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NASA NTRS1994

Diffusive modification of primary zoning in olivine cores in Angrite LEW 87051

Angrite LEW 87051 consists of large olivine crystals set in a fine-grained groundmass that clearly represents a crystallized melt. A few olivines contain Ca-poor, Cr-rich cores that crystallized from a very different melt than the outer part of the crystals constituting the majority of olivine in LEW 87051. We evaluate a model in which the cores formed through fractional crystallization of one melt, then were incorporated into a different melt as xenocrysts, whereupon the original zoning patterns were modified by diffusion. Using a similar approach, we calculate zoning patterns for the cores that would result from perfect fractional crystallization, compare them with the observed zoning, and determine whether the differences could result from diffusive modification consistent with known diffusion rates for Ca, Mn, and Cr. Using distribution coefficients from the 1400 C, IW + 1 experiments, we computed CaO, Cr2O3, and MnO abundances in the hypothetical parent melt by inverting the olivine at the centers of the cores. We further assumed that the primary zoning profile for CaO is essentially unmodified, because the diffusion rate of Ca in olivine is slow. We carried out the fractional crystallization calculation until the calculated Ca content was that observed at break in zoning profiles at the outer edge of the core. We then normalized the distance of this calculated profile to the length of the observed profile in the olivine core and calculated profiles for MnO and Cr2O3. The CaO zoning profile agrees well with the observed profile. The observed MnO profile is slightly higher than the calculated profile near the edge. Diffusion calculations indicate that reversal of the general trend of primary zoning through diffusion would require that diffusion of Cr is 5-10x faster than that of Mn.

Mikouchi, T.↗

DOE OSTI2021

Atypical phase-change alloy Ga 2 Te 3 : atomic structure, incipient nanotectonic nuclei, and multilevel writing

Emerging brain-inspired computing, including artificial optical synapses, photonic tensor cores, neuromorphic networks, etc., needs phase-change materials (PCMs) of the next generation with lower energy consumption and a wider temperature range for reliable long-term operation. Gallium tellurides with higher melting and crystallization temperatures appear to be promising candidates and enable achieving the necessary requirements. Here, using high energy X-ray diffraction and Raman spectroscopy supported by first-principles simulations, we show that vitreous g-Ga 2 Te 3 films essentially have a tetrahedral local structure and sp 3 hybridization, similar to those in the stable fcc Ga 2 Te 3 polymorph and in contrast to a vast majority of typical PCMs. Nevertheless, optical pump–probe laser experiments revealed high-contrast, fast and reversible multilevel SET-RESET transitions raising a question related to the phase change mechanism. A recently observed nanotectonic compression in bulk glassy Ga–Te alloys seems to be responsible for the PCM performance. Incipient nanotectonic nuclei, reminiscent of monoclinic high-pressure HP-Te II and rhombohedral HP-Ga 2 Te 3 , are present as minorities (2–4%) in g-Ga 2 Te 3 but are suggested to grow dramatically with increasing temperature while interacting with appropriate laser pulses. This leads to co-crystallization of HP-polymorphs amplified by a high internal local pressure reaching 4–8 GPa. The metallic HP-forms provide an increasing optical and electrical contrast, favorable for reliable PCM operations, and higher energy efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Spin-singlet topological superconductivity in the attractive Rashba-Hubbard model

Fully gapped, spin-singlet superconductors with antisymmetric spin-orbit coupling in a Zeeman magnetic field provide a promising route to realize superconducting states with non-Abelian topological order and therefore fault-tolerant quantum computation. Here we use a quantum Monte Carlo dynamical cluster approximation to study the superconducting properties of a doped two-dimensional attractive Hubbard model with Rashba spin-orbit coupling in a Zeeman magnetic field. We generally find that the Rashba coupling has a beneficial effect towards s-wave superconductivity. In the presence of a finite Zeeman field, when superconductivity is suppressed by Pauli pair breaking, the Rashba coupling counteracts the spin imbalance created by the Zeeman field by mixing the spins, and thus restores superconductivity at finite temperatures. Further, we show that this favorable effect of the spin-orbit coupling is traced to a spin-flip driven enhancement of the amplitude for the propagation of a pair of electrons in time-reversed states. Moreover, by inspecting the Fermi surface of the interacting model, we show that for sufficiently large Rashba coupling and Zeeman field, the superconducting state is expected to be topologically nontrivial.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2004

Bubble Combustion

A method of energy production that is capable of low pollutant emissions is fundamental to one of the four pillars of NASA s Aeronautics Blueprint: Revolutionary Vehicles. Bubble combustion, a new engine technology currently being developed at Glenn Research Center promises to provide low emissions combustion in support of NASA s vision under the Emissions Element because it generates power, while minimizing the production of carbon dioxide (CO2) and nitrous oxides (NOx), both known to be Greenhouse gases. and allows the use of alternative fuels such as corn oil, low-grade fuels, and even used motor oil. Bubble combustion is analogous to the inverse of spray combustion: the difference between bubble and spray combustion is that spray combustion is spraying a liquid in to a gas to form droplets, whereas bubble combustion involves injecting a gas into a liquid to form gaseous bubbles. In bubble combustion, the process for the ignition of the bubbles takes place on a time scale of less than a nanosecond and begins with acoustic waves perturbing each bubble. This perturbation causes the local pressure to drop below the vapor pressure of the liquid thus producing cavitation in which the bubble diameter grows, and upon reversal of the oscillating pressure field, the bubble then collapses rapidly with the aid of the high surface tension forces acting on the wall of the bubble. The rapid and violent collapse causes the temperatures inside the bubbles to soar as a result of adiabatic heating. As the temperatures rise, the gaseous contents of the bubble ignite with the bubble itself serving as its own combustion chamber. After ignition, this is the time in the bubble s life cycle where power is generated, and CO2, and NOx among other species, are produced. However, the pollutants CO2 and NOx are absorbed into the surrounding liquid. The importance of bubble combustion is that it generates power using a simple and compact device. We conducted a parametric study using CAVCHEM, a computational model developed at Glenn, that simulates the cavitational collapse of a single bubble in a liquid (water) and the subsequent combustion of the gaseous contents inside the bubble. The model solves the time-dependent, compressible Navier-Stokes equations in one-dimension with finite-rate chemical kinetics using the CHEMKIN package. Specifically, parameters such as frequency, pressure, bubble radius, and the equivalence ratio were varied while examining their effect on the maximum temperature, radius, and chemical species. These studies indicate that the radius of the bubble is perhaps the most critical parameter governing bubble combustion dynamics and its efficiency. Based on the results of the parametric studies, we plan on conducting experiments to study the effect of ultrasonic perturbations on the bubble generation process with respect to the bubble radius and size distribution.

Corrigan, Jackie↗

DOE OSTI2021

Observation of current-induced switching in non-collinear antiferromagnetic IrMn 3 by differential voltage measurements

There is accelerating interest in developing memory devices using antiferromagnetic (AFM) materials, motivated by the possibility for electrically controlling AFM order via spin-orbit torques, and its read-out via magnetoresistive effects. Recent studies have shown, however, that high current densities create non-magnetic contributions to resistive switching signals in AFM/heavy metal (AFM/HM) bilayers, complicating their interpretation. Here we introduce an experimental protocol to unambiguously distinguish current-induced magnetic and nonmagnetic switching signals in AFM/HM structures, and demonstrate it in IrMn 3 /Pt devices. A six-terminal double-cross device is constructed, with an IrMn 3 pillar placed on one cross. The differential voltage is measured between the two crosses with and without IrMn 3 after each switching attempt. For a wide range of current densities, reversible switching is observed only when write currents pass through the cross with the IrMn 3 pillar, eliminating any possibility of non-magnetic switching artifacts. Micromagnetic simulations support our findings, indicating a complex domain-mediated switching process.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Photodynamic melting of phase-reversed charge stripes and enhanced condensation

The interplay between charge stripes and pairing has long been a subject of scrutiny in a broad class of unconventional superconductors, as in some cases it is unclear whether this interplay benefits the ensuing superfluidity. Experiments that explore the out-of-equilibrium dynamics of these systems aim to tip the balance toward one phase or the other by selectively coupling to relevant modes. Leveraging the fact that competition between stripes and pairing is not exclusive to fermionic systems, we explore the photoirradiation dynamics of interacting hardcore bosons in which density-wave phase-reversal melting leads to enhanced phase-coherent transport response, as quantified by the dynamic amplification of both the zero-momentum occupancy and the condensate fraction, as well as finite out-of-equilibrium charge stiffness and superfluid weight, for a given system size. Finally, our results, obtained using unbiased methods for an interacting system on a ladder geometry, demonstrate how one can engineer time-dependent perturbations to release suppressed orders, potentially providing insight into the underlying mechanism in related experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

pynucastro: A Python Library for Nuclear Astrophysics

We describe pynucastro 2.0, an open-source library for interactively creating and exploring astrophysical nuclear reaction networks. We demonstrate new methods for approximating rates and use detailed balance to create reverse rates, show how to build networks and determine whether they are appropriate for a particular science application, and discuss the changes made to the library over the past few years. Finally, we demonstrate the validity of the networks produced and share how we use pynucastro networks in simulation codes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

A User Guide to PARET/ANL

PARET was originally created in 1969 at what is now Idaho National Laboratory (INL), to analyze reactivity insertion events in research and test reactor cores cooled by light or heavy water, with fuel composed of either plates or pins. The use of PARET is also appropriate for fuel assemblies with curved fuel plates when their radii of curvatures are large with respect to the fuel plate thickness. The PARET/ANL version of the code has been developed at Argonne National Laboratory (ANL) under the sponsorship of the U.S. Department of Energy/NNSA since the inception of the Reactor Conversion Program. Since Reduced Enrichment for Research and Test Reactors (RERTR) began in 1978, PARET/ANL has been benchmarked to experimental data including SPERT testing, and used to determine the expected transient behavior of a large number of reactors regardless of enrichment both inside and outside the Reactor Conversion Program. This document provides the pertinent information for the use of PARET/ANL Version 7.6. PARET/ANL models the various fueled regions of a reactor core as channels. Each of these channels consists of a single flat fuel plate/pin (including cladding and, optionally, a gap) with water coolant on each side. In slab geometry the coolant channels for a given fuel plate are of identical dimensions (mirror symmetry), but they can be of different thickness in each channel. There can be many channels, but each channel is independent and coupled only through reactivity feedback effects to the whole core. The time-dependent differential equations that represent the system are replaced by an equivalent set of finite-difference equations in space and time, which are integrated numerically. PARET/ANL uses fundamentally the same numerical scheme as RELAP5 for the time-integration of the point-kinetics equations. The one-dimensional thermal-hydraulic model includes temperature-dependent thermal properties of the solid materials, such as heat capacity and thermal conductivity, as well as the transient heat production and heat transfer from the fuel meat to the coolant. Temperature- and pressure-dependent thermal properties of the coolant such as enthalpy, density, thermal conductivity, and viscosity are also used in determining parameters such as friction factors and heat transfer coefficients. The code first determines the steady-state solution for the initial state. Then the solution of the transient is obtained by integration in time and space. Multiple heat transfer, DNB and flow instability correlations are available. The code was originally developed to model reactors cooled by an open loop, which was adequate for rapid transients in pool-type cores. An external loop model appropriate for Miniature Neutron Source Reactors (MNSR’s) was also added to PARET/ANL to model natural circulation within the vessel, heat transfer from the vessel to pool and heat loss by evaporation from the pool. PARET/ANL also contains models for decay heat after shutdown, control rod reactivity versus time or position, time-dependent pump flow, and loss-of-flow event with flow reversal as well as logic for trips on period, power, and flow. Feedback reactivity effects from coolant density changes and temperature changes are represented by tables. Feedback reactivity from fuel heat-up (Doppler Effect) is represented by a four-term polynomial in powers of fuel temperature. Photo-neutrons produced in beryllium or in heavy water may be included in the point-kinetics equations by using additional delayed neutron groups.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Nonlinear saturation of reverse shear Alfvén eigenmodes induced by kinetic electrons

A strong nonlinear saturation mechanism of the reverse shear Alfvén eigenmode (RSAE) induced by thermal electrons is observed in gyrokinetic $\delta$$f$ particle-in-cell simulation. This nonlinear effect occurs at moderate mode amplitude, $\delta$$B$ ⟂ /$B$ < 10 -3 , and is associated with the electron parallel streaming along the perturbed magnetic field lines, the term v $\|$ $\frac{δΒ_{⟂}}{B}$ ∙ ∇$\delta$$f$, in the electron drift-kinetic equation. In the case of an n = 4 RSAE, where n is the toroidal mode number, this magnetic fluttering nonlinearity leads to strong mode coupling and broadening of the saturation spectrum. The nonlinear components, which are highly damped through the interaction between thermal electrons and the parallel electric field, modifies the RSAE mode structure and suppresses energetic particle drive significantly. The split-weight scheme (Chen and Parker 2007 J. Comput. Phys. 220 839–55) is used to simulate kinetic electrons.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Fundamentals of hydrogen storage in nanoporous materials

Abstract Physisorption of hydrogen in nanoporous materials offers an efficient and competitive alternative for hydrogen storage. At low temperatures (e.g. 77 K) and moderate pressures (below 100 bar) molecular H 2 adsorbs reversibly, with very fast kinetics, at high density on the inner surfaces of materials such as zeolites, activated carbons and metal–organic frameworks (MOFs). This review, by experts of Task 40 ‘Energy Storage and Conversion based on Hydrogen’ of the Hydrogen Technology Collaboration Programme of the International Energy Agency, covers the fundamentals of H 2 adsorption in nanoporous materials and assessment of their storage performance. The discussion includes recent work on H 2 adsorption at both low temperature and high pressure, new findings on the assessment of the hydrogen storage performance of materials, the correlation of volumetric and gravimetric H 2 storage capacities, usable capacity, and optimum operating temperature. The application of neutron scattering as an ideal tool for characterising H 2 adsorption is summarised and state-of-the-art computational methods, such as machine learning, are considered for the discovery of new MOFs for H 2 storage applications, as well as the modelling of flexible porous networks for optimised H 2 delivery. The discussion focuses moreover on additional important issues, such as sustainable materials synthesis and improved reproducibility of experimental H 2 adsorption isotherm data by interlaboratory exercises and reference materials.

08 HYDROGEN↗

NASA NTRSDate not supplied

Variance Decomposition of MEDLI2 Reconstructed Heating Using Neural Networks

The Mars Entry, Descent, and Landing Instrumentation (MEDLI2) sensor suite collected data during entry of the Mars 2020 Perseverance rover into Mars’ atmosphere. This suite included a network of MEDLI2 Instrumented Sensor Plugs (MISPs). Each MISP was comprised of a cylinder made of Thermal Protection System (TPS) material with 1-3 embedded thermocouples (TCs), and it was flush mounted into the heatshield or backshell. Data from these in-depth TCs were used to reconstruct the aeroheating environment of the vehicle throughout entry. Surface heating was posed as an inverse problem, with the goal of estimating the surface heating by minimizing an objective function of the difference between MISP temperature measurements during flight and the temperature predictions derived from the Fully Implicit Ablation and Thermal response (FIAT) program. Given an aerothermal environment, FIAT calculates the material response and provides in-depth temperatures throughout the TPS material. To achieve the reverse, an internal tool called FIAT_Opt runs through multiple different environments until the output temperature at the TC depth closely matches the flight data. 95% confidence intervals on the reconstructed surface heating were obtained using Monte Carlo analysis, in which uncertainties in the thermocouple depth and the TPS material properties (e.g., density, thermal conductivity, heat capacity, emissivity) based on flight-lot material testing were included. A variance decomposition method using Sobol indices was employed to assess the sensitivity of the reconstructed peak heating to the TC placement and material property uncertainties. Variance decomposition was found to require tens of thousands of FIAT_Opt runs in order for the Sobol indices to converge. With a single FIAT_Opt run taking on the order of 40 minutes, the required number of computations would take months to complete, even if using multiple CPUs. To mitigate this problem, three machine learning models (ridge regression with cross-validation, random forest regression, and a deep neural network) were trained and tested using the 2000 Monte Carlo runs that were already completed. A subset of 1600 runs were used to train the model (i.e., training set), while the remaining 400 runs were used as the test set. The predictions from the deep neural network (DNN) on the test set showed nearly perfect agreement to the actual values computed with FIAT_Opt (R2 > 0.99). Using the DNN as a surrogate model, the variance decomposition using 50,000 runs was completed within minutes. The resulting Sobol indices showed that the reconstructed peak surface heating was most sensitive to the uncertainties in the thermal conductivity (ST = 0.37) and heat capacity (ST = 0.26). This method can be leveraged to provide requirements for material property measurements needed to improve the accuracy of surface heating prediction and ultimately lead to the reduction of design margins in the future. This presentation will include background on the MEDLI2 suite; the method used for inverse heating estimation; the way that material property uncertainties were accounted for using Monte Carlo analysis; a brief background on variance decomposition; the motivation for using machine learning in this context; how a neural network was trained on the data to enable variance decomposition in a fraction of the time; and the variance decomposition results for one of the MISPs.

Hannah Alpert↗

DOE OSTI2020

Amphiphile Organization in Organic Solutions: An Alternative Explanation for Small-Angle X-ray Scattering Features in Malonamide/Alkane Mixtures

In this work, the role of different intermolecular interactions in the aggregation of amphiphiles in an organic solvent is studied for systems of relevance to liquid-liquid extraction (LLE), a chemical process used to selectively recover metals from complex mixtures. Of specific interest is the role, or lack thereof, of hydrogen bonding, which is often assumed to be a main driver of the organic phase structural organization that has been linked to separation efficacy. Toward that end, a series of malonamide extractants in n-dodecane have been studied in the absence of any extracted aqueous solutes, including water. The series of extractants includes N,N'-dimethyl-N,N'-dibutyltetradecylmalonamide (DMDBTDMA), two of its homologs, and N,N'-dimethyl-N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). This simplified model LLE system enables systematic investigation of the role of dipole-dipole and alkyl tail steric interactions in amphiphile aggregation. Small-angle X-ray scattering (SAXS) profiles computed from molecular dynamics trajectories are in good agreement with experimental SAXS data. Molecular dynamics simulations show that malonamide aggregation results from dipole-driven self-association and lacks characteristic aggregate sizes. Mid-q correlation peaks in the SAXS profiles emerge at high concentration for each malonamide. In those densely packed solutions, the correlation peaks are observed to result from alkyl tail-induced spacing between electron-rich polar head groups, with peak positions determined by the different alkyl tail lengths present in the malonamide molecule. This explanation of the SAXS correlation peaks contrasts with the prevailing literature, which attributes mesoscale features observed in small-angle scattering to the formation of microemulsions. Instead, this work finds that these features are present in the absence of water or any reverse micellar organization of the malonamides. As such, molecular-scale malonamide self-association and packing, rather than microemulsion-based colloidal-scale descriptions, is a more appropriate framework for these LLE systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

First-principles theory of the Dirac semimetal Cd 3 As 2 under Zeeman magnetic field

Time-reversal broken Weyl semimetals have attracted much attention recently, but certain aspects of their behavior, including the evolution of their Fermi surface topology and anomalous Hall conductivity with Fermi-level position, have remained underexplored. A promising route to obtain such materials may be to start with a nonmagnetic Dirac semimetal and break time-reversal symmetry via magnetic doping or magnetic proximity. Here we explore this scenario in the case of the Dirac semimetal Cd 3 As 2 , based on first-principles density-functional calculations and subsequent low-energy modeling of Cd 3 As 2 in the presence of a Zeeman field applied along the symmetry axis. We clarify how each four-fold degenerate Dirac node splits into four Weyl nodes, two with chirality ±1 and two higher-order nodes with chirality ±2. Using a minimal k · p model Hamiltonian whose parameters are fit to the first-principles calculations, we detail the evolution of the Fermi surfaces and their Chern numbers as the Fermi energy is scanned across the region of the Weyl nodes at fixed Zeeman field. We also compute the intrinsic anomalous Hall conductivity as a function of Fermi-level position, finding a characteristic inverted-dome structure. Cd 3 As 2 is especially well suited to such a study because of its high mobility, but the qualitative behavior revealed here should be applicable to other Dirac semimetals as well.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Embodied carbon in the U.S. manufacturing and trade

On average, one quarter of the global carbon footprint is embodied in traded goods. These emissions are a growing issue for global efforts to decarbonize the world economy. Embodied emissions in trade are not accounted for by existing greenhouse gas accounting systems. For example, countries only report their domestic carbon emissions (also known as production-based or territorial accounting) to the Intergovernmental Panel on Climate Change (IPCC). If the embodied carbon in trade were accounted for and reported, the promising climate trends depicted by many countries would be negated or reversed. For example, many achievements of reducing emissions by developed countries under the Kyoto Protocol would actually appear as emissions outsourced to developing countries. Like many other developed countries, the United States is a net importer of embodied greenhouse gas (GHG) emissions in trade. The goal of this study was to calculate the carbon footprint of various sectors of the U.S. economy using the latest available data and based on that, estimate the embodied carbon in certain manufacturing sector products imported and exported by the U.S. First, we conducted an input-output analysis to calculate the carbon footprint of 401 aggregate level sectors of the U.S. economy. After that, for a selected number of manufacturing subsectors /products(hereafter referred to as products),we collected their trade(import/export) data and combined that with their computed carbon footprint to estimate the embodied carbon in import and export of these products for the U.S. While we conducted the carbon footprint analysis for sectors covering the entire U.S. economy (401 sectors), we only conducted the embodied carbon in trade analysis for a few products within specific aggregate level manufacturing sectors,such as computer and electronic product manufacturing (NAICS 334), transport equipment manufacturing (NAICS 336), machinery manufacturing (NAICS 333), and chemical manufacturing (NAICS 325). It is possible to do the detailed embodied carbon analysis for all other products within the various aggregate level manufacturing sectors of the U.S. economy, but given the scope of this study and space constraint of this report, we only present the results for a few products. The results of our analysis for the selected products show the embodied carbon in trade for each product by country and also show the rankings of countries in terms of top importers and exporters of embodied carbon in trade with the U.S. Our results show that in majority of cases, the U.S. is a net importer of embodied carbon in trade. Unless consumption-based accounting is used, the U.S. and other net embodied carbon importing countries may continue to outsource their emissions to meet their climate change mitigation targets under the Paris Agreement, as observed previously with the Kyoto Protocol. Some countries reported reductions that exceeded their Kyoto targets, however, the changes in emissions embodied in imports were comparable to or larger than changes in domestic emissions. Traded emissions undermined emissions reductions in the Kyoto Protocol, and threaten to continue to do so for the Paris Agreement. New climate policies such as California’s Buy Clean act, EU’s proposed border carbon tax adjustment, as well as efforts in the private sector can help address the embodied carbon in traded products.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches

Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Adaptive multigrid domain decomposition solutions for viscous interacting flows

Several viscous incompressible flows with strong pressure interaction and/or axial flow reversal are considered with an adaptive multigrid domain decomposition procedure. Specific examples include the triple deck structure surrounding the trailing edge of a flat plate, the flow recirculation in a trough geometry, and the flow in a rearward facing step channel. For the latter case, there are multiple recirculation zones, of different character, for laminar and turbulent flow conditions. A pressure-based form of flux-vector splitting is applied to the Navier-Stokes equations, which are represented by an implicit lowest-order reduced Navier-Stokes (RNS) system and a purely diffusive, higher-order, deferred-corrector. A trapezoidal or box-like form of discretization insures that all mass conservation properties are satisfied at interfacial and outflow boundaries, even for this primitive-variable, non-staggered grid computation.

Rubin, Stanley G.↗

NASA NTRS1997

Computer-aided design of a proton pump

The use of transmembrane proton gradients in energy transduction is an almost universal feature of life on earth. These proton gradients are established and maintained by specialized assemblies of proteins which actively pump protons across membranes. One broad class of proton pumps uses captured light energy to drive the proton pumping. Our goal is to elucidate the minimum structural requirements of a light-driven proton-pump. There are two basic components to a simple light-driven proton pump: a source of photo-generated protons and a "gate-keeper" which prevents these protons from reattaching themselves to their source. A wide variety of molecules in the membrane, even as simple as polycyclic aromatic hydrocarbons, are capable of releasing protons when illuminated. Our work is therefore focused on the design of the "gate-keeper." Our initial model involves a pair of proton acceptors, coupled to each other by a transient water bridge, and supported in the membrane by a small bundle of peptide helices. Upon illumination, the proton source transfers its proton to the:- first acceptor of the gate-keeper. While the reverse reaction is highly probable, all that is needed to ensure irreversibility is a nonvanishing probability that the proton will be transferred to the second acceptor across a transient water bridge. Back transfer of the proton to the first acceptor, and thence to the proton source, is impeded by the free energy required to move the proton uphill towards the. proton source and by the disruption of the transient water bridge. As a prototypical water-bridged proton transfer system, we are studying the transfer of a proton across a water bridge from a formic acid to a formate anion. With a pK(sub alpha), of 3.7. formic acid is a good model for the acidic amino acids glutamate and aspartate which are good candidates for gate-keeper proton acceptors. Simulations of proton transfer reactions in a membrane are complicated by the quantum mechanical nature of the process breaking and forming chemical bonds.

New, Michael H.↗