unveil a diverse family of secreted RSH enzymes with potential roles in interbacterial antagonism and environmental signaling.

Ahmad, Shehryar↗

Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation

Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions, it is important to understand their relative merits. In the present study, we evaluate the respective scattering cross sections of the two methods and simulate their ability to determine excited state molecular structures in light of currently existing XFEL and MeV source parameters. Using the example of optically excited N-methyl morpholine and simulating the scattering patterns with shot noise, we find that the currently achievable signals are superior with x-ray scattering for equal samples and on a per-shot basis and that x-ray scattering requires fewer detected signal counts for an equal fidelity structure determination. Importantly, within the independent atom model, excellent structure determinations can be achieved for scattering vectors only to about 5 Å−1, leaving larger scattering vector ranges for investigating vibrational motions and wavepackets. Electron scattering has a comparatively higher sensitivity toward hydrogen atoms, which may point to applications where electron scattering is inherently the preferred choice, provided that excellent signals can be achieved at large scattering angles that are currently difficult to access.

74 ATOMIC AND MOLECULAR PHYSICS↗

Studying microbially induced corrosion on glass using ToF-SIMS

Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Finally, possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.

36 MATERIALS SCIENCE↗

Femtosecond symmetry breaking and coherent relaxation of methane cations via x-ray spectroscopy

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic-level insight into photochemistry. Here, we performed a time-resolved study of ultrafast molecular symmetry breaking through geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft x-rays at the carbon K-edge revealed that the distortion occurred within 10 ± 2 femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activated coherent oscillations in the asymmetric scissoring vibrational mode of the symmetry-broken cation, which were detected in the x-ray signal. These oscillations were damped within 58 ± 13 femtoseconds because vibrational coherence was lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens avenues for exploring complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deposition of sulfate aerosols with positive Δ 33 S in the Neoarchean

Anomalous sulfur isotope compositions present in Archean rocks have been intensely scrutinized over the last 20 years because they record key aspects of Earth's atmospheric composition prior to the appearance of free molecular oxygen ca. 2.3 billion years ago. These isotopic compositions can be described as mass anomalous fractionations (MAF) and are produced in the atmosphere as UV light interacts with SO 2 molecules. Most interpretations suggest that atmospheric processes generate a reduced S-phase with a positive ( 33 S-enriched) MAF signature, as measured in pyrites, and an oxidized S-phase with a negative anomaly, as measured in bedded barite deposits. However, recent data for carbonate-associated sulfate (CAS) — a direct proxy for the isotopic composition of sulfur from seawater sulfate — in Neoarchean rocks showed no such negative values, but rather the opposite. To understand if the positive MAF anomalies we measured in Neoarchean CAS reflect secondary processes (diagenetic, metamorphic, handling) instead of original signals of Archean seawater sulfate, we collected additional sample suites with various degrees of preservation and metamorphic alteration across the Campbellrand-Malmani platform in South Africa. Results illustrate that within this comprehensive suite, less-altered samples all contain positive MAF values while secondary processes tend to either remove CAS from the sample and/or decrease the 33 S-enrichment. This positive MAF signal in sulfate is therefore reasonably interpreted as a primary depositional origin, and implies that the assumption that sulfate always carries a negative MAF anomaly throughout the Archean rock record needs to be reconsidered. Our CAS observations suggest that future experiments and calculations should also consider atmospheric and/or sulfur cycling processes that can produce oxidized sulfur with a positive MAF signature.

54 ENVIRONMENTAL SCIENCES↗

Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6

The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗

Superstructured Biomaterials Formed by Exchange Dynamics and Host–Guest Interactions in Supramolecular Polymers

Dynamic and reversible assembly of molecules is ubiquitous in the hierarchical superstructures of living systems and plays a key role in cellular functions. Recent work from the laboratory reported on the reversible formation of such superstructures in systems of peptide amphiphiles conjugated to oligonucleotides and electrostatically complimentary peptide sequences. Here, a supramolecular system is reported upon where exchange dynamics and host–guest interactions between β-cyclodextrin and adamantane on peptide amphiphiles lead to superstructure formation. Superstructure formation with bundled nanoribbons generates a mechanically robust hydrogel with a highly porous architecture that can be 3D printed. Functionalization of the porous superstructured material with a biological signal results in a matrix with significant in vitro bioactivity toward neurons that could be used as a supramolecular model to design novel biomaterials.

36 MATERIALS SCIENCE↗

Sample-minimizing co-flow cell for time-resolved pump–probe X-ray solution scattering

A fundamental problem in biological sciences is understanding how macromolecular machines work and how the structural changes of a molecule are connected to its function. Time-resolved techniques are vital in this regard and essential for understanding the structural dynamics of biomolecules. Time-resolved small- and wide-angle X-ray solution scattering has the capability to provide a multitude of information about the kinetics and global structural changes of molecules under their physiological conditions. However, standard protocols for such time-resolved measurements often require significant amounts of sample, which frequently render time-resolved measurements impossible. A cytometry-type sheath co-flow cell, developed at the BioCARS 14-ID beamline at the Advanced Photon Source, USA, allows time-resolved pump–probe X-ray solution scattering measurements to be conducted with sample consumption reduced by more than ten times compared with standard sample cells and protocols. The comparative capabilities of the standard and co-flow experimental setups were demonstrated by studying time-resolved signals in photoactive yellow protein.

36 MATERIALS SCIENCE↗

Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors

The G12D mutation is among the most common KRAS mutations associated with cancer, in particular, pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM KD values. Deep mutational scanning of a monobody generated hundreds of functional and nonfunctional single-point mutants, which identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Revisiting the three-kaon interaction and its relation with 𝐾⁡(1460)

Here, we test the hypothesis of 𝐾⁡(1460) being a hadronic 𝐽 𝑃 = 0 − molecule through nonperturbative 𝑆-wave $KK\bar{⁢K}$, 𝐾⁢𝜋⁢𝜋, 𝐾⁢𝜋⁢𝜂 coupled-channel dynamics in a three-body unitary isobar approach. The scalar two-body coupled-channel resonances 𝑓 0 ⁡(500), 𝑓 0 ⁡(980), 𝑎 0 ⁡(980), and 𝐾$^*_0$⁡(700) are generated in the subsytems in amplitudes that match phase shifts from experiment. In a first step, previous results in the limit of mass-degenerate, stable 𝑓 0 and 𝑎 0 isobars are reproduced. Once the full seven-coupled channel model is switched on, other 𝑆-matrix effects obscure and modify the resonance signal, including complex thresholds, a two-body cusp, and a triangle singularity at threshold.

Döring, M. [George Washington Univ., Washington, D↗

High throughput single cell multiomics platform [Abstract]

In this collaborative project, PNNL and Scienion will co-develop an integrated microfluidic technology to co-measure the transcriptome and proteome in single cells. The technology will enable us to efficiently separate proteins from mRNA transcripts between two microchips, barcode the molecules, and measure them separately with next-generation sequencing and mass spectrometry, respectively. Multicellular organisms contain diverse cell types and tremendous cell-to-cell heterogeneity that dictates a multitude of biological functions in both physiological and pathological environments. Even in the case of microbes, these genetically identical organisms can randomly differentiate into many subpopulations that assume different roles for the survival of the community. Bulk-scale measurements are insufficient to resolve such complexities. The development and applications of high throughput single-cell omics technologies have transformed our understanding of cellular heterogeneities and their differential responses to internal signaling events or external stimulations. Despite these advances, most current single-cell omic technologies provide information on only one type of biomolecule. Perse, such measurements provide incomplete information because the cell phenotype is determined by multiple layers of biomolecules and the interplay between genome, epigenome, transcriptome, and proteome. For example, mRNA abundance in one cell can not be precisely referred to the corresponding DNA and protein in other cells because of the potential subtle difference in genotype (e.g., somatic mutation or copy number variation) or phenotype (external microenvironment and cell-cell interactions). As such, parallel measurement of multiple biomolecules in the same single cells can offer unique advantages compared with measuring them separately in different single cells. Scienion is a world-leading biotech company focusing on precision liquid handling and its application in single-cell whole-genome sequencing and RNA sequencing. PNNL is the leading institution in ultrasensitive mass spectrometry, microfluidics, and untargeted single-cell proteomics (scProteomics). This collaboration will facilitate a unique fusion between scTranscriptomics capability at Scienion and scProteomics capabilities at PNNL to, for the first time, perform both untargeted transcriptomics and proteomics from the same single cells.

59 BASIC BIOLOGICAL SCIENCES↗

Lipid Droplets: Packing Hydrophobic Molecules Within the Aqueous Cytoplasm

Lipid droplets, also known as oil bodies or lipid bodies, are plant organelles that compartmentalize neutral lipids as a hydrophobic matrix covered by proteins embedded in a phospholipid monolayer. Some of these proteins have been known for decades, such as oleosins, caleosins, and steroleosins, whereas a host of others have been discovered more recently with various levels of abundance on lipid droplets, depending on the tissue and developmental stage. In addition to a growing inventory of lipid droplet proteins, the subcellular machinery that contributes to the biogenesis and degradation of lipid droplets is being identified and attention is turning to more mechanistic questions regarding lipid droplet dynamics. While lipid droplets are mostly regarded as storage deposits for carbon and energy in lipid-rich plant tissues such as seeds, these organelles are present in essentially all plant cells, where they display additional functions in signaling, membrane remodeling, and the compartmentalization of a variety of hydrophobic components. Remarkable metabolic engineering efforts have demonstrated the plasticity of vegetative tissues such as leaves to synthesize and package large amounts of storage lipids, which enable future applications in bioenergy and the engineering of high-value lipophilic compounds. Here, we review the growing body of knowledge about lipid droplets in plant cells, describe the evolutionary similarity and divergence in their associated subcellular machinery, and point to gaps that deserve future attention.

60 APPLIED LIFE SCIENCES↗

Standoff Detection of Chemical Plumes Using Swept-ECQCL Remote Detection Technology: Results from EMRTC Complex Terrain Dual Tracer Experiment

As part of the Complex Terrain Dual Tracer Experiments performed in support of the LYNM program, a swept-wavelength external cavity quantum cascade laser (swept-ECQCL) remote detection system was deployed to measure chemical plume propagation with high temporal resolution. The swept-ECQCL remote detection technology was initially developed at PNNL, and is now under further development at Opticslah, LLC under SBIR funding from DOE (DOE SBIR Phase I Project DE-SC0019855, Remote Detection Technologies, Program Manager Chris Ramos). The swept-ECQCL technology provides a single-frequency infrared laser source which is rapidly scanned over a large wavelength range to measure the infrared absorption of gases, liquids, or solids. Analysis of the measured infrared absorption spectrum is used to detect, identify, and quantify the chemical species which are present. While most previous laser-based techniques used small wavelength tuning ranges to measure only a few isolated spectral lines of a few species, the swept-ECQCL provides the large tuning range needed to measure multiple species simultaneously, and to detect broad absorption features from large molecules or condensed phase materials. In addition, the swept-ECQCL systems have high enough spectral resolution and sensitivity to measure narrow lines of small molecules and determine isotope ratios. The remote detection system for gas plumes is based on the swept-ECQCL technology, and consists of a swept-ECQCL source, infrared detector, control electronics, and beam transmitting and alignment optics. The remote detection system directs the infrared output of the swept-ECQCL to a target retro reflector typically located at ~10-10,000 m distance. The swept-ECQCL wavelength is varied continuously over a large wavelength range (>1000 nm) at rates up to 1000 Hz. The swept ECQCL light reflected from the remote target is collected and focused onto an infrared photodetector. By measuring the detector signal continuously as the swept-ECQCL wavelength is varied, a time-series of absorption spectra are measured for the gases along the beam line of-sight. Based on analysis and fitting of the measured absorption spectra, the time-dependent chemical concentrations of species are determined. Multiple species and mixtures can be detected simultaneously, for all species with absorption features above the sensor noise floor. The sensor output is thus a continuous, high-speed record of identified chemicals along with their concentrations and isotope ratios of interest. The high-speed operation enables low-noise operation in conditions of atmospheric turbulence and allows tracking of fluctuating concentrations in transient chemical plumes as needed for reliable remote detection applications. All components operate with minimal cooling requirements and no cryogens are needed. In addition, the output infrared light is invisible with an intensity below the maximum permissible exposure (MPE) threshold of 100 mW/cm2 for these infrared wavelengths and thus eye safe. The measurement concept for plume detection using the swept-ECQCL remote detection system is as follows. The ECQCL beam is directed toward a remote retro-reflector, which reflects the beam back to the ECQCL system where it is focused onto an infrared photodetector. The line-of-sight from the ECQCL system to the retro-reflector defines the measurement path. The detected infrared signal is recorded continuously and detects the absorption of molecular species along the measurement path. Before a plume release, the system measures absorption from atmospheric constituents, which in this LWIR band consist primarily of lines from H 2 O and CO 2 , with additional weaker absorption from N 2 O, NH 3 , and O 3 possibly contributing. The system then measures any changes in absorption due to the tracer compounds when they enter the measurement path. The shape of absorption features is used to distinguish and identify the different tracer compounds, and the strength of the absorption is used to determine the path-integrated concentration – also called the column density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗