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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Subject-specific multi-scale modeling of the fate of inhaled aerosols

Determining the fate of inhaled aerosols in the respiratory system is essential in assessing the potential toxicity of inhaled airborne materials, responses to airborne pathogens, or in improving inhaled drug delivery. The availability of high-resolution clinical lung imaging and advances in the reconstruction of lung airways from CT images have led to the development of subject-specific in-silico 3D models of aerosol dosimetry, often referred to as computational fluid-particle-dynamics (CFPD) models. As CFPD models require extensive computing resources, they are typically confined to the upper and large airways. These models can be combined with lower-dimensional models to form multiscale models that predict the transport and deposition of inhaled aerosols in the entire respiratory tract. Understanding where aerosols deposit is only the first of potentially several key events necessary to predict an outcome, being a detrimental health effect or a therapeutic response. To that end, multiscale approaches that combine CFPD with physiologically-based pharmacokinetics (PBPK) models have been developed to evaluate the absorption, distribution, metabolism, and excretion (ADME) of toxic or medicinal chemicals in one or more compartments of the human body. CFPD models can also be combined with host cell dynamics (HCD) models to assess regional immune system responses. Here, this paper reviews the state of the art of these different multiscale approaches and discusses the potential role of personalized or subject-specific modeling in respiratory health.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Transcriptional networks underlying a primary ovarian insufficiency disorder in alligators naturally exposed to EDCs

Interactions between the endocrine system and environmental contaminants are responsible for impairing reproductive development and function. Despite the taxonomic diversity of affected species and attendant complexity inherent to natural systems, the underlying signaling pathways and cellular consequences are mostly studied in lab models. To resolve the genetic and endocrine pathways that mediate affected ovarian function in organisms exposed to endocrine disrupting contaminants in their natural environments, we assessed broad-scale transcriptional and steroidogenic responses to exogenous gonadotropin stimulation in juvenile alligators (Alligator missippiensis) originating from a lake with well-documented pollution (Lake Apopka, FL) and a nearby reference site (Lake Woodruff, FL). Here, we found that individuals from Lake Apopka are characterized by hyperandrogenism and display hyper-sensitive transcriptional responses to gonadotropin stimulation when compared to individuals from Lake Woodruff. Site-specific transcriptomic divergence appears to be driven by wholly distinct subsets of transcriptional regulators, indicating alterations to fundamental genetic pathways governing ovarian function. Consistent with broad-scale transcriptional differences, ovaries of Lake Apopka alligators displayed impediments to folliculogenesis, with larger germinal beds and decreased numbers of late-stage follicles. After resolving the ovarian transcriptome into clusters of co-expressed genes, most site-associated modules were correlated to ovarian follicule phenotypes across individuals. However, expression of two site-specific clusters were independent of ovarian cellular architecture and are hypothesized to represent alterations to cell-autonomous transcriptional programs. Collectively, our findings provide high resolution mapping of transcriptional patterns to specific reproductive function and advance our mechanistic understanding regarding impaired reproductive health in an established model of environmental endocrine disruption.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chemical contributions to silicon anode calendar aging are dominant over mechanical contributions

Silicon (Si) anodes are a promising candidate for increasing the energy density of lithium (Li)-ion batteries for electric vehicles. However, they have recently been identified as having poor calendar life that is insufficient for commercial needs, in addition to the well-known issue of their poor cycle life resulting from large volume expansion. Here, a specially designed protocol with variable rest periods between intermittent cycling is used to evaluate the impact of the mechanical disruption of Si and solid electrolyte interphase (SEI) from cycling on calendar aging measurements. Si was found to undergo more mechanical degradation during calendar aging with intermittent cycling than graphite. However, Si anode capacity fade was still dominated by time, especially for rest periods greater than or equal to 1 month between cycling. Postmortem dQ/dV half-cell analysis indicated this was mainly due to Li inventory loss and an increase in electrode resistance. Isothermal microcalorimetry further demonstrated that Si passivation is more disrupted than graphite passivation with intermittent cycling and suggested that there may be a chemical buildup of a detrimental species in the electrolyte, leading to a large spike in heat after the Si and SEI are disrupted by cycling.

25 ENERGY STORAGE↗
DOE OSTI2022

Best Practices in PEC Water Splitting: How to Reliably Measure Solar-to-Hydrogen Efficiency of Photoelectrodes

Photoelectrochemical (PEC) water splitting, which utilizes sunlight and water to produce hydrogen fuel, is potentially one of the most sustainable routes to clean energy. One challenge to success is that, to date, similar materials and devices measured in different labs or by different operators lead to quantitatively different results, due to the lack of accepted standard operating procedures and established protocols for PEC efficiency testing. With the aim of disseminating good practices within the PEC community, we provide a vetted protocol that describes how to prepare integrated components and accurately measure their solar-to-hydrogen (STH) efficiency (η STH ). This protocol provides details on electrode fabrication, η STH test device assembly, light source calibration, hydrogen evolution measurement, and initial material qualification by photocurrent measurements under monochromatic and broadband illumination. Common pitfalls in translating experimental results from any lab to an accurate STH efficiency under an AM1.5G reference spectrum are discussed. A III–V tandem photocathode is used to exemplify the process, though with small modifications, the protocol can be applied to photoanodes as well. Dissemination of PEC best practices will help those approaching the field and provide guidance for comparing the results obtained at different lab sites by different groups.

08 HYDROGEN↗
DOE OSTI2023

NbTaV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution ternary alloys niobium-tantalum-vanadium (Nb-Ta-V). The first-principle code that has been used to run the calculations is the closed-source Vienna Ab-Initio Simulation Package (VASP). The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 8. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 10,500 randomized atomic structures over 105 chemical compositions. The calculations have been collected on NERSC-Perlmutter using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for ternary alloys is AXBYCZ, where A, B, and C refer to the constituents, and X, Y, and Z are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. 0.POSCAR: input file that defines the atomic structure of a system 3. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 4. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 6. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 7. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 8. OUTCARL: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 10. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 11. vasprun.xml: contains similar information to OUTCAR, but in an xml format. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Non-thermal electron acceleration from magnetically driven reconnection in a laboratory plasma

Magnetic reconnection rapidly converts magnetic energy into some combination of plasma flow energy, thermal energy and non-thermal energetic particles. Various reconnection acceleration mechanisms have been theoretically proposed and numerically studied in different collisionless and low-β environments, where β refers to the plasma-to-magnetic pressure ratio. These mechanisms include Fermi acceleration, betatron acceleration, parallel electric field acceleration along magnetic fields and direct acceleration by the reconnection electric field. However, none of them have been experimentally confirmed, as the direct observation of non-thermal particle acceleration in laboratory experiments has been difficult due to short Debye lengths for in situ measurements and short mean free paths for ex situ measurements. Here we report the direct measurement of accelerated non-thermal electrons from magnetically driven reconnection at low β in experiments using a laser-powered capacitor coil platform. We use kilojoule lasers to drive parallel currents to reconnect megagauss-level magnetic fields in a quasi-axisymmetric geometry. The angular dependence of the measured electron energy spectrum and the resulting accelerated energies, supported by particle-in-cell simulations, indicate that the mechanism of direct electric field acceleration by the out-of-plane reconnection electric field is at work. Scaled energies using this mechanism show direct relevance to astrophysical observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Multi-Sourced Collaboration for the Production and Refining of Rare Elements and Critical Metals (Final Technical Report)

The project objective was to develop a feasible and cost-effective method for recovering rare earth elements (REEs) and critical materials (CMs) from coal and coal byproducts, resulting in high-purity individually separated REEs and CMs. The targeted REEs included Y, Pr, Nd, Gd, Dy, and Sm, with a purity of over 99.5%, while the CMs included Co, Mn, Ga, Sr, Li, Ni, Zn, and Ge, with a purity of over 90%. The project aimed to design a prototype facility capable of producing 1-3 tonnes/day of high-purity REO mixes. The work was divided into four designated circuits: 1) REE extraction and concentration, 2) REE separation and purification, 3) RE metal production, and 4) CM production. To achieve these goals, the project involved 11 tasks, including technology reviews, research, process flow diagram development, mass balance estimation, and preliminary technical-economic analysis. The project team included researchers from the University of Kentucky, University of Alabama and Virginia Tech as well as process specialists from Argonne National Laboratory. MP Materials provided technical support regarding rare earth markets and processing while Alliance Coal performed resource assessment. The project included a market analysis for Nd/Pr, Tb, Dy, Gd, Y, Co, Mn, Li, Sr, Ga, Ni, Zn, and Ge. These analyses provided insights into the supply and demand trends as well as historic and future projections of market price relative to purity requirements for these elements. Two coal resources were selected for the project: the West Kentucky No. 13 (Baker) Seam and an undisclosed lignite resource in the Illinois coal basin. The estimated quantities of REEs in these resources were calculated based on production samples and drilling data. It was estimated that there is adequate supply for an operation producing one metric ton daily of higher purity mixed rare earth oxides (MREO) for approximately 20 years at a site located in western Kentucky. In Circuit 1, project data was obtained from a pilot heap leach and REE concentration facility. It was concluded that the existing circuit, which generated a MREO concentrate, two types of CM mixed products, and Li- and Sr-containing waters, would be suitable feed for circuits 2-4. Data from the first-of-its-kind coal coarse refuse heap leach pilot pad played a crucial role in estimating reliable elemental concentrations of the pregnant leaching solution (PLS). The average total REE concentration in the PLS was found to be 28.6 ppm. In Circuit 2, several concepts were explored including a novel process referred to as solvent-assisted chromatography (SAC). This concept involved a novel columnar reactor that incorporated multiple mixer/settlers, thereby enabling the operation of counter-flowing aqueous and organic phases. Unfortunately, due to project time constraints, a complete fundamental modeling analysis could not be completed to fully evaluate the technology. Molten salt electrowinning was considered as an alternative for circuit 3 following circuit 2 purification circuit utilizing the novel SAC process. A mass and energy balance of Nd reduction to metal in a fluoride containing molten salt electrolyte was conducted. Comparisons were made with the current state of Asian molten salt electrorefining, and potential improvements in siphoning rare earth metals (REM) from the reactor were presented. A cost estimate was performed for the production of 1 tonne per day, which yielded a total of $2.29 million for the nine electrowinning (EW) cells required. The selected option for circuits 2 and 3 was a plasma distillation process, which initially separates rare earth elements (REEs) from other elements. This is followed by selective electrowinning in various ionic liquids. The selection was made on the basis of thermodynamic modeling and experimental data previously published by a project partner. The combination offers an innovative approach to integrated refining and RE metal production. For Circuit 4, an extensive literature review was conducted for the processing of the CMs. The ultimate decision was to utilize a combined plasma and ionic liquid process as well to produce individual high-purity concentrates of Zn, Ni, Co, Mn, and Mg. A separate flowsheet for Li and Sr was recommended, which would yield carbonates of these elements. Due to the lack of suitable experimental data at this time, a process recommendation could not be provided but several methods have been proposed for consideration. Lastly, a techno-economic analysis (TEA) was conducted to assess the effectiveness of the proposed process for further investigation. The TEA results revealed a capital expense (CapEx) of $737 million and an annual operational expense (OpEx) of $220 million. Due to the selected elements, the hypothetical heap leach pad can produce 1 metric tonne per day of REO equivalent, but a conscious decision was made to only treat targeted REEs, resulting in the production of 0.4 metric tonne of REM. An estimated annual revenue of $90.87 million was projected based on standard market pricing information provided by the funding agency. During the TEA, ten different modules were evaluated for costing purposes. The precipitation circuit was identified as the largest single operational expense, followed by the Mg/Mn process due to the amount of treated metal. In terms of capital expenditures, the heap leach process incurred the highest cost, followed by the Mg/Mn process. The scalability of the plasma process is a crucial consideration since the reactors cannot be scaled beyond the largest demonstrated size due to their reliance on surface area of the slag and vapor phase. The purity estimate for the REEs are generally 98%±2% to produce a metal. The purity level being lower than the project objective was due to the lack of specific experimental data needed to tighten the tolerance of the estimates. Based on literature and previous experience, the CMs are estimated as follows; Ga (95%+, metal), Sr (95%+, carbonate), Li (95%+, carbonate), Ni (98%±2%, metal), Zn (95%+, metal sponge), Ge (95%+, metal), Co (98%±2%, metal), and Mn (98%±2%, metal).

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Dataset of theoretical multinary perovskite oxides

Perovskite oxides (ternary chemical formula ABO 3 ) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent (chemical formula $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$) chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$ compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, 69,407 $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ compositions were generated in the a - b + a - Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with density functional theory (DFT) using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔH f ) and decomposition enthalpies (ΔH d ) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ perovskite structures using MP-compatible DFT calculations.

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

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗
DOE OSTI2022

IM3/HyperFACETS Thermodynamic Global Warming (TGW) Simulation Datasets

Publication For a thorough description of the methods, see the peer-reviewed paper: Jones, A.D., Rastogi, D., Vahmani, P. et al. Continental United States climate projections based on thermodynamic modification of historical weather. Sci Data 10, 664 (2023). https://doi.org/10.1038/s41597-023-02485-5 Overview The IM3 / HyperFACETS climate simulations provide 40-year historical (1980-2019) as well as four 80-year future simulations (2020-2099) over the U.S. The future simulations are split into near (2020-2059) and far future (2060-2099) segments. The future scenarios span a range of plausible changes in future climate (both Global Circulation Model (GCM) and Representative Concentration Pathways/Shared Socioeconomic Pathway (RCP/SSP) dimensions). The simulations provide climate variables with high spatiotemporal resolution (25 hourly variables and 207 3-hourly variables at 12 km2). The datasets are generated using dynamical downscaling with the WRF (Weather Research and Forecasting) model (version 4.2.1) and therefore preserve physical consistency across variables. WRF is a state-of-the-art, fully compressible, non-hydrostatic, mesoscale numerical weather prediction model. WRF is coupled with an urban canopy model (UCM), which resolves urban surfaces. The future scenarios were developed using a thermodynamic global warming approach where past events are replayed under a range of future warming conditions. These scenarios therefore provide a perspective on potential increases in extreme event intensity, geographic scope, and duration, with previously non-extreme conditions potentially crossing new thresholds to be considered extreme by today's standards. This approach is not intended to estimate future changes in extreme event frequency that might result from changes in large-scale atmospheric dynamics. This dataset has NOT been bias corrected. A bias corrected version of selected variables is under development and will be released here when available. Scenarios Files Data for each scenario is provided in weekly NetCDF files. 25 variables are available at hourly resolution, and 207 variables are available at three-hourly resolution. Spatial resolution is 12km and spans the conterminous United States (CONUS), including some areas of Canada and Mexico, resulting in a grid of 424 by 299 cells. The spatial projection is a Lambert Conformal Conic with the following proj-string: "+proj=lcc +lat_0=40.0000076293945 +lon_0=-97 +lat_1=30 +lat_2=45 +x_0=0 +y_0=0 +R=6370000 +units=m +no_defs". The available scenarios and simulation periods are listed below: historical | 1980 - 2019 rcp45cooler | 2020 - 2059 rcp45cooler | 2060 - 2099 rcp45hotter | 2020 - 2059 rcp45hotter | 2060 - 2099 rcp85cooler | 2020 - 2059 rcp85cooler | 2060 - 2099 rcp85hotter | 2020 - 2059 rcp85hotter | 2060 - 2099 * The first year (1979, 2019, and 2059) of data within each scenario represents a model warmup period and should not be used. These are located in the `spinup_files` directory. Historical year 2020 is considered an extra year of data beyond the simulation period and can be found in the `additional_files` directory. For information on specific variables and a more in-depth discussion of methodology, please refer to the data landing page at https://tgw-data.msdlive.org. Delta Warming Files The global and CONUS warming deltas for each scenario are provided in degrees Celsius annually and monthly. Restart Files Yearly restart files are provided for each scenario which can be used to restart the WRF model at a particular point in time. Spinup Files The first year of data within each simulation period represents a model warmup period and should not be used. The files are provided here for the sake of reproducibility. Additional Files Additional years of data are provided as an extension of the historic simulation.

Jones, Andrew D.↗
DOE OSTI2025

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Roll to Roll (R2R) Manufacturing of Electrolysis Electrodes for Low Cost Hydrogen Production: Cooperative Research and Development Final Report, CRADA Number CRD-18-00780

NREL, Argonne National Laboratory (ANL) and Oak Ridge National Laboratory (ORNL), which are also referred to collectively herein as the "Contractors" will perform electrode ink development and characterization, focusing on 1) inks with appropriate properties for R2R (gravure and slot-die) coating onto PFSA membrane and 2) catalysts suitable for electrolysis. Participant will develop acceptance criteria and characterization methods for direct coating on the membrane. The purpose of this project is to show feasibility for cost reduction of the electrode through increased throughput and improved material utilization. Successful completion of this project will result in more affordable hydrogen production via proton exchange membrane (PEM) electrolysis by substantially reducing the anode precious metal content and catalyst-coated membrane processing costs. Assists laboratory in achieving programmatic scope, adds new capability to the laboratory's core competencies. This project uses and enhances the laboratory's core competencies, and enhances U.S. competitiveness by utilizing DOE developed intellectual property and/or capabilities. This project will benefit the Fuel Cell subprogram within the EERE Fuel Cell Technologies Office (FCTO) by actively developing materials, formulations, components, and processes for PEM electrolyzer stacks for overcoming critical technical barriers to widespread hydrogen production for zero-emission transportation applications. Through this JWS, NREL, ANL and ORNL are assisting a key domestic industry partner, Proton Energy Systems, Inc., in the area of low-cost electrolyzer electrode formulation and coating technology. After completion of this project, NREL, ANL and ORNL will be able to verify whether the direct deposit coating processes investigated are suitable for producing CCMs for PEM electrolyzers, which is of great interest and benefit to the DOE EERE Fuel Cell Technologies Office (FCTO) and H2@Scale missions.

08 HYDROGEN↗
DOE OSTI2020

A Systems Biology Approach to Energy Flow in H 2 Producing Microbial Communities: Microbial Mats

This report describes the results of work conducted at NASA Ames Research Center, in collaboration with investigators at Lawrence Livermore National Laboratory, during the time period 12/15/2014 to 12/15/2017. The work was an extension of a collaboration with LLNL that began in 2008. Work this reporting period focused primarily on tasks related to microbial mats from both the Elkhorn Slough and Baja California field sites, including the analysis and publication of data produced prior to 12/15/2014. During this reporting period, in addition to the microbial mat work, we also conducted a series of experiments with a particular algal-bacterial association (C. sorokiniana and A. brasilense). A number of aspects of this well-characterized algal-bacterial association enabled us not only to further our understanding of interactions between these particular organisms, but to apply that knowledge and techniques to our collection of microorganisms isolated from microbial mats. Microbial mat experiments focused both on intact mat communities and on cultures of organisms isolated from the mats (the Microbial Mat Living Library). In a series of co-culture experiments, we documented both positive and negative interactions amongst heterotrophic and autotrophic isolates of microbial mat microorganisms. One particularly important and novel mat cyanobacterium (ESFC-1) was studied in detail. We developed techniques to pursue an investigation of functional redundancy (the idea that closely related organisms perform identical roles in a community) in cyanobacterial autotrophs in the Elkhorn Slough microbial mat. In those experiments, we documented numerous instances of increases in growth rate between co-cultures of two organisms (relative to their growth rate in isolation) performing what would seem to be identical functional roles. Simplified microbial mat communities consisting of organisms from the Microbial Mat Living Library were constructed and studied in laboratory experiments. The “constructed mats” were grown in standard laboratory glassware and plasticware, but cultures were also combined with artificial materials in an effort to re-create the three-dimensional structure of naturally occurring microbial mats. These constructed mats re-created a number of functions attributable to natural microbial mats (N-fixation, H2-production) and simplified their study using molecular ecological techniques due to the smaller number of microbial “species” present. Cyanobacteria which migrated in response to vertical variations in light intensity (irradiance) obtained characteristic positions in constructed mats that were similar to their positions in natural mats. A detailed investigation of nitrogen cycling in both the Baja California and Elkhorn Slough microbial mats was initiated during this reporting period. The nitrogen cycle in the microbial mats has not been studied in depth, despite the fact that nitrogen usually limits growth in marine environments. The organisms conducting nitrogen cycling in both microbial mats were studied using the genomes available from earlier work on these mats, as well as with a targeted approach using molecular ecological methods developed here. Quantitative measurements of rates of nitrogen transformations were made using stable isotopically labeled nitrogen. The processes quantified and examined using molecular ecological methods included: nitrogen fixation, ammonification, ammonium and nitrate assimilation, denitrification, anaerobic oxidation of ammonium, and dissimilatory nitrate reduction to ammonium. In a series of experiments designed to examine a potential application for microbial mats, we demonstrated that both Elkhorn Slough and Baja California microbial mats were very effective in removing large quantities of both nitrate and ammonium from waste streams containing these compounds at levels where they would be considered to be pollutants. Considerable effort was expended during this reporting period to analyze, and prepare for publication, metagenomes and metatranscriptomes collected from two experimental manipulations of microbial mats. The first, a diel study, was conducted in November 2011, while the second, an investigation of the effects of sulfate on community composition, was conducted during this reporting period. For the earlier study, reference-based and reference-free methods were used to assess microbial ecology and genetic partitioning in these complex microbial systems, and that work is available as a pre-print. Four metagenomes from the same experiment were published. In the second, longer (nearly 200 day) manipulation, rRNA iTag libraries for cDNA and DNA were analyzed to determine the effects of sulfate concentration on microbial mat community composition over the course of the experiment. Work on the algal-bacterial association (Chlorella sorokiniana and Azospirillum brasilense) focused initially on demonstrating the transfer of carbon and nitrogen between the partners, using stable isotopic labeling and the LLNL NanoSIMS. Subsequently, the potential role of diazotrophy (nitrogen fixation) by the bacterial partner in supporting the growth of the association was assessed in a series of experiments. It appears to be the case that, although the bacterial partner demonstrably increases the fitness of the algae under nitrogen limitation, and cells of C. sorokiniana receive nitrogen originally fixed from atmospheric nitrogen by A. brasilense, the amount of nitrogen obtained by diazotrophy is too small to explain the increase in fitness.

08 HYDROGEN↗
DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗
DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗
DOE OSTI2023

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microglia are implicated in the development of paclitaxel chemotherapy-associated cognitive impairment in female mice

Chemotherapy remains a mainstay in the treatment of many types of cancer even though it is associated with debilitating behavioral side effects referred to as “chemobrain,” including difficulty concentrating and memory impairment. The predominant hypothesis in the field is that systemic inflammation drives these cognitive impairments, although the brain mechanisms by which this occurs remain poorly understood. Here, we hypothesized that microglia are activated by chemotherapy and drive chemotherapy-associated cognitive impairments. To test this hypothesis, we treated female C57BL/6 mice with a clinically-relevant regimen of a common chemotherapeutic, paclitaxel (6 i.p. doses at 30 mg/kg), which impairs memory of an aversive stimulus as assessed via a contextual fear conditioning (CFC) paradigm. In this work, paclitaxel increased the percent area of IBA1 staining in the dentate gyrus of the hippocampus. Moreover, using a machine learning random forest classifier we identified immunohistochemical features of reactive microglia in multiple hippocampal subregions that were distinct between vehicle- and paclitaxel-treated mice. Paclitaxel treatment also increased gene expression of inflammatory cytokines in a microglia-enriched population of cells from mice. Lastly, a selective inhibitor of colony stimulating factor 1 receptor, PLX5622, was employed to deplete microglia and then assess CFC performance following paclitaxel treatment. PLX5622 significantly reduced hippocampal gene expression of paclitaxel-induced proinflammatory cytokines and restored memory, suggesting that microglia play a critical role in the development of chemotherapy-associated neuroinflammation and cognitive impairments. This work provides critical evidence that microglia drive paclitaxel-associated cognitive impairments, a key mechanistic detail for determining preventative and intervention strategies for these burdensome side effects.

60 APPLIED LIFE SCIENCES↗