Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase
Abstract not provided
Schormann, Norbert↗
SEARCH · Engineering Papers
Results for “replication”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Pathogenesis of virulent and attenuated foot-and-mouth disease virus in cattle
Background: Understanding the mechanisms of attenuation and virulence of foot-and-mouth disease virus (FMDV) in the natural host species is critical for development of next-generation countermeasures such as live-attenuated vaccines. Functional genomics analyses of FMDV have identified few virulence factors of which the leader proteinase (Lpro) is the most thoroughly investigated. Previous work from our laboratory has characterized host factors in cattle inoculated with virulent FMDV and attenuated mutant strains with transposon insertions within Lpro. Methods: In the current study, the characteristics defining virulence of FMDV in cattle were further investigated by comparing the pathogenesis of a mutant, attenuated strain (FMDV-Mut) to the parental, virulent virus from which the mutant was derived (FMDV-WT). The only difference between the two viruses was an insertion mutation in the inter-AUG region of the leader proteinase of FMDV-Mut. All cattle were infected by simulated-natural, aerosol inoculation. Results: Both viruses were demonstrated to establish primary infection in the nasopharyngeal mucosa with subsequent dissemination to the lungs. Immunomicroscopic localization of FMDV antigens indicated that both viruses infected superficial epithelial cells of the nasopharynx and lungs. The critical differences between the two viruses were a more rapid establishment of infection by FMDV-WT and quantitatively greater virus loads in secretions and infected tissues compared to FMDV-Mut. The slower replicating FMDV-Mut established a subclinical infection that was limited to respiratory epithelial sites, whereas the faster replication of FMDV-WT facilitated establishment of viremia, systemic dissemination of infection, and clinical disease. Conclusion: The mutant FMDV was capable of achieving all the same early pathogenesis landmarks as FMDV-WT, but was unable to establish systemic infection. The precise mechanism of attenuation remains undetermined; but current data suggests that the impaired replication of the mutant is more responsible for attenuation than differences in host immunological factors. These results complement previous studies by providing data of high-granularity describing tissue-specific tropism of FMDV and by demonstrating microscopic localization of virulent and attenuated clones of the same field-strain FMDV.
59 BASIC BIOLOGICAL SCIENCES↗
Breaking the reproducibility barrier with standardized protocols for plant–microbiome research
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.
Novak, Vlastimil↗
Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention
CommunityRx (CRx), an information technology intervention, provides patients with a personalized list of healthful community resources (HealtheRx). In repeated clinical studies, nearly half of those who received clinical “doses” of the HealtheRx shared their information with others (“social doses”). Clinical trial design cannot fully capture the impact of information diffusion, which can act as a force multiplier for the intervention. Furthermore, experimentation is needed to understand how intervention delivery can optimize social spread under varying circumstances. To study information diffusion from CRx under varying conditions, we built an agent-based model (ABM). This study describes the model building process and illustrates how an ABM provides insight about information diffusion through in silico experimentation. To build the ABM, we constructed a synthetic population (“agents”) using publicly-available data sources. Using clinical trial data, we developed empirically-informed processes simulating agent activities, resource knowledge evolution and information sharing. Using RepastHPC and chiSIM software, we replicated the intervention in silico, simulated information diffusion processes, and generated emergent information diffusion networks. The CRx ABM was calibrated using empirical data to replicate the CRx intervention in silico. We used the ABM to quantify information spread via social versus clinical dosing then conducted information diffusion experiments, comparing the social dosing effect of the intervention when delivered by physicians, nurses or clinical clerks. The synthetic population (N = 802,191) exhibited diverse behavioral characteristics, including activity and knowledge evolution patterns. In silico delivery of the intervention was replicated with high fidelity. Large-scale information diffusion networks emerged among agents exchanging resource information. Varying the propensity for information exchange resulted in networks with different topological characteristics. Community resource information spread via social dosing was nearly 4 fold that from clinical dosing alone and did not vary by delivery mode. This study, using CRx as an example, demonstrates the process of building and experimenting with an ABM to study information diffusion from, and the population-level impact of, a clinical information-based intervention. While the focus of the CRx ABM is to recreate the CRx intervention in silico, the general process of model building, and computational experimentation presented is generalizable to other large-scale ABMs of information diffusion.
59 BASIC BIOLOGICAL SCIENCES↗
Spatial and Temporal Organization of Chromosome Duplication and Segregation in the Cyanobacterium Synechococcus elongatus PCC 7942
The spatial and temporal control of chromosome duplication and segregation is crucial for proper cell division. While this process is well studied in eukaryotic and some prokaryotic organisms, relatively little is known about it in prokaryotic polyploids such as Synechococcus elongatus PCC 7942, which is known to possess one to eight copies of its single chromosome. Using a fluorescent repressor-operator system, S. elongatus chromosomes and chromosome replication forks were tagged and visualized. We found that chromosomal duplication is asynchronous and that the total number of chromosomes is correlated with cell length. Thus, replication is independent of cell cycle and coupled to cell growth. Replication events occur in a spatially random fashion. However, once assembled, replisomes move in a constrained manner. On the other hand, we found that segregation displays a striking spatial organization in some cells. Chromosomes transiently align along the major axis of the cell and timing of alignment was correlated to cell division. This mechanism likely contributes to the non-random segregation of chromosome copies to daughter cells.
59 BASIC BIOLOGICAL SCIENCES↗
Keep CALM and CRDT On
Despite decades of research and practical experience, developers have few tools for programming reliable distributed applications without resorting to expensive coordination techniques. Conflict-free replicated datatypes (CRDTs) are a promising line of work that enable coordination-free replication and offer certain eventual consistency guarantees in a relatively simple object-oriented API. Yet CRDT guarantees extend only to data updates; observations of CRDT state are unconstrained and unsafe. We propose an agenda that embraces the simplicity of CRDTs, but provides richer, more uniform guarantees. We extend CRDTs with a query model that reasons about which queries are safe without coordination by applying monotonicity results from the CALM Theorem, and lay out a larger agenda for developing CRDT data stores that let developers safely and efficiently interact with replicated application state.
Computer Science↗
Aligned FTICR-MS, Respiration, and Biochemical Transformation Data from Columbia River Sediment Incubations Associated with: “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism”
Columbia River hyporheic zone sediments from the Hanford Site 300 Area in eastern Washington were incubated in a full factorial design with different organic matter (OM) amendments. The aim of the experiment was to test the influence of OM thermodynamics on aerobic respiration across different organic carbon pools and concentrations. This dataset is comprised of (1) a csv with high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (2) a csv with sample IDs, replicates, amendments, dissolved oxygen (DO) measurements, and sampling time points, (3) a csv with sample IDs, replicates, respiration rates, FTICR summary metrics, and relative abundance of chemical classes; and (4) a csv with the number of chemical transformations in each sample replicate (microcosm). The data are associated with the publication “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism” published in ES&T Letters (Garayburu-Caruso et al., 2020). Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.
54 ENVIRONMENTAL SCIENCES↗
Kinetic and temperature sensitivity properties of soil exoenzymes through the soil profile down to one-meter depth at a temperate coniferous forest (Blodgett, CA)
This dataset contains data on kinetic and temperature sensitivity parameters of the exoenzymes β-glucosidase (BG), leucine/leucyl aminopeptidase (LAP) and acid phosphatase (AP) across a soil profile down to 90 cm depth at Blodgett forest, CA, USA. These data were generated to determine if kinetic and thermal properties of microbial exoenzymes involved in organic matter decomposition varied with soil depth, following variation in soil properties and microbial communities, as part of the study: Alves et al. (2021). Kinetic Properties of Microbial Exoenzymes Vary with Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Frontiers in Microbiology 12:3618. https://doi.org/10.3389/fmicb.2021.735282. This research was performed within the framework of the TES Belowground Biogeochemistry SFA project, in particular association with a long-term field warming experiment of the whole soil profile at Blodgett forest. Samples for this work were collected from locations representative of the field experimental plots. Potential enzyme activity rates were measured using laboratory fluorometric assays with soils collected at 0-10, 10-20, 30-40, 50-60, 60-70 and 80-90 cm deep in biological triplicates (i.e., three soil cores collected at different representative locations). Assays with each soil were conducted over a gradient of eight substrate concentrations per enzyme, and incubated at 4, 10, 16, 25, 35 or 50°C. Enzyme Michaelis-Menten kinetics were modeled over the eight substrate concentrations at each temperature, and the temperature sensitivity of the kinetic parameters was modeled over the six temperatures using linear Arrhenius/Q10 and non-linear Macromolecular Rate Theory (MMRT) models. The dataset includes the fully processed enzyme activity rate data used to model Michaelis-Menten kinetics, calculated kinetic and temperature sensitivity parameters, and basic soil and microbial biomass chemistry for each sample. All data is provided for each individual biological replicate, and kinetic and temperature sensitivity parameters are also provided as means of the biological replicates. The dataset also includes all raw measurement data and code used to parse, combine and perform the analyses described by Alves et al. (2021). For file descriptions, see the file-level metadata files: “enzymes_dataProcessed_flmd.xlsx” (processed data); “enzymes_dataRaw_flmd.xlsx” (compressed raw data and metadata); and “enzymes_code_flmd.xlsx” (compressed code). The experimental design, list of parameters measured, soil and microbial biomass chemistry data, and means of biological replicates for kinetic and temperature sensitivity parameters are also provided as human-readable tables in file “enzymeTraits_design_results_tables.xlsx”.
54 ENVIRONMENTAL SCIENCES↗
Current Status of the Quality of 4H-SiC Substrates and Epilayers for Power Device Applications
ABSTRACT Interfacial dislocations (IDs) and half-loop arrays (HLAs) present in the epilayers of 4H-SiC crystal are known to have a deleterious effect on device performance. Synchrotron X-ray Topography studies carried out on n-type 4H-SiC offcut wafers before and after epitaxial growth show that in many cases BPD segments in the substrate are responsible for creating IDs and HLAs during CVD growth. This paper reviews the behaviors of BPDs in the substrate during the epitaxial growth in different cases: (1) screw-oriented BPD segments intersecting the surface replicate directly through the interface during the epitaxial growth and take part in stress relaxation process by creating IDs and HLAs (Matthews-Blakeslee model [1] ); (2) non-screw oriented BPD half loop intersecting the surface glides towards and replicates through the interface, while the intersection points convert to threading edge dislocations (TEDs) and pin the half loop, leaving straight screw segments in the epilayer and then create IDs and HLAs; (3) edge oriented short BPD segments well below the surface get dragged towards the interface during epitaxial growth, leaving two long screw segments in their wake, some of which replicate through the interface and create IDs and HLAs. The driving force for the BPDs to glide toward the interface is thermal stress and driving force for the relaxation process to occur is the lattice parameter difference at growth temperature which results from the doping concentration difference between the substrate and epilayer.
Dudley, M.↗
The Effects of Assumed Source Depth and Shear-Wave Velocity on Moment Tensors Estimated for Small, Contained Chemical Explosions in Granite
ABSTRACT The Source Phenomenology Experiment (SPE-Arizona) included of a series of chemical explosions detonated within a copper mine in Arizona. This study focuses on ground motions from detonations in the copper mine, which are analyzed to assess the uniqueness of the resulting source representation when the source region propagation characteristics have a range of possible models. P-wave velocities are well constrained by refraction data with less constraint of the S-wave velocities. The effects of explosion source depth and VS are assessed with Green’s functions for a range of models in which VP is held constant. Propagation models with a Poisson’s value of 0.25 and a source depth 30–60 m most accurately replicate the data. The explosion was detonated at a centroid depth of 30 m, so trade-offs in depth are demonstrated. The compensated linear vector dipole and explosion components of the Green’s functions convolved with a Mueller–Murphy source function are compared. Both produce significant energy in the 2–12 Hz band, due to surface-wave contributions with no clear depth dependencies above 20 Hz. The range of propagation models is used with the observational data to invert for the frequency-domain moment tensor. Fits to the data from these inversions have cross-correlation values of 0.64, demonstrating effectiveness in replicating the observations with the assumed propagation path effects and resulting source function. Inversions produce horizontal dipoles (Mxx and Myy), roughly half the maximum amplitude of Mzz, consistent with a compensated linear vector dipole source, which is frequency dependent. Denny and Johnson, Mueller–Murphy, Walter and Ford, and the revised Mueller–Murphy source models, parameterized for granite, are compared to the moment tensors. Despite a nonisotropic moment tensor source, the revised Mueller–Murphy isotropic source model best replicates the long-period moments, overshoot, and corner frequency.
Geochemistry & Geophysics↗
Oil Recovery Prediction for Polymer Flood Field Test of Heavy Oil on Alaska North Slope Via Machine Assisted Reservoir Simulation
The first ever polymer flood field pilot to enhance the recovery of heavy oils on the Alaska North Slope is ongoing. This study constructs and calibrates a reservoir simulation model to predict the oil recovery performance of the pilot through machine-assisted reservoir simulation techniques. To replicate the early water breakthrough observed during waterflooding, transmissibility contrasts are introduced into the simulation model, forcing viscous fingering effects. In the ensuing polymer flood, these transmissibility contrasts are reduced to replicate the restoration of injection conformance during polymer flooding, as indicated by a significant decrease in water cut. Later, transmissibility contrasts are reinstated to replicate a water surge event observed in one of the producing wells during polymer flooding. This event may represent decreased injection conformance from fracture overextension; its anticipated occurrence in the other production well is included in the final forecast. The definition of polymer retention in the simulator incorporates the tailing effect reported in laboratory studies; this tailing effect is useful to the simultaneous history match of producing water cut and produced polymer concentration. The top 24 best-matched simulation models produced at each stage of the history matching process are used to forecast oil recovery. The final forecast clearly demonstrates that polymer flooding significantly increases the heavy oil production for this field pilot compared to waterflooding alone. This exercise displays that a simulation model is only valid for prediction if flow behavior in the reservoir remains consistent with that observed during the history matched period. Critically, this means that a simulation model calibrated for waterflooding may not fully capture the benefits of an enhanced oil recovery process such as polymer flooding. Therefore, caution is recommended in using basic waterflood simulation models to scope potential enhanced oil recovery projects.
Keith, Cody Douglas↗
Phase II Nevada Water Resources Data, Modeling, and Visualization (DMV) Center (Final Report)
Water is unquestionably a critical resource throughout the United States. In the semi-arid west -- an area stressed by increase in human population and sprawl of the built environment -- water is the most important limiting resource. Crucially, science must understand factors that affect availability and distribution of water. To sustain growing consumptive demand, science needs to translate understanding into reliable and robust predictions of availability under weather conditions that could be average but might be extreme. These predictions are needed to support current and long-term planning. Similar to the role of weather forecast and climate prediction, water prediction over short and long temporal scales can contribute to resource strategy, governmental policy and municipal infrastructure decisions, which are arguably tied to the natural variability and unnatural change to climate. Change in seasonal and annual temperature, precipitation, snowmelt, and runoff affect the distribution of water over large temporal and spatial scales, which impact the risk of flooding and the groundwater recharge. Anthropogenic influences and impacts increase the complexity and urgency of the challenge. The goal of this project has been to develop a decision support framework of data acquisition, digital modeling, and 3D visualization. This integrated framework consists of tools for compiling, discovering and projecting our understanding of processes that control the availability and distribution of water. The framework is intended to support the analysis of the complex interactions between processes that affect water supply, from controlled availability to either scarcity or deluge. The developed framework enables DRI to promote excellence in water resource management, particularly within the Lake Tahoe basin. In principle, this framework could be replicated for other watersheds throughout the United States. Phase II of this project builds upon the research conducted during Phase I, in which the hydrologic framework was investigated and the development initiated. Phase II concentrates on practical implementation of the earlier work but emphasizes applications to the hydrology of the Lake Tahoe basin. Phase 1 efforts have been refined and extended by creating a toolset for geographic information systems (GIS) that is usable for disparate types of geospatial and geo-referenced data. The toolset is intended to serve multiple users for a variety of applications. The web portal for internet access to hydrologic and remotely sensed product data, prototyped in Phase I, has been significantly enhanced. The portal provides high performance access to LANDSAT-derived data using techniques developed during the course of the project. The portal is interactive, and supports the geo-referenced display of hydrologic information derived from remotely sensed data, such as various vegetative indices used to calculate water consumption. The platform can serve both internal and external constituencies using inter-operating infrastructure that spans both sides of the DRI firewall. The platform is intended grow its supported data assets and to serve as a template for replication to other geographic areas. An unanticipated development during the project was the use of ArcGIS software on a new computer system, called the IBM PureSytems, and the parallel use of the systems for faster, more efficient image processing. Additional data, independent of the portal, was collected within the Sagehen basin and provides detailed information regarding the processes that control hydrologic responses within mountain watersheds. The newly collected data include elevation, evapotranspiration, energy balance and remotely sensed snow-pack data. A Lake Tahoe basin hydrologic model has been developed, in part to help predict the hydrologic impacts of climate change. The model couples both the surface and subsurface hydrology, with the two components having been independently calibrated. Results from the coupled simulations involving both surface water and groundwater processes show that it is possible to fairly accurately simulate lake effects and water budget variables over a wide range of dry and wet cycles in the historical record. The Lake Tahoe basin is representative of the hydrology, topography and climate throughout the Sierra Nevada Range, and the entire model development is prototypical of the efforts required to replicate the decision support framework to other locales. The Lake Tahoe model in particular, could allow water managers to evaluate more accurately components of the water budget (ET, runoff, groundwater, etc) and to answer important questions regarding water resources in northern Nevada. This report discusses the geographic scale and the hydrologic complexity of the calibrated model developed as part of this project, as well as simulation results for historical and future climate projects To enable human-driven data exploration and discovery, de novo software for a globalized rendering module that extends the capability of our evolving custom visualization engine from Phase I (called SMEngine) has been developed. The new rendering component, called Horizon, supports terrain rendering capable of displaying and interrogating both remotely sensed and modeled data. The development of Horizon necessitated adaptation of the visualization engine to allow extensible integration of components such as the global rendering module and support for associated features. The resulting software is general in its GIS capability, but a specific Lake Tahoe visualization application suitable for immersive decision support in the DRIVE6 virtual reality facility has been developed. During the development, various features to enhance the value of the visualization experience were explored, including the use of hyperspectral image overlays. An over-arching goal of the visualization aspect of the project has been to develop and demonstrate the CAVE (CAVE Automatic Virtual Environment) as a practical tool for hydrologic research.
54 ENVIRONMENTAL SCIENCES↗
The Coal-Seq III Consortium. Advancing the Science of CO 2 Sequestration in Coal Seam and Gas Shale Reservoirs
The Coal-Seq consortium is a government-industry collaborative that was initially launched in 2000 as a U.S. Department of Energy sponsored investigation into CO2 sequestration in deep, unmineable coal seams. The consortium’s objective aimed to advancing industry’s understanding of complex coalbed methane and gas shale reservoir behavior in the presence of multi-component gases via laboratory experiments, theoretical model development and field validation studies. Research from this collaborative effort was utilized to produce modules to enhance reservoir simulation and modeling capabilities to assess the technical and economic potential for CO2 storage and enhanced coalbed methane recovery in coal basins. Coal-Seq Phase 3 expands upon the learnings garnered from Phase 1 & 2, which has led to further investigation into refined model development related to multicomponent equations-of-state, sorption and diffusion behavior, geomechanical and permeability studies, technical and economic feasibility studies for major international coal basins the extension of the work to gas shale reservoirs, and continued global technology exchange. The first research objective assesses changes in coal and shale properties with exposure to CO2 under field replicated conditions. Results indicate that no significant weakening occurs when coal and shale were exposed to CO2, therefore, there was no need to account for mechanical weakening of coal due to the injection of CO2 for modeling. The second major research objective evaluates cleat, Cp, and matrix, Cm, swelling/shrinkage compressibility under field replicated conditions. The experimental studies found that both Cp and Cm vary due to changes in reservoir pressure during injection and depletion under field replicated conditions. Using laboratory data from this study, a compressibility model was developed to predict the pore-volume compressibility, Cp, and the matrix compressibility, Cm, of coal and shale, which was applied to modeling software to enhance model robustness. Research was also conducted to improve algorithms and generalized adsorption models to facilitate realistic simulation of CO2 sequestration in coal seams and shale gas reservoirs. The interaction among water and the adsorbed gases, carbon dioxide (CO2), methane (CH4), and nitrogen (N2) in coalbeds is examined using experimental in situ laboratory techniques to comprehensively model CBM production and CO2 sequestration in coals. An equation of state (EOS) module was developed which is capable of predicting the density of pure components and mixtures involving the wet CBM gases CH4, CO2, and N2 at typical reservoir condition, and is used to inform CO2 injection models. The final research objective examined the effects adsorbed CO2 has on coal strength and permeability. This research studied the weakening or failure of coal by the adsorption of CO2 from empirically derived gas production data to develop models for advanced modeling of permeability changes during CO2 sequestration. The results of this research effort have been used to construct a new and improved model for assessing changes in permeability of coal reservoirs due CO2 injection. The modules developed from these studies and knowledge learned are applied to field validation and basin assessment studies. These data were used to assess the flow and storage of CO2 in a shale reservoir, test newly developed code against large-scale projects, and conduct a basin-oriented review of coal storage potential in the San Juan Basin. The storage potential and flow of CO2 was modeled for shale sequestration of a proprietary Marcellus Shale horizontal gas production well using COMET3 simulation software. Simulation results from five model runs indicate that stored CO2 quantities are linked to the duration of primary production preceding injection. Matrix CO2 saturation is observed to increase in each shale zone after injection with an increase in primary production, and the size of the CO2 plume is also observed to increase in size the longer initial production is sustained. The simulation modules developed around the Coal-Seq experimental work are also incorporated into a pre-existing large-scale numerical simulation model of the Pump Canyon CO2-ECBM pilot in the San Juan Basin. The new model was applied to re-history match the data set to explore the improvements made in permeability prediction against previously published data sets and to validate this module. The assessment of the new data, however, indicates that the impact of the variable Cp is negligible on the overall behavior of the coal for CO2 storage purposes. Applying these new modules, the San Juan Basin and the Marcellus Shale are assessed for their technical ECBM/AGR and CO2 storage potential and the economic potential of these operations. The San Juan Basin was divided into 4 unique geographic zones based on production history, and the Marcellus was divided into nine. Each was assessed based upon each zone’s properties, and simulations were run to assess the potential of full Basin development. Models of a fully developed San Juan Basin suggest the potential for up to 104 Tcf of CO2 storage, and 12.3 Tcf of methane recovery. The Marcellus models suggest 1,248 Tcf of CO2 storage and 924 Tcf of AGR. The economics are deemed favorable where credits cover the cost of CO2 in the San Juan Basin, and in many cases in the Marcellus, but to maximize storage potential, credits need to extend to pay the operator to store CO2.
01 COAL, LIGNITE, AND PEAT↗
Characterization of Covetic Materials for Process Control. Final CRADA report
GDC Industries LLC has been performing process research on covetic materials since its formation in February 2015. With assistance from DOE and the Air Force via SBIR projects, GDC focused on the enhancement of aluminum alloys to covetics to replicate a previously reported electrical conductivity of about 67% IACS (International Annealed Copper Standard). GDC has established a joint development agreement with General Cable Corporation, wherein General Cable agreed to perform numerous extrusions of as cast covetics and subsequent tensile and electrical conductivity tests on the resultant wire. Covetics conversion was proven but the significant improvement is yet to be replicated. To control the experiments towards enhanced process control, a series of designed experiments was created by an expert in process control from the automotive industry. Six process variables were identified and a designed experiment matrix requiring 18 independent conversions was created at GDC. The result of those designed experiments has now allowed GDC to focus on two process variables, namely, residence time and DC current in the conversions with the other four variable held constant. While this work is useful in replicating the earlier enhancements, GDC feels it will not be sufficient for the necessary process knowhow for scale up required by industry as GDC still does not have a direct correlation of the process variables to the actual carbon in the finished covetics. Since 2015, GDC has been aware of the capabilities existing at Argonne National Laboratory for performing carbon analysis that exceeds the precision commonly available to Industry. GDC and ANL submitted a proposal in response to the DOE-EERE – Small Business Vouchers Pliot Program announcement and the proposal was selected for funding. GDC will melt-process covetic aluminum samples following their design of experiment criteria and have the as-casted samples extruded by their partner, General Cable. Argonne will measure the conductivity, analyze carbon content, perform X-ray diffraction, and examine the microstructural features of the samples. Careful process variable measurements will be recorded by each party such that correlations can be developed indicating process parameters that yield the best carbon concentration in covetics.
36 MATERIALS SCIENCE↗
Efficacy and Delivery of Novel FAST Agents for Coronaviruses
We proposed to test and develop advanced delivery for novel agents from our collaborators Facile Accelerated Specific Therapeutics (FAST) platform to reduce coronavirus replication. Sachi Bioworks Inc., Prof. Anushree Chatterjee, and Prof. Prashant Nagpal at the University of Colorado Boulder have developed a bioinformatics and synthesis pipeline to produce sequence specific theranostic agents (agents that can be therapies and/or diagnostics) that are inherently transported into the cytoplasm of mammalian host cells and sequence-specifically interfere in nucleic acid replication. The agent comprises a small nanoparticle (2-5 nm) chosen for ideal cellular transport and/or imaging conjugated to a short, synthetic DNA analog oligomer designed for binding to one or more target viral sequences. The sequence specific binding of the FAST agent to its target prevents nucleic acid replication due to its high affinity binding. While the small nanoparticle facilitates delivery in vitro, we plan to package the FAST agents into a larger nanoparticle (80-300 nm) for future in vivo delivery applications. Our team at Sandia has expertise encapsulating biomolecules including protein, DNA, and RNA into solid lipid nanoparticles (LNP) and lipid coated mesoporous silica nanoparticles (LC-MSN) and shown successful delivery in mouse models to multiple tissues. Our team focused on formulation parameters for FAST agents into lipid nanoparticles (LNP) and lipid coated mesoporous silica nanoparticles (LC-MSN) for enhanced delivery and/or efficacy and in vivo translation. We used lipid formulas that have been shown in literature to facility in vitro and more importantly, in vivo delivery. In our work discussed below, we successfully demonstrate loading and release of FAST agents on silica core and stable LC-MSN in a reasonable size range for in vivo testing.
59 BASIC BIOLOGICAL SCIENCES↗
Detection of Damage Inducing Impact Events in Vibration Test Fixtures Using Holder Exponents
The Shock and Vibration team within the Test Engineering group at Los Alamos National Laboratory (LANL) aids in the development and qualification of weapon systems for the United States Department of Energy (DOE). Performing tests that replicate shock and vibration environments representative of a weapon’s lifetime is critical in ensuring safety, survivability, and reliability. A key factor in shock and vibration testing is accurate representation of the weapon’s boundary conditions in its end use configuration. The boundary conditions representative of a reentry body in flight are particularly difficult to replicate on an electrodynamic shaker. When executing shock and vibration tests on a reentry body, two system axes are tested with the system in a cantilevered configuration. This cantilevered testing configuration results in a moment load being applied to the system while undergoing vibration environments. A special fixture, known as the Flex-Web, was developed to decouple this moment load from the reentry body in order to more accurately represent real world boundary conditions while replicating flight environments.
42 ENGINEERING↗
Fast Reactor Physics Model Verification Studies using ARC and PyARC Workflows
PyARC was recently developed at Argonne National Laboratory to automate many of the tasks required in the ARC (Argonne Reactor Computation) fast reactor simulation workflow, from input file generation, code execution, data transfer between ARC codes, and output postprocessing. PyARC will likely be the path forward to train new users of the ARC codes with the goal of wide adoption by the national laboratories, academia, and industry. In particular, for the ANL-JAEA collaboration under the Civil Nuclear Working Group (CNWG) project agreement NE-01, PyARC will be used to model the Joyo and EBR-II reactors for comparisons with measured data and calculated results from JAEA (Task 3: Fast Reactor Fuel and Core). As an additional avenue for verification and validation, this report investigates the use of PyARC towards a variety of existing ARC-based reactor models, in order to understand its efficacy in replicating the behavior of base ARC codes and better understand any limitations within modeling realistic fast reactor problems. To this end, PyARC was used to model the Joyo MKI, RBEC Benchmark-M, PRISM Mod-B, and EBR-II Run 138B cores, and its results were compared to those from existing ARC-based models. It was found that for hexagonal-based geometries PyARC was able to replicate the behavior of ARC codes to within 10 pcm for small reactor cores, and ~150pcm difference in eigenvalue for larger cores. These discrepancies are attributed primarily to differences in local mesh refinement options between ARC and PyARC, which currently cannot be resolved with PyARC’s latest version (1.6.0). In some of these cases, PyARC was used to model steady-state problems with initial core compositions originating from a prior REBUS depletion calculation. While PyARC was not designed to support such steady-state calculations, workarounds were applied to replicate the behavior of ARC-based calculations as closely as possible. Thus, these results demonstrate the wide extent to which they can be applied to fast reactor problems while still providing immense benefit to the user in terms of automating and standardizing common routines within the fast reactor analysis workflow. This study concluded that PyARC will be suitable for modeling the steady-state conditions of the EBR-II and Joyo fast reactors as part of the CNWG project agreement.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Explosive Soot Challenge (Final Report)
This project assembled a broad ensemble of modeling and experimentation tools to study the morphological and optical properties of detonation soots in explosive fireballs. A gram-scale hemispherical high explosive was studied in a low-pressure controlled environment using in-situ experimentation with diffusely illuminated visible absorption spectroscopy, particle sizing through light scattering techniques, and post-test collections with subsequent morphological analysis. Hydrocode modeling was performed to replicate the detonation flow observations, and subsequent aerosol kinetics models provided particle size distributions and extinction coefficients from the hydrocode results. Experimentally observed soot morphologies agreed with expectation from the literature - a bimodal distribution was found, brought upon by the particles growing to a size where their inertia and fluid wakes are non-negligible. The aerosol kinetics model did not replicate the observed bimodal size distribution for lack of a coagulation kernel to represent the behavior. To recover particulate optical properties, a spectrally resolved absorption spectroscopy method termed Spectral diffuse back-illuminated extinction imaging (SBI-EI) was developed and implemented on two explosive types. Inverting the absorption spectra using a Kramers-Kronig consistent method yielded the complex index of refraction for the soots produced by the explosives. This method resulted in an unrealistic index of refraction for one of the two explosives, and this is suspected to be due to the model neglecting scattering brought upon by the large particle sizes observed. In addition to the core work, three additional studies were performed in parallel. These investigated the impact of scattering on diffuse absorption spectroscopy, studied how soots oxidate and sublimate in a well-controlled shock tube, and laid the theoretical groundwork for a new collision kernel to replicate the bimodal size distribution from the observations. Summaries of these efforts are included at the end of this report.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗