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NVBL (National Virtual Biotechnology Laboratory) Advanced Manufacturing for Medical Supplies for COVID-19

This virtual symposium was held to highlight the impact the U.S. Department of Energy’s (DOE) National Virtual Biotechnology Laboratory (NVBL) has had utilizing the unique capabilities of the DOE to tackle the science and technology challenges associated with COVID-19, and to discuss areas in which the NVBL can have impact in the future. With perspectives from Chris Fall, Director, Office of Science, DOE, and William A. Bookless, Principal Deputy Administrator of the National Nuclear Security Administration, the event featured Presentations from lead investigators reporting progress in: Epidemiological modeling, Therapeutics, Testing, Understanding transport of the virus, and Solving issues around supply chain challenges. In addition, keynote speakers from outside the NVBL discussed the upcoming science and technology needs in computing, testing and surveillance, and vaccines. The event was aimed at the S&T community, media, and general public.

Love, Lonnie↗

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗

The National Virtual Biotechnology Laboratory Symposium: Harnessing the unique strengths of DOE to tackle the biotechnology challenges of COVID-19, October 28, 2020

This virtual symposium was held to highlight the impact the U.S. Department of Energy’s (DOE) National Virtual Biotechnology Laboratory (NVBL) has had utilizing the unique capabilities of the DOE to tackle the science and technology challenges associated with COVID-19, and to discuss areas in which the NVBL can have impact in the future. With perspectives from Chris Fall, Director, Office of Science, DOE, and William A. Bookless, Principal Deputy Administrator of the National Nuclear Security Administration, the event featured Presentations from lead investigators reporting progress in: Epidemiological modeling, Therapeutics, Testing, Understanding transport of the virus, and Solving issues around supply chain challenges. In addition, keynote speakers from outside the NVBL discussed the upcoming science and technology needs in computing, testing and surveillance, and vaccines. The event was aimed at the S&T community, media, and general public.

59 BASIC BIOLOGICAL SCIENCES↗

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗

Energy Material Network Data Hubs

In early 2015 the United States Department of Energy conceived of a consortium of collaborative bodies based on shared expertise, data, and resources that could be targeted towards the more difficult problems in energy materials research. The concept of virtual laboratories had been envisioned and discussed earlier in the decade in response to the advent of the Materials Genome Initiative and similar scientific thrusts. To be effective, any virtual laboratory needed a robust method for data management, communication, security, data sharing, dissemination, and demonstration to work efficiently and effectively for groups of remote researchers. With the accessibility of new, easily deployed cloud technology and software frameworks, such individual elements could be integrated, and the required collaboration architecture is now possible. The developers have leveraged open-source software frameworks, customized them, and merged them into a platform to enable collaborative energy materials science, regardless of the geographic dispersal of the people and resources. After five years in operations, the systems are demonstratively an effective platform for enabling research within the Energy Material Networks (EMN). This paper will show the design and development of a secured scientific data sharing platform, the ability to customize the system to support diverse workflows, and examples of the enabled research and results connected with some of the Energy Material Networks.

97 MATHEMATICS AND COMPUTING↗

Performance Testing of Software Upgrade for SRNL CPC Instrument at the Nuclear Material Laboratory, Office of Safeguards Analytical Services, International Atomic Energy Agency

This report summarizes the performance testing for the Software upgrade for the Savannah River National Laboratory (SRNL) Controlled Potential Coulometry (CPC) instrument. This upgrade is specifically to meet the needs of the Nuclear Material Laboratory, Office of Safeguards Analytical Services, International Atomic Energy Agency at Seibersdorf, Austria. The instrument hardware was upgraded in 2010, but the software continued to operate on a Windows platform using a High Tech Basic (HT Basic) application. HT Basic usage is declining. The IAEA requested an upgrade to the existing coulometer software to Laboratory Virtual Instrument Engineering Workbench (LabVIEW), an object-oriented programming language in wide use and one the NML staff is familiar with. The software was developed by SRNL Software Engineer, with assistance from Electrical Engineer and Scientist. Once developed, the new LabVIEW software was validated, tested with Iron (surrogate for plutonium) and plutonium. Once testing was completed, the software was installed at the International Atomic Energy Agency Nuclear Material Laboratory (IAEA NML) coulometer, and SRNL provided hands on training to NML staff on using the new software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Tuscaloosa Marine Shale Laboratory

The Tuscaloosa Marine Shale (TMS) in Louisiana and Mississippi is an Upper Cretaceous source rock formation sandwiched between the sands of the upper and lower Tuscaloosa sections. The TMS is believed to be the source rock for underlying prolific Tuscaloosa sand formation. The TMS has an unproven estimate of 7,000,000,000 bbls of recoverable oil while its current total average production is about 3,000 bbls of oil per day in 2017. In 2013 and 2014, more than 80 wells were drilled horizontally into the TMS that were fractured using multi-stage fracturing technology. The results from this have been mixed, but recent production for several wells show an appealing initial oil production rate of more than 1000 bbl/day. The preliminary core analysis by industry partners and a few literature studies shows that the TMS is one of the most clay-rich and sensitive shales to water. Due to these and other technical problems, there is high risk for the economic development of TMS compared to other shale plays. The experiences of major industrial players in the TMS show the necessity of open and collaborative efforts to better understand the critical gaps in the development of this challenging and potentially highly economic shale play to enable more cost-efficient and environmentally-sound recovery from this unconventional liquid-rich shale play. The overall objective of this project is to form a consortium of science and industry partners to address the following six major objectives using scientific and technical approaches: 1. To improve wellbore integrity by better understanding the sources of the wellbore instability issues, proposing innovative mud and cement design for the TMS. 2. To improve formation evaluation using laboratory techniques for the evaluation of mineralogical composition, organic content, and produced-water chemistry as well as well log and geophysical analysis. 3. To determine the role of geologic discontinuities on fracture growth and shale creep behavior using digital image correlation technique. 4. To investigate the application of stable CO 2 foam and super-hydrophobic proppants for improved reservoir stimulation. 5. To better understand the nature of water/hydrocarbon/CO 2 flow in clay and organic-rich formation and the role of water/fluid interaction on recovery. 6. To prepare better socio-economic environment for TMS development by community engagement. Subsequently, the TMS virtual laboratory conducted testing and analysis of various properties of rock and formation fluids from the TMS, including but not limited to the following: Analyzing reports and logs to better understand the source of wellbore instability in TMS wells; Experiments to design a customized cement based on TMS requirements; Experiments to obtain the mineralogical and geochemical composition of TMS samples; Seismic analysis of TMS geophysical data to better predict total organic carbon (TOC) content and brittleness in TMS; Well log analysis to better estimate the TOC and geo-mechanical properties of TMS; Experiments on formation water to understand the chemistry of produced water; Experiments to determine the role of lamination and natural fractures on fracture propagation or rock deformation using digital image correlation technique in in-direct tensile tests, semi-circular bend test and creep tests Experiments to determine the stability and rheological properties of nanoparticle-stabilized CO 2 foam in TMS rock samples; Experiments to determine fluid dynamics in un-propped TMS fractures and the role of nano-coating of proppants on fluid dynamics in fractures with proppants; Micro-fluidics experiments to enhance the understanding of fluid dynamics in tight liquidrich pores with high clay content; Socio-economic studies to better engage communities in TMS development.

58 GEOSCIENCES↗

Microstructure homogenization of concrete used in nuclear power plants

Almost all nuclear power plants in the United States are operating past their intended lifetimes or are requesting lifetime extensions. Therefore, understanding changes to the concrete containment structure over time is crucial to evaluate the structure’s continued viability. Concrete materials are heterogeneous particulate composites that exhibit viscoelastic material properties, which can lead to slow deformation over time, causing stress redistribution and the potential for creep cracking. A code to generate random, three dimensional (3D) concrete microstructures has been developed and paired with finite element analysis to predict the long-term viscoelastic properties of concrete. Data from these simulations are used to develop constitutive equations for the viscoelastic behavior of the homogenized concrete. The codes in this work are used to virtualize laboratory experiments, to obtain long-term creep data in a faster, cheaper manner. To validate this work, the simulated creep behavior of concrete is compared to 800 d of experimental data that has been extended to 27 y of data using the Time-Temperature superposition (TTS) principal. Excellent agreement between the simulation results and experimental data is seen.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Performance of pumped counterflow virtual impactors to study aerosol interactions with laboratory generated warm clouds

Pumped Counterflow Virtual Impactors (PCVI) are designed to separate aerosols based on aerodynamic diameter, which is particularly useful for isolating cloud droplets and ice crystals from smaller particles. However, the PCVI transmission efficiency (TE) values reported in the literature show considerable variability, and little information is available on the TEs for cloud liquid droplets. Here, we determined the optimal flow conditions for PCVI sampling for different activation ratios from the MTU Pi-cloud chamber, highlighting the conditions that maximize droplet residual sampling while minimizing interstitial transmission. Even for a lower limit cloud activation ratio = 1:10, an add flow of 1.5 LPM achieves a residual fraction greater than 0.80, with a droplet TE of ∼15% for typical Pi-Chamber droplets with diameters between 3.5 to 10 µm. This framework can be adapted for field cloud measurements based on the cloud conditions of interest. TE for cloud droplets under flow conditions at which ∼99% of the unactivated submicron particles were removed was substantially lower between 8 and 16% than for supermicron dry particles (∼30 to 40% for 3 µm polystyrene latex spheres). In addition, we conducted a comparison of the performances of three similar PCVI units to assess repeatability for dry aerosols and cloud droplets. All three PCVIs performed similarly in rejecting submicron particles smaller than the desired cutoff diameter. One of the units showed lower TEs due to a misalignment of the internal orifice. We discuss a procedure that improved alignment and performance.

54 ENVIRONMENTAL SCIENCES↗

Automated descriptor selection, volcano curve generation, and active site determination using the DescMAP software

The material space for catalyst discovery is expansive. Volcano curves are traditionally employed to provide physical insights into optimal catalyst characteristics for new material selection. Their generation lies on a single descriptor picked using expert knowledge. Here we present DescMAP, a Python-based software, to automate the selection of descriptors, the generation of volcano maps, and the identification of active sites for structure-sensitive reactions. Here, we consider traditional energy-based and geometric descriptors for structure-sensitive reactions. DescMAP is integrated with the Virtual Kinetic Laboratory (VLab) to provide multiple functionalities. It inputs spreadsheets or template files for flexibility and outputs interactive graphs for post-processing. We demonstrate its features using the non-oxidative dehydrogenation of ethane to ethylene over (111) closed-packed surfaces and the methane total oxidation over various Pt facets. It can be easily applied to other complex chemistries and achieves quick screening of potential catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid Acceleration of Diagnostics: RADx (Tech + ATP)

This virtual symposium was held to highlight the impact the U.S. Department of Energy’s (DOE) National Virtual Biotechnology Laboratory (NVBL) has had utilizing the unique capabilities of the DOE to tackle the science and technology challenges associated with COVID-19, and to discuss areas in which the NVBL can have impact in the future. With perspectives from Chris Fall, Director, Office of Science, DOE, and William A. Bookless, Principal Deputy Administrator of the National Nuclear Security Administration, the event featured Presentations from lead investigators reporting progress in: Epidemiological modeling, Therapeutics, Testing, Understanding transport of the virus, and Solving issues around supply chain challenges. In addition, keynote speakers from outside the NVBL discussed the upcoming science and technology needs in computing, testing and surveillance, and vaccines. The event was aimed at the S&T community, media, and general public.

Tromberg, Bruce J.↗

Computing and AI for Pandemic Response: Looking Forward

This virtual symposium was held to highlight the impact the U.S. Department of Energy’s (DOE) National Virtual Biotechnology Laboratory (NVBL) has had utilizing the unique capabilities of the DOE to tackle the science and technology challenges associated with COVID-19, and to discuss areas in which the NVBL can have impact in the future. With perspectives from Chris Fall, Director, Office of Science, DOE, and William A. Bookless, Principal Deputy Administrator of the National Nuclear Security Administration, the event featured Presentations from lead investigators reporting progress in: Epidemiological modeling, Therapeutics, Testing, Understanding transport of the virus, and Solving issues around supply chain challenges. In addition, keynote speakers from outside the NVBL discussed the upcoming science and technology needs in computing, testing and surveillance, and vaccines. The event was aimed at the S&T community, media, and general public.

Brase, James M.↗