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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Atmospheric river representation in the Energy Exascale Earth System Model (E3SM) version 1.0

Abstract. The Energy Exascale Earth System Model (E3SM) project is an ongoing, state-of-the-science Earth system modeling, simulation, and prediction project developed by the US Department of Energy (DOE). With an emphasis on supporting the DOE's energy mission, understanding and quantifying how well the model simulates water cycle processes is of particular importance. Here, we evaluate E3SM version 1.0 (v1.0) for its ability to represent atmospheric rivers (ARs), which play significant roles in water vapor transport and precipitation. The characteristics and precipitation associated with global ARs in E3SM at standard resolution (1∘ × 1∘) are compared to the Modern-Era Retrospective analysis for Research and Applications, version 2 (MERRA2). Global patterns of AR frequencies in E3SM show high degrees of correlation (≥0.97) with MERRA2 and low mean absolute errors (MAEs; <1 %) annually, seasonally, and across different ensemble members. However, some large-scale condition biases exist, leading to AR biases – most significant of which are the double intertropical convergence zone (ITCZ), a stronger and/or equatorward-shifted subtropical jet during boreal and austral winters, and enhanced Northern Hemisphere westerlies during summer. By comparing atmosphere-only and fully coupled simulations, we attribute the sources of the biases to the atmospheric component or to a coupling response. Using relationships revealed in Dong et al. (2021), we provide evidence showing the stronger North Pacific jet in winter and the enhanced Northern Hemisphere westerlies during summer, associated with E3SM's double ITCZ and related weaker Atlantic meridional overturning circulation (AMOC), respectively, which are significant sources of the AR biases found in the coupled simulations.

58 GEOSCIENCES↗
DOE OSTI2014

Experimental design applications for modeling and assessing carbon dioxide sequestration in saline aquifers

This project was a computer modeling effort to couple reservoir simulation and ED/RSM using Sensitivity Analysis, Uncertainty Analysis, and Optimization Methods, to assess geologic, geochemical, geomechanical, and rock-fluid effects and factors on CO 2 injectivity, capacity, and plume migration. The project objective was to develop proxy models to simplify the highly complex coupled geochemical and geomechanical models in the utilization and storage of CO 2 in the subsurface. The goals were to investigate and prove the feasibility of the ED/RSM processes and engineering development, and bridge the gaps regarding the uncertainty and unknowns of the many geochemical and geomechanical interacting parameters in the development and operation of anthropogenic CO 2 sequestration and storage sites. The bottleneck in this workflow is the high computational effort of reactive transport simulation models and large number of input variables to optimize with ED/RSM techniques. The project was not to develop the reactive transport, geomechanical, or ED/RSM software, but was to use what was commercially and/or publically available as a proof of concept to generate proxy or surrogate models. A detailed geologic and petrographic mineral assemblage and geologic structure of the doubly plunging anticline was defined using the USDOE RMOTC formations of interest data (e.g., Lower Sundance, Crow Mountain, Alcova Limestone, and Red Peak). The assemblage of 23 minerals was primarily developed from literature data and petrophysical (well log) analysis. The assemblage and structure was input into a commercial reactive transport simulator to predict the effects of CO 2 injection and complex reactions with the reservoir rock. Significant impediments were encountered during the execution phase of the project. The only known commercial reactive transport simulator was incapable of simulating complex geochemistry modeled in this project. Significant effort and project funding was expended to determine the limitations of both the commercial simulator and the Lawrence Berkeley National Laboratory (LBNL) R&D simulator, TOUGHREACT available to the project. A simplified layer cake model approximating the volume of the RMOTC targeted reservoirs was defined with 1-3 minerals eventually modeled with limited success. Modeling reactive transport in porous media requires significant computational power. In this project, up to 24 processors were used to model a limited mineral set of 1-3 minerals. In addition, geomechanical aspects of injecting CO 2 into closed, semi-open, and open systems in various well completion methods was simulated. Enhanced Oil Recovery (EOR) as a storage method was not modeled. A robust and stable simulation dataset or base case was developed and used to create a master dataset with embedded instructions for input to the ED/RSM software. Little success was achieved toward the objective of the project using the commercial simulator or the LBNL simulator versions available during the time of this project. Several hundred realizations were run with the commercial simulator and ED/RSM software, most having convergence problems and terminating prematurely. A proxy model for full field CO 2 injection sequestration utilization and storage was not capable of being developed with software available for this project. Though the chemistry is reasonably known and understood, based on the amount of effort and huge computational time required, predicting CO 2 sequestration storage capacity in geologic formations to within the program goals of ±30% proved unsuccessful.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Axion Mass Prediction from Adaptive Mesh Refinement Cosmological Lattice Simulations

The quantum chromodynamics (QCD) axion arises as the pseudo-Goldstone mode of a spontaneously broken Abelian Peccei-Quinn (PQ) symmetry. If the scale of PQ symmetry breaking occurs below the inflationary reheat temperature and the domain wall number is unity, then there is a unique axion mass that gives the observed dark matter (DM) abundance. Computing this mass has been the subject of intensive numerical simulations for decades since the mass prediction informs laboratory experiments. Axion strings develop below the PQ symmetry-breaking temperature, and as the string network evolves, it emits axions that go on to become the DM. A key ingredient in the axion mass prediction is the spectral index of axion radiation emitted by the axion strings. We compute this index in this Letter using the most precise and accurate large-scale simulations to date of the axion-string network leveraging adaptive mesh refinement to achieve the precision that would, otherwise, require a static lattice with 262,144 3 lattice sites. We find a scale-invariant axion radiation spectrum to within 1% precision and find no evidence that the spectral index of radiation evolves with time. Accounting for axion production from strings prior to the QCD phase transition leads us to predict that the axion mass should be approximately 𝑚 𝑎 ∈ (45, 65) μ ⁢eV. However, we provide preliminary evidence that axions are produced in greater quantities from the string-domain-wall network collapse during the QCD phase transition, potentially increasing the mass prediction to as much as 300 μ ⁢eV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

SU-F-BRB-02: Towards Quantitative Clinical Decision On Deep Inspiration Breath Hold (DIBH) Or Prone for Left-Sided Breast Irradiation

Purpose: To develop quantitative clinical guidelines between supine Deep Inspiratory Breath Hold (DIBH) and prone free breathing treatments for breast patients, we applied 3D deformable phantoms to perform Monte Carlo simulation to predict corresponding Dose to the Organs at Risk (OARs). Methods: The RPI-adult female phantom (two selected cup sizes: A and D) was used to represent the female patient, and it was simulated using the MCNP6 Monte Carlo code. Doses to OARs were investigated for supine DIBH and prone treatments, considering two breast sizes. The fluence maps of the 6-MV opposed tangential fields were exported. In the Monte Carlo simulation, the fluence maps allow each simulated photon particle to be weighed in the final dose calculation. The relative error of all dose calculations was kept below 5% by simulating 3*10{sup 7} photons for each projection. Results: In terms of dosimetric accuracy, the RPI Adult Female phantom with cup size D in DIBH positioning matched with a DIBH treatment plan of the patient. Based on the simulation results, for cup size D phantom, prone positioning reduced the cardiac dose and the dose to other OARs, while cup size A phantom benefits more from DIBH positioning. Comparing simulation results for cup size A and D phantom, dose to OARs was generally higher for the large breast size due to increased scattering arising from a larger portion of the body in the primary beam. The lower dose that was registered for the heart in the large breast phantom in prone positioning was due to the increase of the distance between the heart and the primary beam when the breast was pendulous. Conclusion: Our 3D deformable phantom appears an excellent tool to predict dose to the OARs for the supine DIBH and prone positions, which might help quantitative clinical decisions. Further investigation will be conducted. National Institutes of Health R01EB015478.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Design and analysis of a wake model for spatially heterogeneous flow

Abstract. Methods of turbine wake modeling are being developed to more accurately account for spatially variant atmospheric conditions within wind farms. Most current wake modeling utilities are designed to apply a uniform flow field to the entire domain of a wind farm. When this method is used, the accuracy of power prediction and wind farm controls can be compromised depending on the flow-field characteristics of a particular area. In an effort to improve strategies of wind farm wake modeling and power prediction, FLOw Redirection and Induction in Steady State (FLORIS) was developed to implement sophisticated methods of atmospheric characterization and power output calculation. In this paper, we describe an adapted FLORIS model that features spatial heterogeneity in flow-field characterization. This model approximates an observed flow field by interpolating from a set of atmospheric measurements that represent local weather conditions. The objective of this method is to capture heterogeneous atmospheric effects caused by site-specific terrain features, without explicitly modeling the geometry of the wind farm terrain. The implemented adaptations were validated by comparing the simulated power predictions generated from FLORIS to the actual recorded wind farm output from the supervisory control and data acquisition (SCADA) recordings and large eddy simulations (LESs). When comparing the performance of the proposed heterogeneous model to homogeneous FLORIS simulations, the results show a 14.6 % decrease for mean absolute error (MAE) in wind farm power output predictions for cases using wind farm SCADA data and a 18.9 % decrease in LES case studies. The results of these studies also indicate that the efficacy of the proposed modeling techniques may vary with differing site-specific operational conditions. This work quantifies the accuracy of wind plant power predictions under heterogeneous flow conditions and establishes best practices for atmospheric surveying for wake modeling.

17 WIND ENERGY↗
DOE OSTI2020

Critical nuclei at hetero-phase interfaces

Two-step nucleation, in which a metastable intermediate phase acts as a precursor for nucleating a thermodynamically stable phase, has been widely observed in many materials systems and solid-state reactions. Among the advantages of two-step nucleation is that the stable phase may nucleate heterogeneously at the hetero-phase interface between the original and the precursory phases. Although heterogeneous nucleation (HN) theories for homo-phase grain boundaries and inert surfaces are well established, our understanding of HN at reactive hetero-phase interfaces remains incomplete. This deficiency stems from the discontinuity of the chemical potential driving force across the hetero-phase interface, which profoundly affects the fundamental properties of the nucleus in a way that is not properly accounted for in existing models. In this work, we incorporate these effects to extend the classical nucleation theory to HN at hetero-phase interfaces. Our extended model demonstrates that the nucleus shape along the minimum energy path is strongly size-dependent, and this additional degree of freedom can result in the reduction of the critical nucleus volume and associated activation energy barrier by orders of magnitude relative to conventional predictions. The simulation results are used to construct a sensitivity map in the parameter space of interfacial energy and bulk driving force ratios, which quantifies the difference in nucleation barriers predicted by different models.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computational Fermi Level Engineering and Doping-Type Conversion of Ga2O3 Via Three-Step Processing

Ga2O3 is being actively explored for power electronics, and other applications due to its ultra- wide bandgap and low projected fabrication cost of high-quality crystals. N-type doping of Ga2O3 can be achieved and tuned, but p-type doping faces fundamental obstacles. Successful engineering of Ga2O3 based devices requires critical control of doping density, Fermi level position, providing opportunities for predictive process simulation. We use first-principles defect equilibrium calculations to simulate a 3-step growth- annealing-quench protocol for hydrogen assisted Mg doping in Ga2O3, taking into account the hydrogen- oxygen-water gas phase equilibrium. We predict type conversion to a net p-type regime following O-rich annealing after growth under reducing conditions in the presence of H2. We show that there is an optimal temperature that maximizes the net acceptor density during the equilibrium annealing step for a given Mg doping level. Quenching of non-equilibrium annealed samples then results in a Fermi level EF below mid-gap down to about EV +1.5 eV, creating a significant number of uncompensated neutral MgGa0 acceptors. This type converted Ga2O3 can create significant built-in field in a p-n junction with an adjoining n-type material and could enable vertical MOSFETs.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗
DOE OSTI2021

Computational Fermi Level Engineering and Doping-Type Conversion of Ga2O3 Via Three-Step Processing

Ga2O3 is being actively explored for power electronics, deep-ultraviolet optoelectronics, and other applications due to its ultra-wide bandgap and low projected fabrication cost of large-size and high-quality crystals. N-type doping of Ga2O3 can be achieved and tuned, but p-type doping faces fundamental obstacles due to deep character of acceptor levels and polaron transport of resulting holes. However, successful engineering of Ga2O3 based devices requires critical control of doping density, Fermi level position, and free carrier concentration, providing opportunities for predictive process simulation. We use first-principles defect theory and defect equilibrium calculations to simulate a 3-step growth-annealing-quench protocol for hydrogen assisted Mg doping in Ga2O3, taking into account the hydrogen-oxygen-water gas phase equilibrium. We predict type conversion to a net p-type regime following O-rich annealing after growth under reducing conditions in the presence of H2. This process is similar to the Mg acceptor activation by H removal in GaN. We show that there is an optimal temperature that maximizes the net acceptor density during the equilibrium annealing step for a given Mg doping level. Quenching of non-equilibrium annealed samples then results in a Fermi level EF below mid-gap down to about EV +1.5 eV, creating a significant number of uncompensated neutral MgGa0 acceptors. The resulting free hole concentration in quenched samples is very low (109 – 1012 cm-3) due to deep energy level of these Mg acceptors, but this type converted Ga2O3 material can create a significant built-in field in a p-n junction with an adjoining n-type material. Additionally, the electron concentration is greatly suppressed in such acceptor-doped Ga2O3, which could enable the use as a current blocking layer to fabricate normally-off (enhancement-mode) vertical Ga2O3 based metal-oxide-semiconductor field effect transistors (MOSFETs), and as a guard ring for edge termination in MOSFETs and Schottky barrier diodes (SBDs) with increased breakdown voltage.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗
DOE OSTI2022

A Kinetic Model for Predicting Trace Gas Uptake and Reaction

A model is developed to describe trace gas uptake and reaction with applications to aerosols and microdroplets. Gas uptake by the liquid is formulated as a coupled equilibria that links gas, surface, and bulk regions of the droplet or solution. Previously, this framework was used in explicit stochastic reaction-diffusion simulations to predict the reactive uptake kinetics of ozone with droplets containing aqueous aconitic acid, maleic acid, and sodium nitrite. With the use of prior data and simulation results, a new equation for the uptake coefficient is derived, which accounts for both surface and bulk reactions. Lambert W functions are used to obtain closed form solutions to the integrated rate laws for the multiphase kinetics; similar to previous expressions that describe Michaelis-Menten enzyme kinetics. Together these equations couple interface and bulk processes over a wide range of conditions and do not require many of the limiting assumptions needed to apply resistor model formulations to explain trace gas uptake and reaction.

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

Survey of Modeling and Simulation Techniques for Advanced Manufacturing Technologies Volume II – Predicting Material Performance from Material Microstructure

This report describes the current state of modeling and simulation techniques for predicting the properties of materials fabricated with advanced manufacturing techniques, given the initial microstructure of the material. The report includes a literature survey and a gap analysis outlining and prioritizing key issues in applying these modeling and simulation techniques to nuclear reactor structural materials. The discussion covers both physics-based and data-driven modeling techniques and includes a broad range of manufacturing techniques and materials that may have future nuclear applications. This report is the second in a two-part series, with the first report covering modeling and simulation methods for predicting the initial, as-manufactured structure of advanced manufacturing materials, given a description of the process. Both reports focus on a set of manufacturing technologies likely to be applied to reactor structural components. Taken together, the two reports provide a complete summary of the current state of processing-structure-properties models for advanced manufacturing as well as a survey of applications to reactor structural materials

42 ENGINEERING↗
DOE OSTI2017

Giant Ly α Nebulae in the Illustris Simulation

Several “giant” Ly α nebulae with an extent ≳300 kpc and observed Ly α luminosity of ≳10{sup 44} erg s{sup −1} cm{sup −2} arcsec{sup −2} have recently been detected, and it has been speculated that their presence hints at a substantial cold gas reservoir in small cool clumps not resolved in modern hydrodynamical simulations. We use the Illustris simulation to predict the Ly α emission emerging from large halos ( M > 10{sup 11.5} M {sub ⊙}) at z ∼ 2 and thus test this model. We consider both active galactic nucleus (AGN) and star driven ionization, and compare the simulated surface brightness maps, profiles, and Ly α spectra to a model where most gas is clumped below the simulation resolution scale. We find that with Illustris, no additional clumping is necessary to explain the extents, luminosities, and surface brightness profiles of the “giant Ly α nebulae” observed. Furthermore, the maximal extents of the objects show a wide spread for a given luminosity and do not correlate significantly with any halo properties. We also show how the detected size depends strongly on the employed surface brightness cutoff, and predict that further examples of such objects will be found in the near future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

First-Principles Grand-Canonical Simulations of Water Adsorption in Proton-Exchanged Zeolites

Water appears by design or as impurities in many important reactive systems. For those catalyzed by porous solid acids, such as widely used zeolites, experimentally quantifying the amount or elucidating the structure of adsorbed water clusters at reaction conditions is challenging, while computational studies (e.g., first-principles molecular dynamics simulations) often need to assume the loading to examine solvation effects. Furthermore, we perform first-principles grand-canonical simulations to predict water adsorption to H-ZSM-5 zeolites under specified experimental conditions. Presampling with inexpensive force fields and a pool-based parallelization algorithm are used to improve simulation efficiency, while molecular dynamics is used to sample configurations involving hydronium species. We observe that H + exchange dramatically increases the hydrophilicity of zeolite MFI and an appreciable amount of water is present at very low relative humidities. At all conditions examined, the zeolitic protons are found to dissociate readily from the surface basic sites and become mobile by participating in the hydrogen-bonded chains of adsorbed water molecules.

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

When more data hurts: Optimizing data coverage while mitigating diversity-induced underfitting in an ultrafast machine-learned potential

Machine-learned interatomic potentials (MLIPs) are becoming an essential tool in materials modeling. However, optimizing the generation of training data used to parametrize the MLIPs remains a significant challenge. This is because MLIPs can fail when encountering local environments too different from those present in the training data. The difficulty of determining a priori the environments that will be encountered during molecular dynamics simulation necessitates diverse, high-quality training data. Here, this study investigates how training data diversity affects the performance of MLIPs using the Ultra-Fast force field (UF 3 ) to model amorphous silicon nitride. We employ expert and autonomously generated data to create the training data and fit four force field variants to subsets of the data. Our findings reveal a critical balance in training data diversity: insufficient diversity hinders generalization, while excessive diversity can exceed the MLIP's learning capacity, reducing simulation accuracy. Specifically, we found that the UF 3 variant trained on a subset of the training data, in which nitrogen-rich structures were removed, offered vastly better prediction and simulation accuracy than any other variant. By comparing these UF 3 variants, we highlight the nuanced requirements for creating accurate MLIPs, emphasizing the importance of application-specific training data to achieve optimal performance in modeling complex material behaviors.

ab initio molecular dynamics↗
DOE OSTI2021

Predicting 1 H NMR relaxation in Gd 3+ -aqua using molecular dynamics simulations

Atomistic molecular dynamics simulations are used to predict 1 H NMR T 1 relaxation of water from paramagnetic Gd 3+ ions in solution at 25 °C. Simulations of the T 1 relaxivity dispersion function r 1 computed from the Gd 3+ – 1 H dipole–dipole autocorrelation function agree within ≃8% of measurements in the range f 0 ≃ 5 ↔ 500 MHz, without any adjustable parameters in the interpretation of the simulations, and without any relaxation models. Here the simulation results are discussed in the context of the Solomon-Bloembergen-Morgan inner-sphere relaxation model, and the Hwang-Freed outer-sphere relaxation model. Below f 0 ≲ 5 MHz, the simulation overestimates r 1 compared to measurements, which is used to estimate the zero-field electron-spin relaxation time. The simulations show potential for predicting r 1 at high frequencies in chelated Gd 3+ contrast-agents used for clinical MRI.

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

Direct comparison of gyrokinetic and fluid scrape-off layer simulations

Typically, fluid simulations are used for tokamak divertor design. However, fluid models are only valid if the scrape-off layer (SOL) is highly collisional. This assumption is valid in many present-day experiments but is questionable in the upstream SOL of some high-power scenarios envisioned for burning plasmas and fusion pilot plants. This paper reports on comparisons between fluid and kinetic simulations of the SOL for upstream parameters and geometry representative of the Spherical Tokamak for Energy Production fusion pilot plant. The SOLPS-ITER (fluid) and Gkeyll (gyrokinetic) codes are operated in a two-dimensional axisymmetric mode, which replaces turbulence with ad-hoc diffusivities. In kinetic simulations, we observe that the ions in the upstream SOL experience significant mirror trapping. This substantially increases the upstream temperature and has important implications for impurity dynamics. We show that the mirror force, which is excluded in SOLPS’s fluid equations, enhances the electrostatic potential drop along the field line in the SOL. We also show that the assumption of equal main ion and impurity temperatures, which is made in commonly used fluid codes, is invalid for the regimes explored here. The combination of these effects results in superior confinement of impurities to the divertor region in kinetic simulations, consistent with our earlier predictions [Kotschenreuther et al., in 29th IAEA 29 Fusion Energy Conference (IAEA, London, UK, 2023)]. This effect can be dramatic, reducing the midplane impurity density by orders of magnitude. These results indicate that in lower collisionality SOL’s the tolerable downstream impurity densities may be higher than would be predicted by fluid simulations, allowing for higher radiated power while avoiding unacceptable core contamination. Our results highlight the importance of kinetic simulations for divertor design and optimization for fusion pilot plants.

Computational fluid dynamics↗
DOE OSTI2015

Angular radiation temperature simulation for time-dependent capsule drive prediction in inertial confinement fusion

The x-ray drive on a capsule in an inertial confinement fusion setup is crucial for ignition. Unfortunately, a direct measurement has not been possible so far. We propose an angular radiation temperature simulation to predict the time-dependent drive on the capsule. A simple model, based on the view-factor method for the simulation of the radiation temperature, is presented and compared with the experimental data obtained using the OMEGA laser facility and the simulation results acquired with VISRAD code. We found a good agreement between the time-dependent measurements and the simulation results obtained using this model. The validated model was then used to analyze the experimental results from the Shenguang-III prototype laser facility. More specifically, the variations of the peak radiation temperatures at different view angles with the albedo of the hohlraum, the motion of the laser spots, the closure of the laser entrance holes, and the deviation of the laser power were investigated. Furthermore, the time-dependent radiation temperature at different orientations and the drive history on the capsule were calculated. The results indicate that the radiation temperature from “U20W112” (named according to the diagnostic hole ID on the target chamber) can be used to approximately predict the drive temperature on the capsule. In addition, the influence of the capsule on the peak radiation temperature is also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities-and their impacts on environmental processes-requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca–Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ~0.6 nm between alginate strands.

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

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

59 BASIC BIOLOGICAL SCIENCES↗