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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Compensating cylindrical Hohlraum mode 4 asymmetry via capsule thickness tailoring and effects on implosions

We report previously, hydrodynamic simulations suggested that precisely tailoring the capsule ablator thickness (shimming) could counterbalance cylindrical Hohlraum Legendre P 4 drive asymmetries at the capsule in laser indirect drive implosions. As a result, the stagnated deuterium–tritium (DT) fuel areal density P 4 asymmetry is reduced, potentially resulting in a nuclear yield increase. Inflight radiographs of various level of shimmed capsules with plastic (CH) ablators showed that shims can indeed control the in-flight capsule shell P 4 asymmetry, with a linear sensitivity to shim amplitude that is close to analytic estimates and simulations. Furthermore, the stagnated DT fuel areal density P 4 asymmetry inferred from downscattered neutron imaging was reduced when the capsule shim was applied, in agreement with simulations matching the inflight shell asymmetry. A nuclear yield improvement via shim was not observed, as predicted, likely due to implosion instabilities and as built capsule shim deviations from an ideal P 4 shape.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Striped Jets in Post–Neutron Star Merger Systems

Abstract Models invoking magnetic reconnection as the particle acceleration mechanism within relativistic jets often adopt a gradual energy dissipation profile within the jet. However, such a profile has yet to be reproduced in first-principles simulations. Here we perform a suite of 3D general relativistic magnetohydrodynamic simulations of post–neutron star merger disks with an initially purely toroidal magnetic field. We explore the variations in both the microphysics (e.g., nuclear recombination, neutrino emission) and system parameters (e.g, disk mass). In all of our simulations, we find the formation of magnetically striped jets. The stripes result from the reversals in the poloidal magnetic flux polarity generated in the accretion disk. The simulations display large variations in the distributions of stripe duration, τ , and power, 〈 P Φ 〉. We find that more massive disks produce more powerful stripes, the most powerful of which reaches 〈 P Φ 〉 ∼ 10 49 erg s −1 at τ ∼ 20 ms. The power and variability that result from the magnetic reconnection of the stripes agree with those inferred in short-duration gamma-ray bursts. We find that the dissipation profile of the cumulative energy is roughly a power law in both radial distance, z , and τ , with a slope in the range of ∼1.7–3; more massive disks display larger slopes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Operational, gauge-free quantum tomography

As increasingly impressive quantum information processors are realized in laboratories around the world, robust and reliable characterization of these devices is now more urgent than ever. These diagnostics can take many forms, but one of the most popular categories is tomography, where an underlying parameterized model is proposed for a device and inferred by experiments. Here, we introduce and implement efficient operational tomography, which uses experimental observables as these model parameters. This addresses a problem of ambiguity in representation that arises in current tomographic approaches (the gauge problem). Solving the gauge problem enables us to efficiently implement operational tomography in a Bayesian framework computationally, and hence gives us a natural way to include prior information and discuss uncertainty in fit parameters. We demonstrate this new tomography in a variety of different experimentally-relevant scenarios, including standard process tomography, Ramsey interferometry, randomized benchmarking, and gate set tomography.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

O 2 -Dependence of reactions of 1,2-dimethoxyethanyl and 1,2-dimethoxyethanylperoxy isomers

Reaction mechanisms of Ṙ and ROȮ radicals derived from low-temperature oxidation of 1,2-dimethoxyethane (CH 3 O(CH 2 ) 2 OCH 3 ) were investigated using speciation from multiplexed photoionization mass spectrometry (MPIMS) measurements via Cl-initiated oxidation, in conjunction with electronic structure calculations. The experiments were conducted at 5 bar, from 450 K – 650 K, and O 2 concentrations from 1 · 10 14 cm –3 – 6 · 10 18 cm –3 to probe the effects on competing reaction channels of 1,2-dimethoxyethanyl (Ṙ) and 1,2-dimethoxyethanylperoxy (ROȮ) isomers. Several species were detected with photoionization spectral fitting – ethene, formaldehyde, methyl vinyl ether, and 2-methoxyacetaldehyde – and, as determined by electronic structure calculations, may form via unimolecular decomposition of 1,2-dimethoxyethanyl or 1,2-dimethoxyethanylperoxy. O 2 -dependent yield ratios show that the formation pathways for all species undergo a competition between O 2 -addition and unimolecular decomposition. Here, adiabatic ionization energies were also calculated and utilized along with exact mass determinations to infer contributions for other species derived exclusively from first- and second-O 2 -addition, including 1,2-dimethoxyethene, cyclic ethers, and dicarbonyls.

1,2-dimethoxyethane↗
DOE OSTI2021

Origin of the isotopic composition of natural perchlorate: Experimental results for the impact of reaction pathway and initial ClO x reactant

Natural perchlorate (ClO 4 - ) exists in many places on Earth, in lunar regolith, meteorites, and on the surface of Mars. Terrestrial natural ClO 4 - has widely variable Cl and O stable isotopic compositions (δ 37 Cl, δ 18 O, Δ 17 O). The δ 18 O and Δ 17 O values of ClO 4 - from the most hyper-arid locations co-vary. ClO 4 - from less arid areas has relatively little 17 O excess and poor Δ 17 O-δ 18 O correlation. ClO 4 - from the Atacama Desert has unusually low δ 37 Cl (<-10‰) and exhibits a positive correlation between δ 37 Cl and δ 18 O, while the δ 37 Cl of ClO 4 - from all other locations varies between -5 and +7‰ with no δ 37 Cl-δ 18 O covariation. To evaluate the impact of different precursors (ClO x ) and reaction pathways on the isotopic composition of ClO 4 - , we measured the isotopic composition of ClO 4 - produced in the laboratory by UV or O 3 mediated aqueous oxidation of Cl-, OCl-, ClO2-, and ClO2° as well as O 3 mediated oxidation of dry NaCl. ClO x oxidation in aqueous or dry systems enriched in O 3 produced ClO 4 - with Δ 17 O values that generally increased with the number of O atoms required and included evidence that the site-specific 17 O anomaly in O 3 was preferentially transferred to ClO 4 - . Based on the inferred number of O atoms sourced from O 3 , and known Cl and O reaction pathways, it appears that ClO 2 ° and ClO 3 * were required intermediates in the production of ClO 4 - in the O 3 experiments. ClO x aqueous oxidation by UV irradiation produced ClO 4 - with a large range of δ 18 O values and little or no 17 O anomaly. ClO 3 - was produced to a much greater extent than ClO 4 - in all experiments except dry oxidation of NaCl by O 3 . The isotopic composition of ClO 3 - was distinct from that of ClO 4 - produced from the same initial reactants. Combined results of O 3 and UV mediated reactions largely bracketed the range of natural ClO 4 - δ 18 O and Δ 17 O values as well as δ 37 Cl values of non-Atacama natural samples, but no conditions produced the low δ 37 Cl values of Atacama ClO 4 - . Finally, our results indicate that variation in production mechanisms, possibly combined with isotopically variable precursors, could be responsible for much of the observed isotopic variation in natural ClO 4 - and ClO 3 - .

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

A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques

Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Elucidating Hydrogen Reaction-Induced Water Desorption from Oxide-Passivated Metal Surfaces for Plasma Applications

Elucidating the mechanisms responsible for sub-microsecond desorption of water and other impurities from electrode surfaces at high heating rates is crucial for understanding pulsed power behavior. Ionization of desorbed impurities in the vacuum regions causes power or current loss; devising methods to limit such desorption during the short time scale of pulsed power is needed to improve corresponding applications. Previous molecular modeling studies have strongly suggested that, under high vacuum conditions, the amount of water impurity desorbing from oxide surfaces on metal electrodes is at a sub-monolayer level at room temperature, which appears insufficient to explain observed pulsed power energy losses at high current densities. In this work, we apply Density Functional Theory (DFT) techniques to show that hydrogen trapped inside iron metal can diffuse into hematite (α-Fe 2 O 3 ) on the metal surface, ultimately reacting with the oxide to form Fe(II) and H 2 O. The latter desorbs at elevated temperature and may explain the anomalous amount of desorbed impurity inferred from pulsed-power experiments. We also apply a suite of characterization techniques to demonstrate that when iron metal is heated to 650 °C, the dominant surface oxide component becomes α-Fe 2 O 3 . The oxide facets exposed are found to be a mixture of (0001), (10-10), and others, in agreement with the DFT models used.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Comprehensive Material Characterization and Simultaneous Model Calibration for Improved Computational Simulation Credibility

Computational simulation is increasingly relied upon for high-consequence engineering decisions, and a foundational element to solid mechanics simulations is a credible material model. Our ultimate vision is to interlace material characterization and model calibration in a real-time feedback loop, where the current model calibration results will drive the experiment to load regimes that add the most useful information to reduce parameter uncertainty. The current work investigated one key step to this Interlaced Characterization and Calibration (ICC) paradigm, using a finite load-path tree to incorporate history/path dependency of nonlinear material models into a network of surrogate models that replace computationally-expensive finite-element analyses. Our reference simulation was an elastoplastic material point subject to biaxial deformation with a Hill anisotropic yield criterion. Training data was generated using either a space-filling or adaptive sampling method, and surrogates were built using either Gaussian process or polynomial chaos expansion methods. Surrogate error was evaluated to be on the order of 10 ⁻5 and 10 ⁻3 percent for the space-filling and adaptive sampling training data, respectively. Direct Bayesian inference was performed with the surrogate network and with the reference material point simulator, and results agreed to within 3 significant figures for the mean parameter values, with a reduction in computational cost over 5 orders of magnitude. These results bought down risk regarding the surrogate network and facilitated a successful FY22-24 full LDRD proposal to research and develop the complete ICC paradigm.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Model of Double Coronal Hard X-Ray Sources in Solar Flares

A number of double coronal X-ray sources have been observed during solar flares by RHESSI, where the two sources reside at different sides of the inferred reconnection site. However, where and how these X-ray-emitting electrons are accelerated remains unclear. Here we present the first model of the double coronal hard X-ray (HXR) sources, where electrons are accelerated by a pair of termination shocks driven by bidirectional fast reconnection outflows. We model the acceleration and transport of electrons in the flare region by numerically solving the Parker transport equation using velocity and magnetic fields from the macroscopic magnetohydrodynamic simulation of a flux rope eruption. We show that electrons can be efficiently accelerated by the termination shocks and high-energy electrons mainly concentrate around the two shocks. The synthetic HXR emission images display two distinct sources extending to >100 keV below and above the reconnection region, with the upper source much fainter than the lower one. The HXR energy spectra of the two coronal sources show similar spectral slopes, consistent with the observations. Our simulation results suggest that the flare termination shock can be a promising particle acceleration mechanism in explaining the double-source nonthermal emissions in solar flares.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Tutorial on Chemical Pressure Analysis: How Atomic Packing Drives Laves/Zintl Intergrowth in K3Au5Tl

The tight atomic packing generally exhibited by alloys and intermetallics can create the impression of their being composed of hard spheres arranged to maximize their density. As such, the atomic size factor has historically been central to explanations of the structural chemistry of these systems. However, the role atomic size plays structurally has traditionally been inferred from empirical considerations. The recently developed DFT-Chemical Pressure (CP) analysis has opened a path to investigating these effects with theory. In this article, we provide a step-by-step tutorial on the DFT-CP method for non-specialists, along with advances in the approach that broaden its applicability. A new version of the CP software package is introduced, which features an interactive system that guides the user in preparing the necessary electronic structure data and generating the CP scheme, with the results being readily visualized with a web browser (and easily incorporated into websites). For demonstration purposes, we investigate the origins of the crystal structure of K3Au5Tl, which represents an intergrowth of Laves and Zintl phase domains. Here, CP analysis reveals that the intergrowth is supported by complementary CP features of NaTl-type KTl and MgCu2-type KAu2 phases. In this way, K3Au5Tl exemplifies how CP effects can drive the merging for geometrical motifs derived from different families of intermetallics through a mechanism referred to as epitaxial stabilization.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Isotope effects at the origin of life: Fingerprints of the Strecker synthesis

We report strecker synthesis creates α-amino acids from prebiotically plausible substrates (cyanide, ammonia, and aldehydes) and is widely hypothesized to be a key mechanism in the chemistry that led to life on Earth and on other planets. To better constrain the synthetic environments and precursors of abiotic α-amino acids, and to determine unique signatures of abiogenic amino acids, we measured the molecular-averaged and site-specific carbon and nitrogen isotope effects for the Strecker synthesis of alanine. The reaction steps of the Strecker synthesis can be divided into two groups: an initial series of reversible amination and nitrile-addition reactions (‘equilibration’) and a second series of irreversible hydrolysis reactions (‘hydrolysis’). The equilibration of cyanide, acetaldehyde, and ammonia with the intermediate, α-aminopropionitrile (α-APN), has a measured 55.1‰ equilibrium nitrogen isotope effect between the 15 N-rich amine nitrogen in α-aminopropionitrile and the 15 N-poor ammonia and a 20.0‰ equilibrium carbon isotope effect between the 13 C-poor C-2 site in α-aminopropionitrile and the 13 C-rich carbonyl carbon in acetaldehyde. The first irreversible hydrolysis step is inferred to have an up to 10‰ normal carbon fractionation (i.e., faster for 12 C, slower for 13 C) for the whole molecule, but it also has one or more side reactions that deplete the reactive α-APN reservoir by up to 15‰. The second hydrolysis step has a 15.4‰ normal kinetic isotope effect on the amide (C-1) site of alaninamide, which becomes the carboxyl site of alanine. Other α-amino acids will likely experience similar nitrogen isotope fractionations between ammonia and their amine sites, and similar carbon isotope fractionations between the carbonyl carbon in reactant aldehydes or ketones and the intermediate α-aminonitrile, and between cyanide and the carboxyl site. Therefore, these isotope effects allow us to predict the carbon and nitrogen isotopic contents and intramolecular structures of α-amino acids formed by Strecker synthesis based on their substrates’ isotopic compositions, or to infer the isotopic compositions of substrates from which amino acids formed, for example in the case of the amino-acid-rich carbonaceous chondrites. The site-specific C and N isotopic compositions of amino acids formed by Strecker chemistry contrast with those typical of terrestrial biosynthetic amino acids, so these data also provide a means of discriminating between biogenic and abiogenic α-amino acids.

58 GEOSCIENCES↗
DOE OSTI2021

High frequency impedance characteristics of a tunable microplasma device

Computational studies on high frequency impedance characteristics of a microplasma device are reported. While microplasma is ignited using a primary excitation signal, frequency response of plasma impedance is determined by a secondary high frequency probe signal with significantly lower voltage amplitude such that it does not influence the plasma parameters. Here, the computational model utilizing the drift–diffusion approximation is first validated by comparing with experimental data for microplasmas ignited at pressures ranging from 1 to 5 Torr. In spite of quantitative discrepancies, good overall agreement is obtained between the measured frequency response of impedance of the discharge. Comparisons are also presented for various plasma parameters including mean electron number density, sheath thickness, mean electron temperature, and collision frequency that were inferred from the impedance measurements. The computational model is then used to perform simulations of near-atmospheric pressure microplasmas with the probe signal frequency ranging from 3 to 20 GHz. The simulations demonstrate the presence of a resonance frequency at which the impedance vanishes. More importantly, it is shown that this resonant frequency can be tuned effectively by suitably modifying the operating parameters (gap size, pressure, and excitation voltage). The simulated impedance characteristics are used to determine the effective plasma inductance and capacitance using a non-linear fitting approach, thereby showing the dependence of these electrical parameters on the plasma operating conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Extreme Heating of Minor Ions in Imbalanced Solar-wind Turbulence

Minor ions in the solar corona are heated to extreme temperatures, far in excess of those of the electrons and protons that comprise the bulk of the plasma. These highly nonthermal distributions make minor ions sensitive probes of the collisionless processes that heat the corona and power the solar wind. The recent discovery of the "helicity barrier" offers a mechanism in which imbalanced Alfvénic turbulence in low-β plasmas preferentially heats protons over electrons, generating high-frequency, proton-cyclotron-resonant fluctuations. We use the hybrid-kinetic particle-in-cell code Pegasus++ to drive imbalanced Alfvénic turbulence in a 3D low-β plasma with additional passive ion species, He 2+ and O 5+ . A helicity barrier naturally develops, followed by clear phase-space signatures of oblique proton-cyclotron-wave heating and Landau-resonant heating from the imbalanced Alfvénic fluctuations. The former results in characteristically arced ion velocity distribution functions, whose non-bi-Maxwellian features are shown by linear ALPS calculations to be critical to the heating process. Additional features include a steep transition-range electromagnetic spectrum, proton-cyclotron waves propagating in the direction of the imbalance, significantly enhanced proton-to-electron heating ratios, ion temperatures that are considerably more perpendicular with respect to magnetic field, and extreme heating of heavier species in a manner consistent with mass scalings inferred from spacecraft measurements. None of these features are realized in an otherwise equivalent simulation of balanced turbulence. If seen simultaneously in the fast solar wind, these signatures of the helicity barrier would testify to the necessity of incorporating turbulence imbalance in a complete theory for the evolution of the solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework

Motivation Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role in immune-mediated selection and can leave strong signatures in virus sequences; however, existing sequence-based within-host virus modeling frameworks do not explicitly include a human leukocyte antigen (HLA)-aware CTL response. Results We extended our previously published within-host sequence evolution simulator, wavess, to include an explicit CTL response, and share a method for identifying HLA-specific CTL epitopes given a founder virus sequence. We also updated the model to permit a variable recombination rate, which allows for modeling non-adjacent genes, segmented genomes, and recombination hotspots. These extensions to wavess allow for more accurate simulation of viruses and virus genes, particularly in regions of the genome where the immune response is dominated by CTLs (rather than antibodies). It also provides the foundation for investigations of how these newly-added biological mechanisms influence within-host evolution. Availability and implementation The core of wavess is written in Python 3, with helper functions written in R. It is available at https://github.com/MolEvolEpid/wavess.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Inference-Based Quantum Sensing

In a standard quantum sensing (QS) task one aims at estimating an unknown parameter θ, encoded into an n-qubit probe state, via measurements of the system. The success of this task hinges on the ability to correlate changes in the parameter to changes in the system response $\mathscr{R}$⁡(θ) (i.e., changes in the measurement outcomes). For simple cases the form of $\mathscr{R}$⁡(θ) is known, but the same cannot be said for realistic scenarios, as no general closed-form expression exists. Here, in this Letter, we present an inference-based scheme for QS. We show that, for a general class of unitary families of encoding, $\mathscr{R}$⁡(θ) can be fully characterized by only measuring the system response at 2⁢n+1 parameters. This allows us to infer the value of an unknown parameter given the measured response, as well as to determine the sensitivity of the scheme, which characterizes its overall performance. We show that inference error is, with high probability, smaller than δ, if one measures the system response with a number of shots that scales only as Ω⁢(log 3 ⁡(n)/δ 2 ). Furthermore, the framework presented can be broadly applied as it remains valid for arbitrary probe states and measurement schemes, and, even holds in the presence of quantum noise. We also discuss how to extend our results beyond unitary families. Finally, to showcase our method we implement it for a QS task on real quantum hardware, and in numerical simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Investigation of the fine structure of antihydrogen

At the historic Shelter Island Conference on the Foundations of Quantum Mechanics in 1947, Willis Lamb reported an unexpected feature in the fine structure of atomic hydrogen: a separation of the 2S 1/2 and 2P 1/2 states. The observation of this separation, now known as the Lamb shift, marked an important event in the evolution of modern physics, inspiring others to develop the theory of quantum electrodynamics. Quantum electrodynamics also describes antimatter, but it has only recently become possible to synthesize and trap atomic antimatter to probe its structure. Mirroring the historical development of quantum atomic physics in the twentieth century, modern measurements on anti-atoms represent a unique approach for testing quantum electrodynamics and the foundational symmetries of the standard model. Here we report measurements of the fine structure in the n = 2 states of antihydrogen, the antimatter counterpart of the hydrogen atom. Using optical excitation of the 1S–2P Lyman-α transitions in antihydrogen, we determine their frequencies in a magnetic field of 1 tesla to a precision of 16 parts per billion. Assuming the standard Zeeman and hyperfine interactions, we infer the zero-field fine-structure splitting (2P 1/2 –2P 3/2 ) in antihydrogen. The resulting value is consistent with the predictions of quantum electrodynamics to a precision of 2 per cent. Using our previously measured value of the 1S–2S transition frequency, we find that the classic Lamb shift in antihydrogen (2S 1/2 –2P 1/2 splitting at zero field) is consistent with theory at a level of 11 per cent. Our observations represent an important step towards precision measurements of the fine structure and the Lamb shift in the antihydrogen spectrum as tests of the charge–parity–time symmetry8 and towards the determination of other fundamental quantities, such as the antiproton charge radius, in this antimatter system.

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

Description of Sensor Assignment Optimization Method as Deployed on a Multi-Node Cluster

Data analytic methods are being developed to address the problem of how to assign a sensor set in a nuclear facility such that a requisite level of process monitoring capability is realized and that the sensor set is sufficiently rich to determine the status of the individual sensors with respect to need for calibration. There is an awareness in the nuclear industry that data analytics combined with rich sensor sets represent a means to improve operations and reduce costs. In the industry the calibration problem has been previously approached as an empirical data-driven problem with several methods having been developed. However, the experience of the utilities over the past ten years with these methods indicates that the absence of physics-based information renders the data-driven approach less reliable. Complicating factors such as the inherent variability of operation (both equipment alignment and operating condition) can confound a pure data-driven approach while there are no rigorous guidelines for determining what constitutes an adequate sensor set. The solution under development to overcome these shortcomings supplements the data analytic method with process information in a so-called process-constrained data-analytic approach. Simple balance equations are written for generic components (e.g., mechanical pump, valve, and heat exchanger). These do not require a priori knowledge of process parameters, such as heat transfer coefficients or friction factors. All that is needed on the part of the utility user is to identify the components and how they are connected. This report describes the development of a parallel computing capability for determining the optimal sensor set. The optimal sensor set problem suffers from the curse of dimensionality. Computation time increases exponentially as the size of the system grows. To overcome this difficulty a pre-conditioner algorithm is developed to find an approximate solution close the actual solution. This serves as a seed for the full-blown algorithm and acts to constrain the space that must searched. The optimization algorithms are described and the implementation on a parallel computing platform is described. The application of the method to a use case we are solving in collaboration with our utility partner served to illustrate how the default sensor set in a nuclear plant may not provide sufficient coverage to infer sensor calibration status.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate in varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of bending propensities of BMC hexamers (BMC-H), the most abundant shell constituents. Published data show that some BMC-H, like β -carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted us to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the arrangement adopted in crystals by BMC-H that experimentally form curved objects, leading to very similar arrangements to those found in structures of recomposed BMC shells. Simulations on triplets of planar-behaving hexamers, which were previously reconfigured to comply with such organization, confirmed that bending propensity is mostly defined by the precise lateral positioning of hexamers, rather than by BMC-H identity. Finally, an interfacial lysine was pinpointed as the most decisive residue in controlling PduA spontaneous curvature. Globally, results presented herein should contribute to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

59 BASIC BIOLOGICAL SCIENCES↗