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Optimal Development of Transferable Machine Learning Interatomic Potentials using Active Learning
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Section 3 Reporting: Preserve America
Brookhaven National Laboratory (BNL) is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and countless advances in science and technology. For over 75 years, the Laboratory has played a leading role in the Department of Energy (DOE) Science and Technology mission and continues to contribute to the DOE’s missions in energy resources, environmental quality, and national security. The Laboratory is operated and managed by Brookhaven Science Associates (BSA), which was founded by the Research Foundation for the State University of New York on behalf of Stony Brook University, and Battelle, a non-profit applied science and technology organization. BNL is committed to longstanding partnerships with researchers, academic institutions, industry, students, teachers, and the surrounding community. BNL is located near the center of Suffolk County on Long Island, New York within Brookhaven Township, about 60 miles east of New York City. Most of BNL’s principal facilities are located near the center of the 5,265-acre (8.23 square mile) site (Figure 1). The developed area encompasses approximately 1,820 acres, consisting of: ▪ 500 acres originally developed by the Army (as part of WW II Camp Upton) and still used for offices and other operational buildings. ▪ 200 acres occupied by large, specialized research facilities. ▪ 520 acres occupied by outlying facilities, such as the Sewage Treatment Plant, research agricultural fields, housing facilities, and fire breaks. ▪ 400 acres of roads, parking lots, and connecting areas. ▪ 200 acres developed for the Long Island Solar Farm. The balance of the site, approximately 3,400 acres, is largely wooded and represents a native pine barrens ecosystem. In November 2000, DOE set aside 530 acres of undeveloped land at BNL as the Upton Ecological and Research Reserve. The Upton Reserve preserves this portion of the pine barrens ecosystem and provides an area for ecological research and education activities.
Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers
Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.
A Custom Machine to Convey Radiologically Impacted Cohesive Soils to the Orion ScanSortSM System - 20382
An established method to reduce the volume of material required to be disposed of as radioactive waste is conveyor-based sorting of potentially radiologically impacted soils. With the Orion ScanSortSM system, potentially impacted soils are conveyed beneath radiation detectors and sorted into above and below criteria bins based on the detectors' response. Confident measurements can only be efficiently achieved when the soil column being conveyed has a reasonably consistent geometry. Highly cohesive soils present a very significant challenge as they tend to clump and adhere to the conveyor hopper, strike-off bar, and belt skirting. This causes voids and valleys in the soil column that affect the measurement geometry and reduce the confidence in the measurement. The reduction in confidence necessitates a longer residence time (i.e. reduction in conveyor belt speed and processing rates) or that the soils in highly unfavorable geometries be dispositioned as impacted or segregated for resurvey (should site logistics support that option). These outcomes may increase the volume of material required to be dispositioned as radiological waste and have a negative impact on project cost and schedule. To minimize impact to sorting operations, Wood designed and built a customized Extruder, to optimize the soil column prior to assay. The design was developed and refined to minimize the volume of highly cohesive soils presented in highly unfavorable geometries in the soil column in order to confidently assess and disposition such soils in a high-production environment. The Extruder is a customized 90 cm wide flat conveyor that has an oversized hopper with a pair of motor-driven rollers that force the soils in the hopper through an opening of adjustable height. The soils are extruded through the opening to produce a soil column that is ∼75 cm wide and ∼8-18 cm deep with a design rate of 225 metric tons/hr. The Extruder was recently deployed with the Orion ScanSort{sup SM} System to a site in northeast Ohio. The site has highly cohesive soils that result from the weathering of glacial sediments and consist of clay and clay loam, resulting in poor drainage and high moisture content. The project infrastructure only supported two bins of material (above and below criteria), which necessitated that soils with unfavorable geometries be discharged into the above criteria bin, along with material determined to have been contaminated. The Extruder was extremely successful in producing a stable soil column with favorable geometries for radiological assay. During production, less than 0.5% (by mass) of the soils processed were presented in unsatisfactory geometries requiring disposition as radioactive waste. The Extruder did not get clogged due to the cohesive soils (as is typical with conventional conveyors) and required very little maintenance, again minimizing impacts to sorting operations. The conveyor belt speed was operated at 14 cm/s with a typical belt loading of ∼109 kg/m resulting in a mean process rate of ∼49 metric tons/hr. The process rate was constrained by other project logistics, rather than by the capabilities of the Extruder, which was operated at less than 20% of the maximum design speed (75 cm/s). It is concluded that the Extruder is highly likely to produce a stable highly cohesive soil column suitable for efficient and confident radiological assay in production environments of 250 short tons/hr or more. The Extruder has the capability to drastically reduce the duration and costs of projects with radiologically impacted highly cohesive soils. (authors)
DOE Award No.: DE-FE0023919 Phase 3 Scientific/Technical Report
This is the Phase 3 Report for the ‘Deepwater Methane Hydrate Characterization and Scientific Assessment or Genesis of Methane Hydrates in the Gulf of Mexico (GOM2)’ research project (DOE Award No. DE-FE0023919). The report summarizes activities from January 16, 2018 to September 30, 2019. The project is led by the University of Texas at Austin (UT). The objective is to gain insight into the nature, formation, occurrence and physical properties of methane hydrate-bearing sediments for the purpose of methane hydrate resource appraisal through the planning and execution of drilling, coring, logging, testing and analytical activities that assess the geologic occurrence, regional context, and characteristics of marine methane hydrate deposits in the Gulf of Mexico outer continental shelf (OCS). We determined that it would not be possible to pursue the project with the International Ocean Discovery Program (IODP) and then developed a revised science and operations plan to maximize the science using a commercial vessel within the budget that is available. We improved the scientific capability of the UT pressure core center by adding the ability to X-ray pressure cores, and the ability to cut and store multiple core samples for experimental analysis. We transferred pressure cores to peer institutions, including the National Energy Technology Lab (NETL) the United States Geological Survey (USGS Woods Hole). We made advances in understanding the composition and source of gasses locked in the methane hydrate from Green Canyon 955 (GC-955). We developed approaches to determine the in-situ salinity of hydrate-bearing samples, revealing that the in situ salinity of the GC 955 reservoir is just above that of seawater. We determined that the GC-955 hydrate reservoir is composed of sandy silt with a high concentration of hydrate interbedded with clayey silt with no hydrate present. We determined that some or all of the intervals bounding the hydrate reservoir are composed of material similar to the reservoir (sandy silt with hydrate and clayey silt with no hydrate), but with a lower net to gross. We determined that the reservoir effective permeability at a hydrate saturation of ~80-90 % is ~0.1 mD (or 1.0×10-16 m2) to ~0.5 mD (or 5.0×10-16 m2) and the intrinsic permeability is ~12 mD (or 1.2×10-14 m2). The GC-955 reservoir in-situ porosity of sandy silt is 0.38 to 0.40 and is largely independent of effective stress, and that the porosity of clayey silt is 0.33 at an in situ effective stress of 3.8 MPa to ~0.37 at zero effective stress. We developed a systematic, repeatable approach to studying hydrate reservoir properties by reconstituting individual lithofacies from dissociated pressure cores. We determined index properties of GC-955 reservoir, including liquid limit and plasticity, porosity, capillary behavior, and particle size distribution. We developed a more robust pressure coring technology. We finalized and published the UT-GOM2-1 Expedition Volume and we finalized a dedicated volume on the UT-GOM2-1 expedition that will be published in the American Association of Petroleum Geologists Bulletin (AAPG) in spring 2020.
Air classification of forest residue for tissue and ash separation efficiency
The goal of this Case Study was to evaluate the performance of air classification of logging residues toward meeting conversion CMAs for carbon and ash contents, as compared to the static status quo Base Case system in which the residues are first dried and then ground in a hammer mill with a 6 mm screen and fines < 1.18 mm are removed. Also considered were moisture and ash impacts on throughput and Overall Operating Effectiveness (OOE), as well as delivered feedstock cost and minimum fuel selling price (MFSP). Laboratory data on the impacts of fan speed and moisture content on the separation efficiency of soil ash, needles and bark from white wood were received from FCIC Subtask 5.2. Average throughput and energy consumption data were obtained from the Bioenergy Feedstock National User Facility (BFNUF) for the same air classifier. These data were utilized to develop the necessary response surface equations to perform throughput analysis using discrete event simulation. Because the Base Case status quo system utilizes drying prior to grinding, we modeled the Case Study with drying prior to air classification and subsequent grinding of the separated white wood to isolate the individual quality and cost impacts of air classification relative to the Base Case system. Key takeaways from this Case Study are that air classification improves the quality of the final material, but increases the production cost, especially when lights are disposed; this becomes a tradeoff between increased conversion yield and the extra cost. Removing material should be done as early in the process as possible. Each operation that occurs prior to removing the material increases the cost of the disposed material and leads to wasted energy expenditures. As processes are included or modified, the impact on monetary and energy cost should be included in the decision process. Identifying alternative uses and the associated value for material that is separated from the feedstock stream will have a significant impact on the delivered cost of the material. Although there was an increase in production cost by adding air classification, there was a resulting benefit to the MFSP when meeting or exceeding all of the conversion CMAs; this was an important finding that should be explored further with FCIC Subtask 8.3 and potentially FCIC Task 6.
Development of a universal method for high yield of furfural and hydrogen from raw lignocellulosic biomass
In order to develop a universal method for the co-production of furfural and hydrogen from raw lignocellulosic biomass, three types of substrates (maple wood, wheat straw, and tall fescue) were investigated, integrating chemical and electrochemical technologies. The results show both furfural and pure hydrogen were produced from all the biomass substrates, and the substrate type, composition, concentration, and size all affected furfural and hydrogen production. The highest furfural production of 154 mg g -1 substrate was achieved from wheat straw. The highest conversion rate of 67% for the waste furfural residue was realized, and 335 ml pure hydrogen per gram of furfural residue with a Faradaic efficiency of 99.3% was obtained with a new electrolytic cell. A reaction mechanism for hydrogen evolution from furfural residue and a rule for co-production of furfural and hydrogen from raw biomass were proposed. The facts show that a promising universal method for the co-production of furfural and hydrogen from lignocellulosic biomass has been developed.
Evidence of restricted heat transport in National Ignition Facility Hohlraums
We present experimental evidence of restricted electron thermal conduction in the high-Z coronal plasma regions of laser-driven Hohlraums on the National Ignition Facility. Four separate measurements, three of which are direct observations of Hohlraum dynamics, corroborate this finding. (1) The velocity of the coronal plasma ablated and heated by the outer-cone laser beams is determined by time-dependent imaging of the gold plasma plume, or “bubble.” The velocities of the incoming plume (perpendicular to the Hohlraum axis) are consistent with high-fidelity 2D radiation-hydrodynamic simulations using flux-limited thermal electron conduction with a flux multiplier f = 0.03. Simulations using f = 0.15, which is very nearly classical Spitzer–Härm transport, predict plume velocities slower than measured. (2) Specific features in time-resolved images of the Hohlraum wall at an angle of 19° are also more consistent with f = 0.03 simulations compared to f = 0.15. (3) Spectroscopic tracers were added to the Hohlraum wall in the outer-beam bubble region. The ratios of hydrogen-like to helium-like line emission are sensitive to the electron temperature of the bubble. The hydrogen-like to helium-like ratios extracted from the time-integrated spectra of manganese and cobalt tracers from two observation angles are consistent with f = 0.03 and not with f = 0.15. (4) The time of peak capsule emission, or “bang time,” an integrated measurement, is also more consistent with f = 0.03 than with f = 0.15. Overall, while these findings do not identify the causes of restricted thermal conduction in Hohlraums, they motivate future experiments to test specific hypotheses and focus on model development in the regions of the plasma exhibiting restricted transport.
Developing machine learned potentials for high temperature applications
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KBase Educators Handbook
The KBase Educators Handbook is a community resource for educators teaching biology, computational biology, and bioinformatics using KBase. The Handbook includes supporting documentation on how to join and access community-developed resources for teaching with KBase, best practices, and guidelines on how to contribute to the KBase Educators Community.
Leveraging the bioeconomy for carbon drawdown
Stringent climate change mitigation scenarios rely on large-scale drawdown of carbon dioxide from the atmosphere. Amongst drawdown technologies, bioenergy with carbon capture and sequestration (BECCS) has received considerable attention in the climate mitigation literature. Recently, attention has shifted further from a relatively narrow focus on BECCS to a broader focus on Biomass Carbon Removal and Storage (BiCRS). The concept of BiCRS has the potential to enable a future where the climate mitigation value of biomass resources is more valuable than the energy value, due to the potential to remove and sequester large quantities atmospheric CO2. This article provides a qualitative overview of prominent BiCRS technologies from which a set of the most promising technologies are assessed quantitively through life cycle assessment. There are numerous opportunities to incorporate carbon removal and management within the bioeconomy, but the majority of immediate carbon removal potential exists in four bioproducts: bioenergy, bioplastics, biochar, and wood products. We analyze the life cycle greenhouse gas emissions and disposition of sequestered carbon over 10 000 years for four bioproducts representative of each broader category: an advanced BECCS pathway, biopolyethylene, oriented strand board, and biochar soil amendment. We find that the BECCS pathway has the greatest magnitude and durability of CO2 storage over all time horizons. However, non-BECCS pathways achieve 34–64% of the drawdown magnitude relative to BECCS and retain 55–67% of their initial drawdown over 100 years (central estimate). We identify three engineering strategies for enhancing carbon drawdown: reducing biomass supply chain emissions, maximizing carbon stored in long-lived products, and extending the term of carbon storage. Finally, we highlight the need to characterize both the magnitude and permanence of carbon drawdown as a means for policymakers and technology developers to deploy limited biomass resources to maximize mitigation benefits.
Synergies and Entanglement in Secondary Cell Wall Development and Abiotic Stress Response in Trees
A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For Populus and other forest trees, quality traits involve alterations in the secondary cell wall (SCW) of wood for traditional uses, as well as for a growing diversity of biofuels and bioproducts. Alterations in wood properties that are desirable for specific end uses can have negative effects on growth and stress tolerance. Understanding of the diverse roles of SCW genes is necessary for the genetic improvement of fast-growing, short-rotation trees that face perennial challenges in their growth and development. Here, we review recent progress into the synergies and antagonisms of SCW development and abiotic stress responses, particularly, the roles of transcription factors, SCW biogenesis genes, and paralog evolution.
Effect of Internal Structure on Warpage in a Large-Scale Additive Manufacturing Process With Bio-Derived Composites
Extrusion-based large-format additive manufacturing (LFAM) often results in unintended deformation and failures due to thermal residual stress between layers. This LFAM involves a hot molten polymer deposited on a previously deposited and cooled layer, generating a temperature mismatch between the layers. The temperature discrepancy causes a thermal contraction mismatch, generating thermal residual stress. Due to the residual stress, printed structures experience warpage and delamination Therefore, understanding the heat distribution behavior is essential to preventing undesired deformation and failures. The goal of this study is to investigate the effect of infill patterns on heat distribution and deformation in an LFAM system. Wood fiber-reinforced polylactic acid was used as a sustainable and low-cost reinforcement material. A numerical model was developed to predict the temperature and deformation field with thermo-mechanical properties, which were measured by a dynamic mechanical analysis and a thermal expansion test. Simulations were performed on a box geometry with three different infill patterns. The simulation model was verified with temperature data gathered from an infrared camera. The results show good agreement between predicted and measured temperature profiles. The developed simulation model was applied to a roof tray with different infill patterns for a case study. We found that the different thermal mass distributions resulting from the various infill patterns affected the heat distribution and deformation. These findings contribute to a better understanding of the thermal and mechanical behavior of LFAM.
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.
U-gas +Cool GTL™ - A New Integrated Process for Direct Biomass Conversion to Liquid Fuels
The U-Gas gasification technology, marketed by Sungas, is a proven fluid bed gasification technology for biomass conversion. U-Gas has been tested on a wide variety of biomass feeds including wood and waste streams. The U-Gas Technology has successfully converted wood for more than 20 years in a gasification plant in Skive Denmark at the 150t/d size. GTI has also recently developed the Cool GTL process for converting biogas to high quality gasoline, jet, and diesel fuels. The technoeconomics and LCA for the combination of the two technologies results an integrated optimized process, which will be discussed. The Cool GTL process is still in development and the development should be complete by 2023. Cool GTL converts high CO2 content feeds to synthesis gas with a 2-2.4/1 H2/CO ratio suitable for fuels synthesis. The process is based on a novel, highly stabile CO2/steam reforming catalyst. The 2.0-2.4/1 H2/CO synthesis gas ratio is always achieved, independently of feed CO2 content, by adjusting the amount of water added according to the amount of CO2 in the feed. The reformer catalyst has been tested for 500 hours and shows no measurable deactivation. The product from the reformer then goes directly to a low temperature slurry bed Fischer Tropsch reactor with an integrated finishing hydroisomerization reactor which makes hydrocarbon liquids from the synthesis gas. With this configuration no wax is produced. The technoeconomics and carbon intensity for the integration of UGas and the Cool GTL processes will be compared to other biomass conversion approaches. The use of electrolysis to boost H2 in the feed and increase liquid production will also be analyzed as a potential process improvement with sensitivities to the cost of electricity and the use of renewable electricity.
Next Generation Logistics Systems for Delivering Optimal Biomass Feedstocks to Biorefining Industries in the Southeastern U.S.
The diverse portfolio of biomass sources that is available in the Southeastern U.S., including a significant supply of pine “residue”, represents a valuable strategic position for the region. Through blends formulated based on critical properties, this project will take full advantage of the range in biomass properties afforded by the portfolio to produce a consistent, high-performance feedstock for the industry, while lowering cost. Key developments being targeted to enable this potential include whole-tree transport to a state-of-the-art merchandising depot that will further access biomass from ongoing, forest industry operations. The approach will more effectively utilize the tree and distribute cost, while minimizing in-woods contamination of the woody biomass component. To implement this vision, information on the chemical composition and changes that are induced during multiple preprocessing steps (size reduction, moisture removal, densification, etc.) is needed. New NIR sensor technology will be developed for online monitoring of important biomass properties. The data will be incorporated into a statistical process control platform to improve process efficiency and meet required specifications. Advanced process models are being developed to inform the techno-economic and life-cycle assessment of the program’s impact. The new system will ultimately reduce operational risks from supply chain disruptions, and allow operation of larger-scale biorefineries.