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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Insights Into Lightning K‐Leader Initiation and Development From Three Dimensional Broadband Interferometric Observations

Abstract We report detailed observations of K‐leaders and the activity between them with the three‐dimensional Broadband Interferometric Mapping and Polarization system (BIMAP‐3D) at Los Alamos National Laboratory. It is found that K‐leaders have a general propagation trend of initial acceleration and then gradual deceleration, and the corresponding very high frequency (VHF) radiation power is exponentially correlated with the leader speed. Based on the 3D development and simultaneous electric field change measurement, some simple K‐leaders can be modeled with time‐evolving point charges at the propagating leader tip and at the stationary origin. We found that the charge magnitude increases during the initial acceleration stage and stays relatively constant for the rest of the development. K‐leaders are observed to interact with other branches; the branches affect the leader's propagation speed, and may affect the charge transfer. After the occurrence of a K‐leader, VHF emissions are quenched for several milliseconds. VHF sources then reappear in an impulsive and scattered manner as “twinkling,” and these sources are found not uniquely on the so‐called needles, but also on the main channel. These twinkling sources start near the apparent positive leader tip, and extend back toward the direction of the flash origin at about 10 5 m/s, while the apparent positive tip continues to extend forward at about 10 4 m/s. The twinkling extending toward the direction of flash origin appears to initiate the following K‐leader, although it may be interrupted by a K‐leader along a different branch, or simply die out without more K‐leader activity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations in biological samples, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the diffraction-limited three-dimensional distribution of the orientations and positions of ensembles of fluorescent dipoles that label biological structures. We share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model the distributions based on the polarization-dependent efficiency of excitation and detection of emitted fluorescence, using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labeled giant unilamellar vesicles, fast-scarlet-labeled cellulose in xylem cells, and phalloidin-labeled actin in U2OS cells. Additionally, we observe phalloidin-labeled actin in mouse fibroblasts grown on grids of labeled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

Science & Technology - Other Topics↗
DOE OSTI2024

Understanding spatial and temporal drivers of variation in tree hydraulic processes and their consequences for climate feedbacks (Final Technical Report)

This is the final technical report from the first phase of a project that changed institutions. The grant was titled “Understanding spatial and temporal drivers of variation in tree hydraulic processes and their consequences for climate feedbacks.” The overall objectives of this project were to (1) provide model‐compatible datasets of key plant hydraulic traits and status for model evaluation, parameterization and validation and (2) use these data to pinpoint ecosystem responses to a changing hydroclimate by addressing both long‐term climatic drying and episodic extreme droughts. We planned to address the objectives with three research activities to quantify plant responses to chronic water stress and episodic drought: (1) generate high frequency observations of soil and plant hydraulic data across different landscape positions at multiple sites, (2) quantify plant hydraulic trait plasticity in response to experimental soil moisture reduction in situ in two central hardwood forests, and (3) simulate the carbon consequences of incorporating plant hydrodynamics and plant acclimation to water stress in the DOE‐sponsored plant hydrodynamics model FATES‐HYDRO. As of the transfer of this project to another institution, we had made substantial progress on activities 1 and 2, and started activity 3.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

DASSH-F: Subchannel Based Thermal Analysis

The DASSH thermal analysis code is designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. The advantage of using DASSH over a hand calculation is that it has a more rigorous treatment of the pin power distribution and coolant heat transfer within an assembly and between assemblies. The advantage of using DASSH over a conventional 3D subchannel code or a computational fluid dynamics code (CFD) is that it can obtain the desired solution in a matter of minutes in serial with minor computer memory needs. The DASSH methodology for pin lattice models is virtually identical to SUPERENERGY-2 with additional functionalities taken from follow on work to SUPERENERGY-2 done at ANL in the 1980s. DASSH today is an integral component of the Argonne Fast Reactor analysis suite for reactor design work. DASSH obtains the power distribution from a coupled neutron-gamma heating calculation in GAMSOR (including DIF3D) at each time point of a companion fuel cycle analysis calculation with REBUS. The domain in DASSH assumes a hexagonal grid typical for fast reactors with much of the geometry information taken from the DIF3D model. DASSH assumes the assemblies that are loaded into each grid position are ducted to control the coolant flow. The user can alternatively provide their own geometry and power profile instead of inheriting it from DIF3D. Considerable detail is given on the subchannel formulation of DASSH in this document. Much of the formulation and design of the code builds upon research done by previous authors with little new investigation. Thus the decisions made in developing the subchannel model used in DASSH have their origins over 50 years ago. Much of the heat transfer methodology in DASSH is built upon correlations for both the coolant mixing and heat transfer coefficients for pins and ducts. DASSH is thus not a rigorous treatment of a given problem, but a rapid assessment of the temperature field that has known limitations with respect to an experimental measurement or CFD calculation. The DASSH input and output are detailed along with usage of the software. The DASSH output provides tables of evaluated material properties and key coolant and pin temperature results. DASSH can create Python scripts that generate domain summary pictures. DASSH can also generate assembly temperature maps and VTK output files which allow the DASSH solution to be visualized. As the primary purpose of the DASSH software is to compute the coolant and fuel pin temperature distribution for a given model of a reactor, much of the output focus is giving the user quick summary tables needed to assess the performance of a given orifice flow specification. The present version of DASSH has a crude orifice search capability and a sufficient orifice flow search capability. The flow search tries to meet user specified constraints for 1) peak 2-sigma clad temperature, 2) peak coolant temperature, and 3) desired bulk outlet temperature. This document serves as the manual for the Fortran based DASSH software that was developed to replace the Python version of DASSH developed as part of the VTR program.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Structure-controlled intramolecular charge transfer in asymmetric pyrene-based luminogens: synthesis, characterization and optical properties

Full-colour emitting materials have been widely studied driven by their promising potential application in fluorescence imaging and optoelectronic devices. In this paper, the synthesis and charactization of four asymmetric D–A type pyrene-based luminogens 2 is presented. Here, the experimental results revealed that this type of pyrene derivative possesses tunable optical properties by introducing D/A groups at the 1-, 3-positions and K-region (5-position) of the pyrene core. Wide emission bands from deep blue (429 nm) to yellow (567 nm) were obtained in different solutions or states. Combined with the theoretical calculations, this work provides an efficient strategy to develop pyrene-based full-colour photoelectric materials.

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

A Novel Technique for Distributed Measuring of Strain in the Vadose Zone

Characterizing water content and pressure changes in the vadose zone is important to understanding a variety of geologic processes, ranging from permeability, to evapotranspiration, and aquifer recharge. Changes in water content, or pressure, cause strain in the solid porous medium of the vadose zone, and it is possible that measuring those strains could be used a characterization tool. The Coherence-length-gated Microwave Photonics Interferometry (CMPI) technique measures strain at high resolution along many intervals defined by pairs of reflectors distributed along an optical fiber. This technique has recently been developed at Clemson University, and it has the spatial, and temporal resolution to characterize the strains that are expected to occur with hydrologic changes in the vadose zone. However, the technique has never been used to measure strain in porous media, so its capabilities remain uncertain. The objective of this thesis is to evaluate the ability of using CMPI to measure strain changes in the vadose zone. The research approach consists of conducting laboratory tests using a column filled with sand that was subjected to changes in water content and pressure. An optical fiber with CMPI reflectors was deployed in a high surface area ribbon and used to measure strain along the axis of the column. The column was made from 8-inch, Schedule 40 PVC pipe (75 cm tall, 20 cm inner diameter) and filled with medium-grained sand (K = 2.5x10-6 m/s, porosity = 0.28, Coefficient of Uniformity = 2, van Genuchten (n = 4.34 and  = 0.00039 m-1), Young’s Modulus = 18 – 47 MPa). Five pressure and four temperature sensors attached to probes inserted into the wall. The optical fiber includes five reflectors spaced 10 cm apart on the inside and outside of the column along the vertical axis. Strain measurements are made between pairs of reflectors. The reflectors are created in 250-micron-diameter acrylate-coated single mode Corning SMF28e+ optical fiber using a femtosecond laser. The optical fiber was laminated between two pieces of polyester film creating a large surface area to transfer strain from the porous media to the optical fiber. The experiments were conducted by filling the column from the bottom or infiltrating water from the top. The water was allowed to equilibrate to room temperature prior to each test in order to limit thermoelastic strain. Five injection tests with a rate of 250 ml/min and three infiltration tests at varying rates were conducted, and the results show patterns of strain and pressure are generally similar. Hydrologic conditions define three zones based on the pressure magnitude and distribution. 1.) Ambient Zone where the pressure heads are quasi-static and the pressure gradient is roughly unity (head gradient of zero). This is the uppermost zone and is characterized by negative pressures. 2.) Transition Zone where the pressures increase from ambient to zero, are changing relatively rapidly and the pressure gradient is relatively steep (pressure head gradients of 2). The Transition zone is 10 to 15 cm thick. 3.) Positive Pressure Zone where the pressure is positive, the rate of change is slower than in the transition zone and the gradient is flatter (pressure head gradient 1.1 to 1.2). This is the lowest zone in the column. Injection of water causes the pressure to increase and the three zones to move upward. The Transition zone moves at a rate of approximately 0.0002 m/s +/- .00005, according to analyses of pressure profiles. This is the same as the average velocity of the water calculated as volumetric flux/effective porosity =5.4x10-5 m/s/0.28. Strain signals in the range of 10s  were observed with a noise level of generally less than 0.1  (signal to noise ratio of greater than 100) during injection and drainage. The spatial and temporal distributions of strain caused by injection depend on the location of the moving pressure zones. The locations of the different pressure zones were determined from pressure profiles at different times and these data were transferred to strain time series. This showed that strain in the Ambient pressure zone is either unchanged or slightly compressive, whereas strain in Transition zone is tensile and roughly proportional to the pressure change, and strain ranges from tensile to compressive in the Positive Pressure zone. In general, the strain is variable at the top of the Positive Pressure zone, but it appears to be consistently tensile lower in the zone. The spatial distribution of strain causes three distinct stages in the strain times series measured between pairs of CMPI reflectors. The strain is unchanged or slightly compressive during Stage 1, it increases (positive strain is tensile) approximately linearly at a rate of 0.02 to 0.03 μ/s during the Stage 2, and then flattens out in Stage 3. The strain increases again during Stage 4 of the time series. The pressure also changes in stages. It is unchanged during Stage 1 and then increases relatively rapidly at a rate of between 4 and 10 Pa/s during Stage 2 and continues to increase during Stages 3 and 4, but at a rate slightly slower than during Stage 2 (from 2.5 to 3.5 Pa/s). The rates of pressure and strain change are consistent with basic analyses. The rate of pressurization is similar to the calculated velocity of flow in the saturated zone, and this is similar to the measured velocity of the strain increase. The ratio of the pressurization rate and strain rate during Stage 2 (2.5 (Pa/s) /0.03 (μ/s)) is 80 MPa, which is approximately equal to the upper range expected considering the uniaxial compression and the Young’s Modulus of the sand. An interesting effect occurs when the upper surface of the sand becomes saturated. Significant compression (several 10s of ) occurs as the pressure and saturation increase at the upper surface. Compression occurs throughout the column, but the effect is greatest at the top of the column. The rate of compression is fastest slightly before ponding occurs, but it slows markedly and nearly stops when water starts to accumulate at the surface (ponding). This effect reverses when the surface of the sand is drained, resulting in tension throughout the column. The compression caused by this effect can be as large or larger than the tensile strain that accumulated during filling. This effect was unexpected because increasing pressure is normally associated with tensile strain. Nevertheless, this effect was observed consistently in all tests where the pressure changes at the upper surface, including tests where water was injected from below or infiltrated from above. This effect behaves as if the pore pressure at the upper surface of the sand exerts a normal force on the boundary (increasing pore pressure exerts a downward compression on the boundary). The results of these laboratory experiments indicate that CMPI can measure strain caused by fluid pressure changes in the vadose zone with a signal to noise ratio of 100 or more. Injection and drainage cause a strain signal that is complex, but repeatable. The magnitudes of the strain signal are consistent with magnitudes that are expected based on poroelastic calculations using independently measured properties of the sand. These results indicate that the CMPI technique with an optical fiber laminated in a polyester ribbon generates data that represent the strain distribution during hydrologic processes of imbibition and drainage in variably saturated sand. This suggests that distributed strain measurements using CMPI could be a viable approach for evaluating processes in the vadose zone, laying the groundwork for future field implementation.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Electronic interactions and stability issues at the copper-graphene interface in air and in alkaline solution under electrochemical control

A micro-electrochemical cell is sealed with a polymer-free single-layer graphene (SLG) membrane to monitor the stability of Cu nanoparticles (NPs) attached to SLG, as well as the interfacial electronic interactions between Cu NPs and SLG both in air and in a mildly alkaline aqueous solution under electrochemical control. A combination of techniques, including in-situ Kelvin probe force microscopy (KPFM) and ex-situ electron microscopy, are applied. When Cu NPs are metallic at cathodic potentials, there is a relatively bias-independent offset in the SLG work function due to charge transfer at the Cu-SLG contact. When Cu NPs are oxidized at anodic potentials, on the other hand, the work function of SLG also depends on the applied bias in a quasi-linear fashion due to electrochemical gating, in addition to charge transfer at the CuOx-SLG contact. Furthermore, Cu NPs were found to oxidize and detach from SLG when kept under anodic potentials for a few hours, whereas they remain adhered to SLG at cathodic potentials. This is attributed to water intercalation at the CuO-SLG interface associated with the enhanced hydrophilicity of positively polarized graphene, as supported by the absence of Cu detachment following oxidation by galvanic corrosion in air.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms

We report optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance. Yet, the scalability and transferability of machine learning models remain as challenges in creating a complete pipeline for the simulation and analysis of large molecular systems. In this work we present a scalable Bayesian optimization framework, which leverages dynamic spawning of jobs through the Message Passing Interface (MPI) to run multiple parallel molecular dynamics simulations within a parent MPI job to optimize heat transfer at the silicon and aluminum (Si/Al) interface. We found a maximum of 50% increase in the ITC when introducing a two-layer intermixed region that consists of a higher percentage of Si. Because of the random nature of the intermixing, the magnitude of increase in the ITC varies. We observed that both homogeneity/heterogeneity of the intermixing and the intrinsic stochastic nature of molecular dynamics simulations account for the variance in ITC.

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

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

First Ever Polymer Flood Field Pilot To Enhance The Recovery Of Heavy Oils On Alaska’s North Slope - Pushing Ahead One Year Later

In June 2018 the team embarked on an ambitious project to address the slow development pace of Alaska’s 20+ billion barrels heavy oil resource via the first ever polymer flood pilot. Following the successful commencement of the pilot in August 2018, the field demonstration, supporting laboratory experiments and numerical simulation have steadily progressed. A significant amount of valuable data and lessons learned have been collected, and are reported in this paper. The ongoing pilot and the research activities is making headway toward the primary objective of validating the use of polymer flooding for extracting heavy oil in Alaska’s challenging environment. The pilot is conducted in two pre-existing pairs of horizontal injectors and producers in an isolated fault block of the Schrader Bluff heavy oil reservoir at the Milne Point Field. A customized polymer blending and pumping unit injects HPAM polymer at a concentration of 1,750 ppm to achieve a target viscosity of 45 cP. Supporting coreflood laboratory experiments have focused on quantification of polymer retention in the rock, and effect of injection water salinity, polymer, and their combinations on oil recovery. The injection and production response of the pilot flood pattern is utilized to develop a history matched reservoir simulation model for forecasting oil recovery beyond the pilot. Finally, specially designed laboratory experiments address anticipated operating concerns regarding post-polymer breakthrough such as oil-water separation efficiency and polymer induced fouling of heater tubes. Polymer has been injected continuously since startup except for two short equipment modification shutdowns, and more recently a prolonged disruption due to polymer hydration issues at the J-pad field site. Cumulatively, over 600,000 lbs. of polymer has been injected, corresponding to ~7%PV. The two producers show significant decrease in the water cut, gradually increasing oil rate, and no polymer breakthrough. Two main observations from the coreflood are a significant uncertainty in polymer retention values, and positive oil recovery response to low salinity water (2,600 mg/liter TDS). The heterogeneity in the flood pattern presents some challenges in obtaining a robust history matched simulation model. Experimental results on produced fluids treatment indicate the formation of a dense polymer deposit, at certain conditions, on heating tubes that can negatively impact the heat transfer efficiency. The scientific knowledge, including the lessons learned during unanticipated shutdowns, quality control, logistics and field data that is being acquired from this effort has referential value for other planned EOR projects. Finally, by all indications, the polymer field pilot is steadily progressing toward achieving the ultimate goal of unlocking the massive heavy oil resources on Alaska North Slope (ANS).

Dandekar, Abhijit↗
DOE OSTI2023

Soft error-mitigating semiconductor design system and associated methods

A soft error-mitigating semiconductor design system and associated methods that tailor circuit design steps to mitigate corruption of data in storage elements (e.g., flip flops) due to Single Events Effects (SEEs). Required storage elements are automatically mapped to triplicated redundant nodes controlled by a voting element that enforces majority-voting logic for fault-free output (i.e., Triple Modular Redundancy (TMR)). Storage elements are also optimally positioned for placement in keeping with SEE-tolerant spacing constraints. Additionally, clock delay insertion (employing either a single global clock or clock triplication) in the TMR specification may introduce useful skew that protects against glitch propagation through the designed device. The resultant layout generated from the TMR configuration may relax constraints imposed on register transfer level (RTL) engineers to make rad-hard designs, as automation introduces TMR storage registers, memory element spacing, and clock delay/triplication with minimal designer input.

Miryala, Sandeep↗
DOE OSTI2024

Soft error-mitigating semiconductor design system and associated methods

A soft error-mitigating semiconductor design system and associated methods that tailor circuit design steps to mitigate corruption of data in storage elements (e.g., flip flops) due to Single Events Effects (SEEs). Required storage elements are automatically mapped to triplicated redundant nodes controlled by a voting element that enforces majority-voting logic for fault-free output (i.e., Triple Modular Redundancy (TMR)). Storage elements are also optimally positioned for placement in keeping with SEE-tolerant spacing constraints. Additionally, clock delay insertion (employing either a single global clock or clock triplication) in the TMR specification may introduce useful skew that protects against glitch propagation through the designed device. The resultant layout generated from the TMR configuration may relax constraints imposed on register transfer level (RTL) engineers to make rad-hard designs, as automation introduces TMR storage registers, memory element spacing, and clock delay/triplication with minimal designer input.

Miryala, Sandeep↗
DOE OSTI2020

Spectral solar irradiance on inclined surfaces: A fast Monte Carlo approach

Estimating spectral plane-of-array (POA) solar irradiance on inclined surfaces is an important step in the design and performance evaluation of both photovoltaic and concentrated solar plants. This work introduces a fast, line-by-line spectral, Monte Carlo (MC) radiative transfer model approach to simulate anisotropic distributions of shortwave radiation through the atmosphere as photon bundles impinge on inclined surfaces. This fast Monte Carlo approach reproduces the angular distribution of solar irradiance without the undesirable effects of spatial discretization and thus computes detailed POA irradiance values on surfaces at any orientation and also when surfaces are subjected to the anisotropic ground and atmospheric scattering. Polarization effects are also easily incorporated into this approach that can be considered as direct numerical simulation of the physics involved. Here, we compare our Monte Carlo radiative transfer model with the most widely used empirical transposition model, Perez4, under various conditions. The results show that the Perez4 model reproduces the more detailed Monte Carlo simulations with less than 10% deviation under clear skies for all relevant surface tilt and azimuth angles. When optically thin clouds are present, observed deviations are larger, especially when the receiving surface is strongly tilted. Deviations are also observed for large azimuth angle differences between the receiving surface and the solar position. When optically thick clouds are present, the two models agree within 15% deviation for nearly all surface orientation and tilt angles. The overall deviations are smaller when compared with cases for optically thin clouds. The Perez4 model performs very well (6.0% deviation) in comparison with the detailed MC simulations for all cases, thus validating its widespread use for practical solar applications. When detailed atmospheric profiles and cloud optical properties are available, the proposed fast Monte Carlo radiative model reproduces accurate spectral and angular POA irradiance levels for various atmospheric and cloud cover conditions, surface orientations, and different surface and ground properties.

42 ENGINEERING↗
DOE OSTI2022

Imaging Wavepackets in Real-Space & Disentangling Ultrafast Solvation Dynamics with High-Energy Ultrafast X-ray Scattering

The microscopic information of solute and solute-solvent motions can be measured using ultrafast diffuse x-ray scattering, and compared to molecular dynamics simulations, as demonstrated in studies of solvated molecular systems done in X-ray free-electron lasers. However, for the typical photon energies used in these experiments, the photon momentum transfer range was limited to lower Q values where the signals arising from different parts of the studied system overlap significantly. Recently, this limitation was greatly alleviated by extending the photon energy at the Linac Coherent Light-Source (LCLS), significantly increasing the accessible momentum transfer range. This improvement is transformative for ultrafast diffuse x-ray scattering measurements, enabling for the first time to disentangle the solute scattering difference signal, that persists to higher Q values, from the bulk solvent and solute-solvent cross-terms difference signals. In addition, it enhances the prediction ability of modeling and simulation methods such as the hybrid QM/MM approach. The extended Q range also opens the way to resolve in real-space details regarding coherent wavepackets motions beyond their center-of-mass positions. Here, we present the first results on high-energy (18keV) diffuse x-ray scattering in solution, demonstrating high fidelity time-resolved scattering and analysis of the photoexcited model photocatalysts PtPOP ([Pt2(POP)4]4-), and IrDimen ([Ir2(dimen)4]2+) in several solvents. These complexes provide ideal systems for demonstrating the ability of high-Q ultrafast scattering and QM/MM simulations to decompose ultrafast solvation dynamics into specific changes in the solute-solvent pair distribution function with a particular focus on how electronically excited states change the interaction between the solvent and photo-catalytically active metal sites. We introduce an approach to further utilize the high-energy capability and demonstrate a single-shot ultra-wide-angle X-ray Scattering modality using two perpendicular detectors, spanning a scattering angle range of more than 100 degrees, allowing to extend the accessible momentum transfer range up to Q~14 Å-1. We develop a model-free method to invert the x-ray scattering signals and enable the recovery of multiple pair-density motions that happen simultaneously, allowing us to directly measure in real-space nuclear wavepacket motions. . [1] Natan, Adi. "Real-Space Inversion and Super-Resolution of Ultrafast X-ray Scattering using Natural Scattering Kernels." arXiv preprint arXiv:2107.05576 (2021)

Natan, Adi↗
DOE OSTI2020

Tuning the Cation–Anion Interactions by Methylation of the Pyridinium Cation: An X-ray Photoelectron Spectroscopy Study of Picolinium Ionic Liquids

Here, X-ray photoelectron spectroscopy is used to investigate the impact of methylation on the electronic environment of pyridinium cations. Because of the electron-donating effect of the methyl group, there is a significant increase in electron density on the cationic nitrogen. The shift of the N 1s binding energy is inversely proportional to the anion basicity. The methylation position on the electronic environment of the cationic nitrogen is investigated. The N 1s binding energy follows the trend: 1-octylpyridinium > 1-octyl-3-picolinium > 1-octyl-4-picolinium > 1-octyl-2-picolinium, which is in good agreement with the cation acidity. The increase in the inductive effect subsequently weakens the cation–anion interactions through charge transfer from the anion to the cation, causing a subtle change in the electronic environment of the anion. Such an effect is noticeably reflected in the Br 3d binding energy. It shows that the Br 3d 5/2 binding energy of 1-octyl-2-picolinium bromide is 0.2 eV lower than that of 1-octylpyridinium bromide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cluster Dynamics Simulations of Intra-Granular Fission Gas Bubble Size and Pressure Evolution in UO 2

Fission gases such as xenon (Xe) play a critical role in determining the behavior and response of nuclear fuel. Given that Xe has little solubility in UO 2 , it accumulates and forms bubbles, which significantly impact fuel performance. Intra- and inter-granular bubble nucleation and growth can lead to fuel swelling, and once bubbles interconnect at grain boundaries, fission gas can be released into the plenum. At low temperatures, limited uranium vacancy mobility can restrict swelling, therefore causing the bubbles to become highly pressurized. Consequently, this can induce micro-cracking, promote fission gas release (increasing the likelihood of cladding failure), and even lead to fuel pulverization under accident conditions such as a loss of coolant accident. As bubble evolution is strongly influenced by local temperature and fission rate, markedly different behavior occurs across the radial profile of the fuel pellet. Capturing the mechanisms that underpin bubble evolution is therefore important to predict these behaviors in the fuel. Previous models describing important mechanisms informed by lower length scale simulations have been developed under the NEAMS program. These can describe the evolution of a single bubble type (i.e., single value for radius and pressure) at each position in the pellet, for instance using the Centipede cluster dynamic code. However, in reality, a full distribution in bubble sizes and pressures exists within the microstructure at a given position in the pellet. To address this the cluster dynamics code Xolotl, which can predict Xe and vacancy phase space (i.e., bubble distributions) for intra-granular bubbles, has been used before. Prior work benchmarked the Xolotl code against the Centipede cluster dynamics code to ensure compatibility and to verify that mobile defect properties are adequately transferred between the two codes, along with some physics improvements. In this work, we go further by introducing a physics-based set of improvements that will allow us to accurately predict bubble size distributions and internal bubble pressures under representative UO 2 irradiation conditions. The improvements include (i) coupling bubble-defect reaction energies to a virial equation of state (EOS), (ii) including a bubble surface tension contribution, (iii) incorporating radiation-induced re-solution of Xe and vacancies, (iv) enabling pressure-driven dislocation loop punching through an effective emission of interstitial clusters informed by interstitial loop energetics, (v) accounting for radiation induced athermal diffusion of Xe, and (vi) implementing a Booth-type grain boundary sink representation for all mobile defects and defect clusters. After these modifications, we observe good agreement of Xolotl fission gas bubble size and concentration predictions with legacy experimental measurements. Additionally, it allows the distribution of Xe bubble pressures and radius to also be predicted and compared to data produced through the Advanced Fuels Campaign (AFC) program. Here, we have done this by running simulations under conditions similar to the AFC post-irradiation examination (PIE) samples irradiated at North Anna 2 light water reactor (LWR). Our results shows excellent agreement with these experimental measurements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae 1,2 . These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching 3-6 . Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Further, only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties 7 , we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

59 BASIC BIOLOGICAL SCIENCES↗