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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Bringing weak transitions to light

Abstract Weak transitions between quantum states are of fundamental importance for a broad range of phenomena from analytical biochemistry to precision physics, but generally challenge experimental detection. Due to their small cross sections scaling with the absolute square of their transition matrix elements, spectroscopic measurements often fail in particular in the presence of competing background processes. Here we introduce a general concept to break this scaling law and enhance the transition probability by exploiting a stronger laser-coupled pathway to the same excited state. We demonstrate the concept experimentally by attosecond transient absorption spectroscopy in helium atoms. The quasi-forbidden transitions from the ground state 1s 2 to the weakly coupled doubly excited 2p3dandsp 2,4− states are boosted by an order of magnitude. Enhancing single-photon-suppressed transitions can find widespread applicability, from spectral diagnostics of complex molecules in life and chemical sciences to precision spectroscopy of weak transitions in metastable atomic nuclei in the search for new physics.

Science & Technology - Other Topics↗
DOE OSTI2023

Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Abstract The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N -terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N - and O - glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities

Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Analytical tools capable of quickly detecting both glycan and lignin deconstruction are needed to support the development and characterization of efficient enzymes/enzyme cocktails. Previously we have described nanostructure-initiator mass spectrometry-based assays for the analysis of glycosyl hydrolase and most recently an assay for lignin modifying enzymes. Here we integrate these two assays into a single multiplexed assay against both classes of enzymes and use it to characterize crude commercial enzyme mixtures. Application of our multiplexed platform based on nanostructure-initiator mass spectrometry enabled us to characterize crude mixtures of laccase enzymes from fungi Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity on both carbohydrate and aromatic substrates. Using time-series analysis we determined that crude laccase from Ab has the higher GH activity and that laccase from Mt has the higher activity against our lignin model compound. Inhibitor studies showed a significant reduction in Mt GH activity under low oxygen conditions and increased activities in the presence of vanillin (common GH inhibitor). Ultimately, this assay can help to discover mixtures of enzymes that could be incorporated into biomass pretreatments to deconstruct diverse components of lignocellulosic biomass.

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

Kerfeld - Dwyer Data 20240614.sf3

Mass spectrometry data for the DERA-RPI complex submission related to Supplemental Figure S3 in Dwyer et. al., Communications Biology.

Analytical biochemistry↗
DOE OSTI2023

Sequence Design of Random Heteropolymers as Protein Mimics

Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo–Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.

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

Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes

A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK) 5 , (EKKE) 5 , (ERER) 5 , (ERRE) 5 , and (EKER) 5 . The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE) 5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE) 5 , as well as the sequences with the equivalent amino acid content, (ERER) 5 , exhibited no aggregate formation under equivalent pH and concentration conditions.

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

Functionalized Polymersomes from a Polyisoprene-Activated Polyacrylamide Precursor

Self-assembled polymer nanoparticles have tremendous potential in biomedical and environmental applications. For all applications, tailored polymer chemistries are critical. In this study, we demonstrate a precursor approach in which an activated, organic solvent-soluble block polymer precursor is modified through mild postpolymerization modifications to access new polymer structures. We synthesized and characterized poly(isoprene)-block-poly(di-Boc acrylamide) diblock polymers. This activated-acrylamide-based polymer was then reacted with amines or reductants in the absence of catalysts to yield the hydrophilic blocks polyacrylamide, poly(hydroxypropylene), and poly(N-ethyl acrylamide). The resulting amphiphilic block polymers self-assembled in water to form polymersomes, as confirmed by cryo-electron microscopy and confocal microscopy. The approach also enables simple functionalization with specialized ligands, which we demonstrated by tagging polymers with an amino-fluorophore and imaging by confocal microscopy. Here, we expect that the methodologies established in this study will open doors to new and useful solution nanostructures with surface chemistries that can be optimized for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural and biochemical insights into NEIL2’s preference for abasic sites

Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.

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

Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer

Abstract 5-Fluorouracil (5-FU) is the first-line chemotherapeutic agent in colorectal cancer, and resistance to 5-FU easily emerges. One of the mechanisms of drug action and resistance of 5-FU is through DNA incorporation. Our quantitative reverse-transcription PCR data showed that one of the translesion synthesis (TLS) DNA polymerases, DNA polymerase η (polη), was upregulated within 72 h upon 5-FU administration at 1 and 10 μM, indicating that polη is one of the first responding polymerases, and the only TLS polymerase, upon the 5-FU treatment to incorporate 5-FU into DNA. Our kinetic studies revealed that 5-fluoro-2′-deoxyuridine triphosphate (5FdUTP) was incorporated across dA 41 and 28 times more efficiently than across dG and across inosine, respectively, by polη indicating that the mutagenicity of 5-FU incorporation is higher in the presence of inosine and that DNA lesions could lead to more mutagenic incorporation of 5-FU. Our polη crystal structures complexed with DNA and 5FdUTP revealed that dA:5FdUTP base pair is like dA:dTTP in the active site of polη, while 5FdUTP adopted 4-enol tautomer in the base pairs with dG and HX increasing the insertion efficiency compared to dG:dTTP for the incorrect insertions. These studies confirm that polη engages in the DNA incorporation and bypass of 5-FU.

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

Application of Quantum Computing to Biochemical Systems: A Look to the Future

Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only treated with different levels of theory, but computed with hybrid classical and quantum algorithms. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with traditional algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Comparative Energetics of Various Membrane Distillation Configurations and Guidelines for Design and Operation

This paper presents a comparative performance study of single-stage desalination processes with major configurations of membrane distillation (MD) modules. MD modules covered in this study are (a) direct contact MD (DCMD), (b) vacuum MD (VMD), (c) sweeping gas MD (SGMD), and (d) air gap MD (AGMD). MD-based desalination processes are simulated with rigorous theoretical MD models supported by molecular thermodynamic property models for the accurate calculation of performance metrics. The performance metrics considered in MD systems are permeate flux and energy efficiency, i.e., gained output ratio (GOR). A general criterion is established to determine the critical length of these four MDs (at fixed width) for the feasible operation of desalination in a wide range of feed salinities. The length of DCMD and VMD is restricted by the feed salinity and permeate flux, respectively, while relatively large AGMD and SGMD are allowed. The sensitivity of GOR flux with respect to permeate conditions is investigated for different MD configurations. AGMD outperforms other configurations in terms of energy efficiency, while VMD reveals the highest permeate production. With larger MD modules, utilization of thermal energy supplied by the hot feed for evaporation is in the order of VMD > AGMD > SGMD > DCMD. Simulation results highlight that energy efficiency of the overall desalination process relies on the efficient recovery of spent for evaporation, suggesting potential improvement in energy efficiency for VMD-based desalination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Life Cycle Assessment of Innovative Carbon Dioxide Selective Membranes from Low Carbon Emission Sources: A Comparative Study

Carbon capture has been an important topic of the twenty-first century because of the elevating carbon dioxide (CO2) levels in the atmosphere. CO2 in the atmosphere is above 420 parts per million (ppm) as of 2022, 70 ppm higher than 50 years ago. Carbon capture research and development has mostly been centered around higher concentration flue gas streams. For example, flue gas streams from steel and cement industries have been largely ignored due to lower associated CO2 concentrations and higher capture and processing costs. Capture technologies such as solvent-based, adsorption-based, cryogenic distillation, and pressure-swing adsorption are under research, but many suffer from higher costs and life cycle impacts. Membrane-based capture processes are considered cost-effective and environmentally friendly alternatives. Over the past three decades, our research group at Idaho National Laboratory has led the development of several polyphosphazene polymer chemistries and has demonstrated their selectivity for CO2 over nitrogen (N2). Poly[bis((2-methoxyethoxy)ethoxy)phosphazene] (MEEP) has shown the highest selectivity. A comprehensive life cycle assessment (LCA) was performed to determine the life cycle feasibility of the MEEP polymer material compared to other CO2-selective membranes and separation processes. The MEEP-based membrane processes emit at least 42% less equivalent CO2 than Pebax-based membrane processes. Similarly, MEEP-based membrane processes produce 34–72% less CO2 than conventional separation processes. In all studied categories, MEEP-based membranes report lower emissions than Pebax-based membranes and conventional separation processes.

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

Development of Structure–Property Relationships for Ammonium Transport through Charged Organogels

Ammonia is a promising carbon-free fuel, but current methods to produce ammonia are energy intensive. New methods are thereby needed, with one promising method being electrochemical nitrogen reduction cells. Efficient cell operation requires robust catalysts but also efficient membrane separators that permit the selective transport of ions while minimizing the transport of the products across the cell. Commercial membranes have an unknown morphology which makes designing improved cells challenging. To address this problem, we synthesized a series of membranes with controlled crosslinking density and chemical composition to understand their impact on ammonium transport. Higher crosslinking density led to lower ammonium permeability. At the highest crosslinking density, similar ammonium permeability was observed independent of the water volume fraction and hydrophobicity of the monomers. These results suggest new directions to develop membranes with reduced ammonium crossover to improve the efficiency of these electrochemical cells.

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

Recognition of V3+/V4+/V5+ Multielectron Reactions in Na3V(PO4)2: A Potential High Energy Density Cathode for Sodium-Ion Batteries

Na3V(PO4)2 was reported recently as a novel cathode material with high theoretical energy density for Sodium-ion batteries (SIBs). However, whether V3+/V4+/V5+ multielectron reactions can be realized during the charging process is still an open question. In this work, Na3V(PO4)2 is synthesized by using a solid-state method. Its atomic composition and crystal structure are verified by X-ray diffraction (XRD) and neutron diffraction (ND) joint refinement. The electrochemical performance of Na3V(PO4)2 is evaluated in two different voltage windows, namely 2.5–3.8 and 2.5–4.3 V. 51V solid-state NMR (ssNMR) results disclose the presence of V5+ in Na2-xV(PO4)2 when charging Na3V(PO4)2 to 4.3 V, confirming Na3V(PO4)2 is a potential high energy density cathode through realization of V3+/V4+/V5+ multielectron reactions.

25 ENERGY STORAGE↗