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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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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 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 OSTI2021

Update of Erosion Conditions and Assessment of Mitigation Options for the L-Bar Site

The L-Bar former uranium milling site was remediated and closed per regulations and is now under the long-term stewardship of the U.S. Department of Energy, Office of Legacy Management (DOE/LM). Since assuming stewardship in 2004, DOE/LM has observed erosion and sedimentation processes at the L-Bar Site that will challenge meeting the design closure criteria in the long term, and therefore erosion control structures were installed in several areas. Portions of these structures were subsequently damaged by summer convective storm events and they are being redesigned. At the request of DOE/LM, Desert Research Institute (DRI) reviewed the proposed redesign plans of the erosion control structures. The purpose of this review is to support DOE/LM decisions regarding mitigation of ongoing erosion processes, including assessing possible repair of the existing erosion control structures, as well as plan for effective long-term site management. This design review is performed in reference to the Uranium Mill Tailings Radiation Control Act (UMTRCA) standards contained in 40 CFR 192.02 that require containment of residual radioactive material be effective for up to 1,000 years (if achievable, but certainly for 200 years), limit radon release, protect groundwater, and minimize future maintenance. The erosion control structures under review are not subject to the UMTRCA standard directly, but they contribute to the performance of the overall containment system by virtue of their relationship with the large diversion channels bounding the disposal cell. The 11 design drawings included in “Erosion Control Alternatives Analysis, L-Bar, New Mexico, Disposal Site, LTS-111-0043-08-002,” dated January 11, 2019, and listed in Appendix A, and supporting calculations in Weston (2019) are the focus of the review. Additionally, DOE/LM provided supporting data such as a 2018 photogrammetry-based digital elevation model of the site, precipitation records collected from an on-site weather station, and sedimentation records collected at an on-site basin. This assessment includes review of the proposed design to mitigate current site conditions but also addresses site changes between the initial erosion assessment report (Miller et al., 2012) and current conditions. The analysis is at a predesign engineering level and does not include development of hydraulic or sediment transport models. Site precipitation data are included in Miller et al. (2012). The natural conditions of the site, the design of site diversion systems, observed erosion at the site, and predesign engineering analysis are used to develop a holistic view of the challenges to L-Bar Site stability and possible responsive actions.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2010

Recovery Act : Near-Single-Crystalline Photovoltaic Thin Films on Polycrystalline, Flexible Substrates

III-V photovoltaics have exhibited efficiencies above 40%, but have found only a limited use because of the high cost of single crystal substrates. At the other end of the spectrum, polycrystalline and amorphous thin film solar cells offer the advantage of low-cost fabrication, but have not yielded high efficiencies. Our program is based on single-crystalline-like thin film photovoltaics on polycrystalline substrates using biaxially-textured templates made by Ion Beam-Assisted Deposition (IBAD). MgO templates made by IBAD on flexible metal substrate have been successfully used for epitaxial growth of germanium films. In spite of a 4.5% lattice mismatch, heteroepitaxial growth of Ge was achieved on CeO2 that was grown on IBAD MgO template. Room temperature optical bandgap of the Ge films was identified at 0.67 eV indicating minimal residual strain. Refraction index and extinction coefficient values of the Ge films were found to match well with that measured from a reference Ge single crystal. GaAs has been successfully grown epitaxially on Ge on metal substrate by molecular beam epitaxy. RHEED patterns indicate self annihilation of antiphase boundaries and the growth of a single domain GaAs. The GaAs is found to exhibit strong photoluminescence signal and, an existence of a relatively narrow (FWHM~20 meV) band-edge excitons measured in this film indicates a good optoelectronic quality of deposited GaAs. While excellent epitaxial growth has been achieved in GaAs on flexible metal substrates, the defect density of the films as measured by High Resolution X-ray Diffraction and etch pit experiments showed a high value of 5 * 10^8 per cm^2. Cross sectional transmission electron microscopy of the multilayer architecture showed concentration of threading dislocations near the germanium-ceria interface. The defect density was found decrease as the Ge films were made thicker. The defects appear to originate from the MgO layer presumably because of large lattice mismatches between the various layers. The defect density in GaAs was reduced by a factor of five by adding a step of in-situ deposition of Ge by MBE on the sputtered Ge prior to GaAs growth. We have investigated device design strategies that would support development of high-efficiency devices in presence of dislocation densities of 10^8 cm^-2 present in our epitaxial GaAs films. Results from modeling work show that with a proper emitter, base and doping selection, the modeled efficiency of a GaAs cells with dislocation densities of 10^9 and 10^8 cm^-2 could be increased from 1% and 7% to 11% and 17% respectively. Under AM0, this single junction GaAs solar cell, has optimized value of emitter and base thickness of around 0.7 and 1.7 microns respectively, to give a maximum efficiency of 24.2%. We have fabricated complete GaAs solar cells using our Ge films on metal substrates. Pattern resolution of few microns with well-defined grid line of 30 microns has been realized on few cm square flexible templates. The ability to grow single-crystalline-like Ge films on flexible, polycrystalline substrates by reel-to-reel tape processing now provides an immense potential to fabricate high quality III-V photovoltaics on flexible, inexpensive substrates.

14 SOLAR ENERGY↗
DOE OSTI2010

Recovery Act: "Near-Single-Crystalline Photovoltaic Thin Films on Polycrystalline, Flexible Substrates" (Final Report)

III-V photovoltaics have exhibited efficiencies above 40%, but have found only a limited use because of the high cost of single crystal substrates. At the other end of the spectrum, polycrystalline and amorphous thin film solar cells offer the advantage of low-cost fabrication, but have not yielded high efficiencies. Our program is based on single-crystalline-like thin film photovoltaics on polycrystalline substrates using biaxially-textured templates made by Ion Beam-Assisted Deposition (IBAD). MgO templates made by IBAD on flexible metal substrate have been successfully used for epitaxial growth of germanium films. In spite of a 4.5% lattice mismatch, heteroepitaxial growth of Ge was achieved on CeO 2 that was grown on IBAD MgO template. Room temperature optical bandgap of the Ge films was identified at 0.67 eV indicating minimal residual strain. Refraction index and extinction coefficient values of the Ge films were found to match well with that measured from a reference Ge single crystal. GaAs has been successfully grown epitaxially on Ge on metal substrate by molecular beam epitaxy. RHEED patterns indicate self annihilation of antiphase boundaries and the growth of a single domain GaAs. The GaAs is found to exhibit strong photoluminescence signal and, an existence of a relatively narrow (FWHM~20 meV) band-edge excitons measured in this film indicates a good optoelectronic quality of deposited GaAs. While excellent epitaxial growth has been achieved in GaAs on flexible metal substrates, the defect density of the films as measured by High Resolution X-ray Diffraction and etch pit experiments showed a high value of 5 x 10 8 per cm 2 . Cross sectional transmission electron microscopy of the multilayer architecture showed concentration of threading dislocations near the germanium-ceria interface. The defect density was found decrease as the Ge films were made thicker. The defects appear to originate from the MgO layer presumably because of large lattice mismatches between the various layers. The defect density in GaAs was reduced by a factor of five by adding a step of in-situ deposition of Ge by MBE on the sputtered Ge prior to GaAs growth. We have investigated device design strategies that would support development of high-efficiency devices in presence of dislocation densities of 10 8 cm -2 present in our epitaxial GaAs films. Results from modeling work show that with a proper emitter, base and doping selection, the modeled efficiency of a GaAs cells with dislocation densities of 10 9 and 10 8 cm -2 could be increased from 1% and 7% to 11% and 17% respectively. Under AM0, this single junction GaAs solar cell, has optimized value of emitter and base thickness of around 0.7 and 1.7 microns respectively, to give a maximum efficiency of 24.2%. We have fabricated complete GaAs solar cells using our Ge films on metal substrates. Pattern resolution of few microns with well-defined grid line of 30 microns has been realized on few cm square flexible templates. The ability to grow single-crystalline-like Ge films on flexible, polycrystalline substrates by reel-to-reel tape processing now provides an immense potential to fabricate high quality III-V photovoltaics on flexible, inexpensive substrates.

14 SOLAR ENERGY↗
DOE OSTI2012

Modeling CANDU-6 liquid zone controllers for effects of thorium-based fuels

We use the DRAGON code to model the CANDU-6 liquid zone controllers and evaluate the effects of thorium-based fuels on their incremental cross sections and reactivity worth. We optimize both the numerical quadrature and spatial discretization for 2D cell models in order to provide accurate fuel properties for 3D liquid zone controller supercell models. We propose a low computer cost parameterized pseudo-exact 3D cluster geometries modeling approach that avoids tracking issues on small external surfaces. This methodology provides consistent incremental cross sections and reactivity worths when the thickness of the buffer region is reduced. When compared with an approximate annular geometry representation of the fuel and coolant region, we observe that the cluster description of fuel bundles in the supercell models does not increase considerably the precision of the results while increasing substantially the CPU time. In addition, this comparison shows that it is imperative to finely describe the liquid zone controller geometry since it has a strong impact of the incremental cross sections. This paper also shows that liquid zone controller reactivity worth is greatly decreased in presence of thorium-based fuels compared to the reference natural uranium fuel, since the fission and the fast to thermal scattering incremental cross sections are higher for the new fuels. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

The effect of original and initial saturation on residual nonwetting phase capillary trapping efficiency

Injection of supercritical carbon dioxide (CO 2 ) into geological formations is a strategy for both atmospheric greenhouse gas reduction (climate change mitigation) and enhanced oil recovery. To understand CO 2 trapping efficiency, the capillary trapping behaviors that immobilize subsurface fluids were analyzed at the pore-scale using pairs of proxy fluids representing the range of in situ nonwetting and wetting fluid properties encountered in geologic storage reservoirs. The pairs of fluids were cycled through imbibition and drainage processes using a flow cell apparatus containing a sintered glass bead column. Computed x-ray microtomography (microCT) was used to identify immobilized nonwetting fluid after imbibition and drainage events. From microCT images, the trapped residual (post-secondary imbibition) nonwetting phase was spatially correlated to both the original (post-primary imbibition) and the initial (post-primary drainage) nonwetting phase; this relationship is referred to here as the original saturation dependence (SO-dependence) and initial saturation dependence (SI-dependence), respectively. Significant trends of decreasing SO- and SI-dependence with increasing wetting and nonwetting fluid phase viscosities were observed. This finding implies that the amount of CO 2 injected and ultimately trapped is dependent on the nonwetting phase (e.g. oil or gas) already present in the formation, as well as on the manner in which supercritical CO 2 is initially injected, which are factors not considered in current trapping models. To explore the potential effect that varying viscosity and interfacial tension (IFT) might have on this process, we report on a variety of fluid pairs with different viscosities and IFT.

42 ENGINEERING↗
DOE OSTI2019

Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence

The evolution of complex nervous systems was accompanied by the expansion of numerous protein families, including cell-adhesion molecules, surface receptors, and their ligands. These proteins mediate axonal guidance, synapse targeting, and other neuronal wiring-related functions. Recently, 32 interacting cell surface proteins belonging to two newly defined families of the Ig superfamily (IgSF) in fruit flies were discovered to label different subsets of neurons in the brain and ventral nerve cord. They have been shown to be involved in synaptic targeting and morphogenesis, retrograde signaling, and neuronal survival. Here, we show that these proteins, Dprs and DIPs, are members of a widely distributed family of two- and three-Ig domain molecules with neuronal wiring functions, which we refer to as Wirins. Beginning from a single ancestral Wirin gene in the last common ancestor of Bilateria, numerous gene duplications produced the heterophilic Dprs and DIPs in protostomes, along with two other subfamilies that diversified independently across protostome phyla. In deuterostomes, the ancestral Wirin evolved into the IgLON subfamily of neuronal receptors. We show that IgLONs interact with each other and that their complexes can be broken by mutations designed using homology models based on Dpr and DIP structures. The nematode orthologs ZIG-8 and RIG-5 also form heterophilic and homophilic complexes, and crystal structures reveal numerous apparently ancestral features shared with Dpr-DIP complexes. The evolutionary, biochemical, and structural relationships we demonstrate here provide insights into neural development and the rise of the metazoan nervous system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Resolution Versus Error for Computational Electron Microscopy

Images that are collected via scanning transmission electron microscopy (STEM) can be undersampled to avoid damage to the specimen while maintaining resolution [1, 2]. We have used BPFA to impute missing data and reduce noise [3]. The reconstruction is typically evaluated using the peak signal-to-noise ratio (PSNR). This measure is too conservative for STEM images and we propose that the Fourier ring correlation (FRC) is used instead to evaluate the reconstruction. We are not concerned with exact reconstruction of the truth image, and therefore PSNR is a conservative estimation of the quality of the reconstruction. Instead, we are concerned with the visual resolution of the image and whether atoms can be distinguished. We have evaluated the reconstruction of a simulated STEM image using the FRC and compared the results with the PSNR measurements. The FRC captures the resolution of the image and is not affected by a large MSE if the atom peaks are still distinguishable. The noisy and reconstructed images are shown in Figure 1. The simulated STEM image was sampled at 100%, 80%, 40%, and 20% of the original pixels to simulate an undersampled scan. The reconstruction was done using BPFA with a patch size of 10 x 10 and no overlapping patches. Not having overlapping patches produces inferior results but they are still acceptable. The dictionary size is 64 and 30 iterations were completed during each reconstruction. The 100% image was denoised instead of reconstructed. Poisson noise was applied to the simulated image with λ values of 500, 50, and 5 to simulate lower imaging dose. The original simulated STEM image was also included in our calculations and was generated using a dose of 1000. The simulated STEM image is 100 by 100 pixels and has essentially no high frequency components. The image reconstruction tends to smooth the data, also resulting in no high frequency components. This causes the FRC of the two images to be large at higher resolutions and may be misleading. For this reason, the BPFA has no overlap to avoid excessive smoothing. Moreover, the resolution of the simulated image is approximately 9.2 (1/nm), so we only look that far in the frequency domain when performing FRC. If the FRC curve does not crossover the threshold, a resolution value of 9.2 is used. We emphasize that our reported results are conservative. The FRC and PSNR values using the ground truth and the reconstructed images are shown in Tables 1 and 2. The left side show the metrics without using BPFA (missing pixels) and the right side show the metrics after using BPFA. When we did not use BPFA, the Fourier transform was estimated [4]. Some threshold curves have been studied [5], but they are derived for additive noise models. Since we have a Poisson noise model, we have used the more conservative threshold of 0.5 for our calculations. Ten images were used to construct each cell of tables in the form of the mean of the metric plus or minus its standard deviation. As expected, the PSNR dies off much quicker than the FRC values for the same image. For the 100% and 80% sampled versions of the truth image, the resolution only dies off when the dose is 5. However, the PSNR dies off rapidly as the dose is reduced. For the 1000, 500, and 50 dose images, the FRC is the maximum, or close, until we undersample at 20%. The PSNR for these values tapers down as we get into the bottom right hand corner of the table, even though the resolution remains high. Overall, we find that undersampled images can be reconstructed to acceptable resolution even when the dose per pixel is also reduced[6]. References: [1]A Stevens, H Yang, L Carin et al. Microscopy 63(1), (2014), pp. 41. [2]A Stevens, L Kovarik, P Abellan et al. Advanced Structural and Chemical Imaging 1(1), (2015), pp. 1. [3]M Zhou, H Chen, J Paisley et al. Image Processing, IEEE Transactions on 21(1), (2012), pp. 130. [4]V. Y. Liepin’sh. Automatic control and computer sciences 30(3), (1996), pp. 20.

Luzi, Lorenzo↗
DOE OSTI2013

Diverse Secreted Effectors Are Required for Salmonella Persistence in a Mouse Infection Model

Salmonella enterica serovar Typhimurium causes typhoid-like disease in mice and is a model of typhoid fever in humans. One of the hallmarks of typhoid is persistence, the ability of the bacteria to survive in the host weeks after infection. Virulence factors called effectors facilitate this process by direct transfer to the cytoplasm of infected cells thereby subverting cellular processes. Secretion of effectors to the cell cytoplasm takes place through multiple routes, including two separate type III secretion (T3SS) apparati as well as outer membrane vesicles. The two T3SS are encoded on separate pathogenicity islands, SPI-1 and -2, with SPI-1 more strongly associated with the intestinal phase of infection, and SPI-2 with the systemic phase. Both T3SS are required for persistence, but the effectors required have not been systematically evaluated. In this study, mutations in 48 described effectors were tested for persistence. We replaced each effector with a specific DNA barcode sequence by allelic exchange and co-infected with a wild-type reference to calculate the ratio of wild-type parent to mutant at different times after infection. The competitive index (CI) was determined by quantitative PCR in which primers that correspond to the barcode were used for amplification. Mutations in all but seven effectors reduced persistence demonstrating that most effectors were required. One exception was CigR, a recently discovered effector that is widely conserved throughout enteric bacteria. Deletion of cigR increased lethality, suggesting that it may be an anti-virulence factor. The fact that almost all Salmonella effectors are required for persistence argues against redundant functions. This is different from effector repertoires in other intracellular pathogens such as Legionella.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2011

Response to ''Comment on 'Scalings for radiation from plasma bubbles''' [Phys. Plasmas 18, 034701 (2011)]

In the preceding Comment, Corde, Stordeur, and Malka claim that the trapping threshold derived in my recent paper is incorrect. Their principal argument is that the elliptical orbits I used are not exact solutions of the equation of motion in the fields of the bubble. The original paper never claimed this--rather I claimed that the use of elliptical orbits was a reasonable approximation, which I based on observations from particle-in-cell simulations. Integration of the equation of motion for analytical expressions for idealized bubble fields (either analytically [I. Kostyukov, E. Nerush, A. Pukhov, and V. Seredov, Phys. Rev. Lett. 103, 175003 (2009)] or numerically [S. Corde, A. Stordeur, and V. Malka, ''Comment on 'Scalings for radiation from plasma bubbles,' '' Phys. Plasmas 18, 034701 (2011)]) produces a trapping threshold wholly inconsistent with experiments and full particle-in-cell (PIC) simulations (e.g., requiring an estimated laser intensity of a{sub 0{approx}}30 for n{sub e{approx}}10{sup 19} cm{sup -3}). The inconsistency in the particle trajectories between PIC and the numeric model used by the comment authors arises due to the fact that the analytical fields are only approximately true for ''real'' plasma bubbles, and lack certain key features of the field structure. Two possible methods of resolution to this inconsistency are either to find ever more complicated but accurate models for the bubble fields or to find approximate solutions to the equations of motion that capture the essential features of the self-consistent electron trajectories. The latter, heuristic approach used in my recent paper produced a threshold that is better matched to experimental observations. In this reply, I will also revisit the problem and examine the relationship between bubble radius and electron momentum at the point of trapping without reference to a particular trajectory.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

High-efficiency perovskite photovoltaic modules achieved via cesium doping

Perovskite solar modules have been attracting increasing attention due to their market potential, yet publications concerned with theintrinsic scale-up potential of different perovskite compositions remain relatively scarce. On the other hand, while great success is being made towards improving the power conversion efficiency (PCE) of perovskite solar cells (PSCs) by cesium cation (Cs + ) doping of the perovskite, more attention is being paid to the perovskite phase stabilization effect of Cs + doping, and less to other properties that are critical to understand and futher improve the PSC's. In this work, moderately-Cs-doped MAPbI 3 was employed as a model perovskite material in order to exclude the phase stabilization effect. Our systematic study revealed the influence of Cs + in organic-inorganic hybrid perovskites on the crystal structure, crystallization process, trap state density, band structure and charge (i.e., ions or photo-carriers) transport. Markedly, it has been observed that Cs + doping can greatly increase the carrier diffusion length in the perovskite films, thus improving the potential to scale-up PSC's.The PCE of small area devices (0.09 cm 2 ) was increased to 21.72% from 19.73%, with decreased hysteresis behavior and increased operational stability (T85 = 1000 h) after Cs + doped, where T85 refers to the retention of 85% of the initial PCE. Moreover, a PCE of 21.08% was obtained for a Cs + -containing perovskite module with an active area > 30 cm 2 , which demonstrates a better "reproducibility" than the reference sample (MAPbI3-based perovskite modules, PCE = 18.26%).

14 SOLAR ENERGY↗
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 OSTI2016

Canards in a minimal piecewise-linear square-wave burster

We construct a piecewise-linear (PWL) approximation of the Hindmarsh-Rose (HR) neuron model that is minimal, in the sense that the vector field has the least number of linearity zones, in order to reproduce all the dynamics present in the original HR model with classical parameter values. This includes square-wave bursting and also special trajectories called canards, which possess long repelling segments and organise the transitions between stable bursting patterns with n and n + 1 spikes, also referred to as spike-adding canard explosions. We propose a first approximation of the smooth HR model, using a continuous PWL system, and show that its fast subsystem cannot possess a homoclinic bifurcation, which is necessary to obtain proper square-wave bursting. We then relax the assumption of continuity of the vector field across all zones, and we show that we can obtain a homoclinic bifurcation in the fast subsystem. We use the recently developed canard theory for PWL systems in order to reproduce the spike-adding canard explosion feature of the HR model as studied, e.g., in Desroches et al., Chaos 23(4), 046106 (2013).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Finite-element simulation of the liquid-liquid transition to metallic hydrogen

Hydrogen at high temperature and pressure undergoes a phase transition from a liquid molecular phase to a conductive atomic state, or liquid metallic hydrogen, sometimes referred to as the plasma phase transition (PPT). The PPT phase line was observed in a recent experiment studying laser-pulse heated hydrogen in a diamond anvil cell in the pressure range ~100–170 GPa for temperatures up to ~2000 K. Here, the experimental signatures of the transition are (i) a negative pressure-temperature slope, (ii) a plateau in the heating curve, assumed to be related to the latent heat of transformation, and (iii) an abrupt increase in the reflectance of the sample. We present a finite-element simulation that accurately takes into account the position and time dependence of the heat deposited by the laser pulse. We calculate the heating curves and the sample reflectance and transmittance. This simulation confirms that the observed plateaus are related to the phase transition; however, we find that large values of latent heat are needed and may indicate that dynamics at the transition are more complex than considered in current models. Finally, experiments are proposed that can distinguish between a change in optical properties due to a transition to a metallic state or due to closure of the band gap in molecular hydrogen.

08 HYDROGEN↗
DOE OSTI2015

HIV Molecular Immunology 2014

HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Biosafety Level 3 Recon Training

The Biosafety Level 3 Recon training is a 3D virtual tool developed for the Counter WMD Analysis Cell (CWAC) and the Asymmetric Warfare Group (AWG) by the Application Modeling and Development Team within the NEN-3 International Threat Reduction Group. The training simulates a situation where friendly forces have secured from hostile forces a suspected bioweapons development laboratory. The trainee is a squad member tasked to investigate the facility, locate laboratories within the facility, and identify hazards to entrants and the surrounding area. Before beginning the 3D simulation, the trainee must select the appropriate MOPP level for entering the facility. The items in the simulation, including inside and outside the bioweapon facility, are items that are commonly used by scientists in Biosafety Level (BSL) laboratories. Each item has clickable red tags that, when activated, give the trainee a brief description of the item and a controllable turn-around view. The descriptions also contain information about potential hazards the item can present. Trainees must find all tagged items in order to complete the simulation, but can also reference descriptions and turn-around view of the items in a glossary menu. Training is intended to familiarize individuals whom have little or no biology or chemistry background with technical equipment used in BSL laboratories. The revised edition of this simulation (Biosafety Level 3 Virtual Lab) changes the trainee into a investigator instead of a military combatant. Many doors now require a virtual badge swipe to open. Airlock doors may come in sets such that the open door must be closed before the next door in the set can be opened. A user interface was added so that the instructor can edit the information about the items (the brief descriptions mentioned above) using the simulation software instead of the previous method of manually entering the material in xml settings files. Facility labels, such as "No Parking" and "Men's room", were changed from Korean, into English. No other changes were made.

59 BASIC BIOLOGICAL SCIENCES↗