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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies

The DOE R&D program under the Spent Fuel Waste Science Technology (SFWST) campaign has made key progress in modeling and experimental approaches towards the characterization of chemical and physical phenomena that could impact the long-term safety assessment of heat-generating nuclear waste disposition in deep clay/shale/argillaceous rock. International collaboration activities such as heater tests and postmortem analysis of samples recovered from these have elucidated key information regarding changes in the engineered barrier system (EBS) material exposed to years of thermal loads. Chemical and structural analyses of sampled bentonite material from such tests has as well as experiments conducted on these are key to the characterization of thermal effects affecting bentonite clay barrier performance and the extent of sacrificial zones in the EBS during the thermal period. Thermal, hydrologic, and chemical data collected from heater tests and laboratory experiments has been used in the development, validation, and calibration of THMC simulators to model near-field coupled processes. This information leads to the development of simulation approaches (e.g., continuum vs. discrete) to tackle issues related to flow and transport at various scales of the host-rock and EBS design concept. Consideration of direct disposal of large capacity dual-purpose canisters (DPCs) as part of the back-end SNF waste disposition strategy has generated interest in improving our understanding of the effects of elevated temperatures on the EBS design. This is particularly important for backfilled repository concepts where temperature plays a key role in the EBS behavior and long-term performance. This report describes multiple R&D efforts on disposal in argillaceous geologic media through development and application of coupled THMC process models, experimental studies on clay/metal/cement barrier and host-rock (argillite) material interactions, molecular dynamic (MD) simulations of water transport during (swelling) clay dehydration, first-principles studies of metaschoepite (UO 2 corrosion product) stability, and advances in thermodynamic plus surface complexation database development. Drift-scale URL experiments provides key data for testing hydrological-chemical (HC) model involving strong couplings of fluid mixing and barrier material chemical interactions. The THM modeling focuses on heater test experiments in argillite rock and gas migration in bentonite as part of international collaboration activities at underground research laboratories (URLs). In addition, field testing at an URL involves in situ analysis of fault slip behavior and fault permeability. Pore-scale modeling of gas bubble migration is also being investigated within the gas migration modeling effort. Interaction experiments on bentonite samples from heater test under ambient and elevated temperatures permit the evaluation of ion exchange, phase stability, and mineral transformation changes that could impact clay swelling. Advances in the development, testing, and implementation of a spent nuclear fuel (SNF) degradation model coupled with canister corrosion focus on the effects of hydrogen gas generation and its integration with Geologic Disposal Safety Assessment (GDSA). GDSA integration activities includes evaluation of groundwater chemistries in shale formations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen–deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein–solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation ( E a ) for the Stokes shifts decay rates and the millisecond C–H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.

Science & Technology - Other Topics↗
DOE OSTI2021

Ice Nucleating Particle Connections to Regional Argentinian Land Surface Emissions and Weather During the Cloud, Aerosol, and Complex Terrain Interactions Experiment

Abstract Here, we present a multi‐season study of ice‐nucleating particles (INPs) active via the immersion freezing mechanism, which took place in north‐central Argentina, a worldwide hotspot for mesoscale convective storms. INPs were measured untreated, after heating to 95°C, and after hydrogen peroxide digestion. No seasonal cycle of INP concentrations was observed. Heat labile INPs, which we define as “biological” herein, dominated the population active at −5 to −20°C, while non‐heat‐labile organic INPs (decomposed by peroxide) dominated at lower temperatures, from −20 to −28°C. Inorganic INPs (remaining after peroxide digestion), were minor contributors to the overall INP activity. Biological INP concentration active around −12°C peaked during rain events and under high relative humidity, reflecting emission mechanisms independent of the background aerosol concentration. The ratio of non‐heat‐labile organic and inorganic INPs was generally constant, suggesting they originated from the same source, presumably from regional arable topsoil based on air mass histories. Single particle mass spectrometry showed that soil particles aerosolized from a regionally common agricultural topsoil contained known mineral INP sources (K‐feldspar and illite) as well as a significant organic component. The INP activity observed in this study correlates well with agricultural soil INP activities from this and other regions of the world, suggesting that the observed INP spectra might be typical of many arable landscapes. These results demonstrate the strong influence of regional continental landscapes, emitting INPs of types that are not yet well represented in global models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Chasing Fast Dynamos in the Plasma Lab

Self-generating magnetic field research is performed through the operation of the newly built Madison Plasma Dynamo Experiment (MPDX). MPDX is designed to explore a hitherto unexplored part of parameter space where dynamos operate in nature. Dynamos are systems which continuously transform kinetic energy from plasma flow into magnetic energy. Before this project, MPDX had demonstrated the ability to create steady-state, unmagnetized high conductivity, low viscosity plasmas in the lab and shown that sheared flows can be driven from the plasma boundary using an electrostatic stirring technique; the resulting Reynolds numbers and Alfvén Mach numbers easily match those required for our dynamo scenarios. The research activities included: (1) systematic undertaking of a set of plasma hydrodynamics experiments, exploring several different flow geometries, measuring plasma viscosity, how toroidal and poloidal flows self-consistently interact, observing the transition to turbulence and experimentally understanding the boundary conditions (on flow and magnetic field) that make this system unique, (2) searching for slow, laminar dynamos, and (3) searching for fast, turbulent dynamos. Discovering the conditions under which dynamos self-generate magnetic fields and then understanding how this field changes plasma dynamics is one of the most compelling questions in all of plasma astrophysics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Muon Time-of-Flight studies for cosmic background rejection in the Short Baseline Near Detector

The Short-Baseline Neutrino (SBN) program at Fermilab is a cutting-edge project in experimental neutrino physics. One of its main goals is to systematically investigate the possible existence of eV-scale sterile neutrinos. This phenomenon has been hypothesized to explain some anomalies found in short-range experiments and, if confirmed, would imply a substantial extension of the Standard Model. SBN also offers an important opportunity to deepen the understanding of neutrino-nucleus interactions in the GeV energy range, through the use of Liquid Argon Time Projection Chambers (LArTPC) detectors, a fundamental technology also for the future DUNE experiment. The SBN experimental infrastructure consists of three detectors aligned along the Booster Neutrino Beamline at Fermilab. Among them, the detector located closest to the neutrino source, SBND (Short-Baseline Near Detector), positioned approximately 110 meters from the target, plays a key role in directly characterizing the initial neutrino flux. This allows for a direct comparison with the measurements from the far detector, ICARUS, located about 600 meters from the source, in order to search for potential signs of anomalous neutrino oscillations. My master's thesis focuses on the commissioning and characterization activities of the SBND detector, with particular reference to the Cosmic Ray Tagger (CRT). The CRT is a subsystem for identifying and rejecting events produced by cosmic rays, which constitute the main source of background for surface experiments like SBND. The activity began with the commissioning of the final components of the detector, as well as their validation to verify their correct functioning and signal acquisition. A central part of my work involved studying the veto efficiency of the CRT system, analyzing the rate of cosmic ray-induced events to quantify any loss of neutrino-induced events caused by cosmic background. This allowed for a more precise evaluation of the systematic impact of the CRT on the useful physics sample. A further phase of my analysis involved an in-depth study of the temporal correlation between the CRT signals and those acquired by the LArTPC's internal photodetector system, consisting of photomultiplier tubes and X-ARAPUCA devices. The objective is to explore the possibility of using combined temporal information as an additional criterion for discriminating between cosmic signals and signals genuinely due to neutrino interaction. Preliminary results indicate the presence of characteristic temporal signatures that could be exploited to improve event selection and increase the purity of the neutrino-induced sample. These methodologies will certainly contribute to the optimization of SBND analysis strategies and, more generally, to a better understanding of background mechanisms in next-generation LArTPC experiments.

Corallo, Annalea [Ferrara U.]↗
DOE OSTI2021

Transformation of atomically dispersed platinum in SAPO-37 into platinum clusters: catalyst for ethylene hydrogenation

Atomically dispersed supported platinum catalysts were synthesized by the reaction of Pt(acac) 2 (acac = acetylacetonato) with the silicoaluminophosphate molecular sieve SAPO-37, with infrared spectra showing that the reaction involved SAPO OH groups. Extended X-ray absorption fine structure (EXAFS) spectra show that, after heating in air to 623 K, each platinum atom on average was bonded to approximately two oxygen atoms of the SAPO support, with no evidence of platinum clusters. X-ray absorption near edge spectra (XANES) indicate a platinum formal oxidation state of approximately +2. Here, these supported mononuclear species lacked catalytic activity for ethylene hydrogenation at 1 bar and room temperature, but activity arose during catalysis in a once-through flow reactor/X-ray absorption spectroscopy cell, as the XANES white line intensity decreased, indicating reduction of the platinum, and the EXAFS-determined Pt–Pt coordination number (CN) increased from essentially zero to 2.7 ± 0.5 after 2 h, indicating the formation of platinum clusters of only a few atoms each. The data indicate the almost instantaneous formation of the clusters and identify them as the catalytically active species. Subsequent exposure of the catalyst to ethylene as in situ EXAFS and XANES data were recorded led to a decrease in the Pt–Pt coordination number to 1.6 ± 0.3 and an increase in the white line intensity, indicating partial oxidative fragmentation of the clusters by ethylene. Platinum clusters in SAPO-37 formed in separate experiments by exposure to H 2 prior to catalysis were also catalytically active for ethylene hydrogenation. Here, the data thus show how to dial in the catalytic activity by forming platinum clusters by exposure of mononuclear platinum to H 2 and how to dial back the activity by oxidative fragmentation of the clusters by reaction with ethylene, all under mild conditions; the ethylene : H 2 ratio of the reactant gas determines the average platinum nuclearity and thus the catalytic activity.

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

Stellar s-process neutron capture cross sections on 78,80,84,86 Kr determined via activation, atom trap trace analysis and decay counting

We present a detailed account of neutron capture experiments of astrophysical relevance on 78,80,84,86 Kr (n, γ) reactions at the border between weak and main s process. The experiments were performed with quasi-Maxwellian neutrons from the Liquid-Lithium Target (LiLiT) and the mA-proton beam at 1.93 MeV (2-3 kW) of the Soreq Applied Research Accelerator Facility (SARAF). The setup yields high-intensity approximate to 40 keV quasi-Maxwellian neutrons (3-5 x10 10 n/s) closely reproducing the conditions of s-process stellar nucleosynthesis. A sample of 100 mg of atmospheric, pre-nuclear-age Kr gas contained in a Ti spherical shell was activated in the LiLiT neutron field. The abundances of long-lived Kr isotopes ( 81,85g Kr) were measured by atom counting via atom trap trace analysis (ATTA) at Argonne National Laboratory and low-level counting (LLC) at University of Bern. This work is the first measurement of a nuclear cross section using atom counting via ATTA. The activities of short-lived Kr isotopes ( 79,85m,87 Kr) were measured by gamma-decay counting with a high-purity germanium detector. Maxwellian-averaged cross sections for s-process thermal energies are extracted. By comparison to reference values, our nucleosynthesis network calculations show that the experimental cross sections have a strong impact on calculated abundances of krypton and neighboring nuclides, in some cases improving agreement between theory and observations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Reaction Pathways over ZnZrO 2 -Based Catalysts and Catalytic Sorbents

Reactive capture and conversion (RCC) is a process intensification approach that integrates CO 2 capture and hydrogenation within a single unit, removing the CO 2 purification and storage steps of traditional process flow schemes. This alters the catalytic step from a traditional steady-state (SS) flow process to a transient capture and conversion cycle, which could lead to product distributions distinct from those observed in conventional SS experiments. Such differences are investigated in the combined capture and hydrogenation of carbon dioxide to methanol over a ZnZrO 2 catalyst and a ZnZrO 2 + NaNO 3 /Mg 3 AlO x catalytic sorbent (CS) using fixed-bed kinetic measurements, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and steady-state isotopic transient kinetic analysis-DRIFTS (SSITKA-DRIFTS). Under SS conditions, ZnZrO 2 produced methanol through sequential hydrogenation of HCOO* and CH 3 O* intermediates. On the contrary, CO was attributed primarily to CO 2 dissociation at oxygen vacancies, as supported by isotopic shifts and measured reaction orders. For the CS, isotopic switching experiments suggested that monodentate carbonate species (CO 3 2− , abbreviated as m-CO 3 2− ) act as active intermediates that can be hydrogenated to HCOO* and subsequently to CH 3 O. Under RCC conditions, in situ DRIFTS and isotopic experiments reveal that m-CO 3 2− species formed during the CO 2 capture step follow two competing routes upon H 2 exposure: (i) direct hydrogenation to methane on the sorbent domain or (ii) migration of m-CO 3 2− to the ZnZrO 2 domain, where they are hydrogenated to methanol through the HCOO pathway. Overall, RCC enables carbonate hydrogenation routes not observed under SS cofeed conditions. Thus, the reaction pathways and rates during RCC can be different from operation under conventional SS conditions, and the product distribution is determined here by competition between carbonate hydrogenation on sorbent sites and migration to ZnZrO 2 for methanol synthesis.

CCUS↗
DOE OSTI2020

Mitigation of backgrounds from cosmogenic 137 Xe in xenon gas experiments using 3 He neutron capture

136 Xe is used as the target medium for many experiments searching for 0νββ. Despite underground operation, cosmic muons that reach the laboratory can produce spallation neutrons causing activation of detector materials. A potential background that is difficult to veto using muon tagging comes in the form of 137 Xe created by the capture of neutrons on 136 Xe. This isotope decays via beta decay with a half-life of 3.8 minutes and a Q β of ~4.16 MeV. This work proposes and explores the concept of adding a small percentage of 3 He to xenon as a means to capture thermal neutrons and reduce the number of activations in the detector volume. When using this technique we find the contamination from 137 Xe activation can be reduced to negligible levels in tonne and multi-tonne scale high pressure gas xenon neutrinoless double beta decay experiments running at any depth in an underground laboratory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Mitigation of Backgrounds from Cosmogenic $^{137}$Xe in Xenon Gas Experiments using $^{3}$He Neutron Capture

\Xe{136} is used as the target medium for many experiments searching for \bbnonu. Despite underground operation, cosmic muons that reach the laboratory can produce spallation neutrons causing activation of detector materials. A potential background that is difficult to veto using muon tagging comes in the form of \Xe{137} created by the capture of neutrons on \Xe{136}. This isotope decays via beta decay with a half-life of 3.8 minutes and a \Qb\ of $\sim$4.16 MeV. This work proposes and explores the concept of adding a small percentage of \He{3} to xenon as a means to capture thermal neutrons and reduce the number of activations in the detector volume. When using this technique we find the contamination from \Xe{137} activation can be reduced to negligible levels in tonne and multi-tonne scale high pressure gas xenon neutrinoless double beta decay experiments running at any depth in an underground laboratory.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Evaluation of the NSUF Reactor Activation and Damage (RAD) Calculator damage component

The Nuclear Science User Facilities (NSUF) provide researchers access to nuclear research facilities and expertise all over the United States and at the Belgian Center for Nuclear Research (SCK/CEN). One special capability of the NSUF is providing access to nuclear research and test reactors often used for conducting material testing experiments. These services are provided at no cost to the researcher through a competitive, peer-reviewed process. With so many proposals being submitted simultaneously, an NSUF information management resource called the Combined Materials Experiment Toolkit (CoMET) was implemented to speed up the review process and give users access to the information and tools necessary for designing meaningful experiments and writing the best proposals possible. One of CoMET’s tools is the Reactor Activation and Damage (RAD) Calculator. For those with little or no background in it, neutron irradiation in research and test reactors can be a challenging subject to include in a proposal. That is why the RAD Calculator was created to assist users with providing estimates of irradiation and post-irradiation conditions, enabling them to select the best neutron irradiation and post-irradiation examination facilities for reaching their experiment goals. The RAD Calculator is a general scoping tool that estimates radiation damage in terms of DPA, in addition to the resulting radioactivity of the material post-irradiation. This report evaluates the neutron damage component of the RAD Calculator. The evaluation of the activation component of the calculator is covered in report INL/EXT-20-58080.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Quantifying the contribution of Fc-mediated effector functions to the antiviral activity of anti–HIV-1 IgG1 antibodies in vivo

In combating viral infections, the Fab portion of an antibody could mediate virus neutralization, whereas Fc engagement of Fc-γ receptors (FcγRs) could mediate an array of effector functions. Evidence abounds that effector functions are important in controlling infections by influenza, Ebola, or HIV-1 in animal models. However, the relative contribution of virus neutralization versus effector functions to the overall antiviral activity of an antibody remains unknown. To address this fundamental question in immunology, here we utilized our knowledge of HIV-1 dynamics to compare the kinetics of the viral load decline (ΔVL) in infected animals given a wild-type (WT) anti–HIV-1 immunoglobulin G1 (IgG1) versus those given a Fc-Null variant of the same antibody. In three independent experiments in HIV-1–infected humanized mice and one pivotal experiment in simian–human immunodeficiency virus (SHIV)-infected rhesus macaques, an earlier and sharper decline in viral load was consistently detected for the WT antibody. Quantifications of the observed differences indicate that Fc-mediated effector functions accounted for 25–45% of the total antiviral activity in these separate experiments. In this study, Fc-mediated effector functions have been quantified in vivo relative to the contribution of virus neutralization mediated by the Fab.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Protein structural changes on a CubeSat under rocket acceleration profile

Catalyzing life-sustaining reactions, proteins are composed by 20 different amino acids that fold into a compact yet flexible three-dimensional architecture, which dictates what their function(s) might be. Determining the spatial arrangement of the atoms, the protein’s 3D structure, enables key advances in fundamental and applied research. Protein crystallization is a powerful technique to achieve this. Unlike Earth’s crystallization experiments, biomolecular crystallization in space in the absence of gravitational force is actively sought to improve crystal growth techniques. However, the effects of changing gravitational vectors on a protein solution reaching supersaturation remain largely unknown. Here, we have developed a low-cost crystallization cell within a CubeSat payload module to exploit the unique experimental conditions set aboard a sounding rocket. We designed a biaxial gimbal to house the crystallization experiments and take measurements on the protein solution in-flight with a spectrophotometry system. After flight, we used X-ray diffraction analysis to determine that flown protein has a structural rearrangement marked by loss of the protein’s water and sodium in a manner that differs from crystals grown on the ground. We finally show that our gimbal payload module design is a portable experimental setup to take laboratory research investigations into exploratory space flights.

42 ENGINEERING↗
DOE OSTI2023

Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the “Active” state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the “Active” state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Iron corrosion in the “inert” supercritical CO 2 , ab initio dynamics insights: How impurities matter

Metal corrosion from exposure to supercritical fluids is a long-standing challenge lacking atomistic understanding for effective corrosion prevention in diverse important applications. Here, in this work, reactions relevant to corrosion in supercritical CO 2 (sCO 2 ), with H 2 O and NO 2 as impurities, are revealed using ab initio molecular dynamics and enhanced sampling methods. While little reactivity is observed in bulk sCO 2 , the iron surface is found to play a crucial almost-catalytic role in its own corrosion, activating the inert CO2 and hence facilitating $\ast$HCO 3 – and $\ast$CO 3 2– formation at the interface. Moreover, the hydrogen bond network of $\ast$H 2 O assists the H shuttling to the activated CO 2 and impurities, forming reactive species observed in experiments. Such atomistic insight elucidates the reaction mechanisms of metal corrosion in aqueous and supercritical fluids and can point to possible remedies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Scale-Up Studies for the Dehydration of C 4+ Alcohols into Drop-In Diesel Fuel

Herein, we demonstrate the production of liter quantities of drop-in diesel-range ethers from biomass-derived alcohols. We report scale-up resultsfor the dehydration of a mixture of C 4+ alcohols using powder and pellet zeolite Ycatalyst in continuous flow and batch reactors. The activity of zeolite Y decreaseswith the introduction of an alumina binder. Large alcohols, as well as branchedand secondary alcohols, increase the coke content over the pellet Y catalyst. Thepellet formulation had lower carbon balances and selectivity to C 10+ ethers,suggesting that the pellet formulation increases alcohol absorption and cokeproduction. Crushing the pellet Y catalyst to smaller particle sizes does notrecover the activity of zeolite Y in its powder form. Cold flow experiments showthat particle agglomeration contributes to pressure buildup in the continuous flowreactor. C 10+ ether blends can be produced in batch reactors at high alcohol conversion regimes. One liter of a diesel #2 blend wasproduced by scaling up this reaction. The final blend consists of a substantial portion of C 10+ ethers (63.7 wt %), followed by heavyunknown products (27.4 wt %). Furthermore, the final alcohol and butyl ether concentration values were 7.3 and 1.5 wt %, respectively. Theblendstock reported in this paper can satisfy diesel #2 ASTM standards for density, cloud point, flashpoint, and cetane number.

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

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems1. In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP–AMP synthase–stimulator of interferon genes (cGAS–STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response2, 3–4. Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.

Doherty, Erin E↗
DOE OSTI2020

Comparing GGA, GGA+ U , and meta-GGA functionals for redox-dependent binding at open metal sites in metal–organic frameworks

Metal–organic frameworks (MOFs) with open metal sites have been widely investigated for the selective adsorption of small molecules via redox mechanisms where charge transfer can take place between the binding site and the adsorbate of interest. Quantum-chemical screening methods based on density functional theory have emerged as a promising route to accelerate the discovery of MOFs with enhanced binding affinities toward various adsorbates. However, the success of this approach is linked to the accuracy of the underlying density functional approximations (DFAs). In this work, we compare commonly used generalized gradient approximation (GGA), GGA+U, and meta-GGA exchange-correlation functionals in modeling redox-dependent binding at open metal sites in MOFs using O 2 and N 2 as representative small molecules. We find that the self-interaction error inherent to the widely used Perdew, Burke, and Ernzerhof (PBE) GGA predicts metal sites that are artificially redox-active, as evidenced by their strong binding affinities, short metal–adsorbate bond distances, and large degree of charge transfer. The incorporation of metal-specific, empirical Hubbard U corrections based on the transition metal oxide literature systematically reduces the redox activity of the open metal sites, often improving agreement with experiment. Additionally, the binding behavior shifts from strong chemisorption to weaker physisorption as a function of U. The M06-L meta-GGA typically predicts binding energies between those of PBE-D3(BJ) and PBE-D3(BJ)+U when using empirically derived U values from the transition metal oxide literature. Despite the strong sensitivity of the binding affinities toward a given DFA, the GGA, GGA+U, and meta-GGA approaches often yield the same qualitative trends and structure–property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗