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DOE OSTI2021

Final CTAP Report

Sandia will provide technical assistance to Helpful Engineering to develop and test the Universal Citizen Protection Device (UCPD) which is a UV-based filter-less PPE concept that aims to keep the Sars-CoV-2 virus out of eyes, nose and mouth with a 99%+ reliability. The heart of the device would be a concealed UV Chamber that decontaminates all air going in and out of the PPE. Helpful Engineering’s goal is to build this device to be reusable and cost less than $100 to construct and can be worn for 8 hours. The UCPD is an open source project, and once developed, prototyped, tested and approved, it will be shared with interested manufacturers globally.

42 ENGINEERING↗

DOE OSTI2021

Science and Technology Review June 2021

When the COVID-19 pandemic hit, Lawrence Livermore National Laboratory scientists came together, leveraging many different disciplines and technologies to address this global challenge. Livermore focused on three areas of research: creating alternatives for medical equipment in short supply, such as ventilators and nasal swabs; developing methods to help detect the SARS-CoV-2 virus responsible for COVID-19; and designing medical countermeasures such as antibodies and antivirals to combat the disease.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Evaluation of Three RNA Extraction Kits with a 2019-nCoV Assay

The following characteristics of three RNA extraction kits (Norgen Biotek Total RNA Purification Kit, #17200; Bioneer AccuPrep Viral RNA Extraction Kit, #K-3033; and Promega Maxwell HT Viral TNA Kit, #AX2340) were evaluated: Limits of detection for quantitative synthetic RNA using the Centers for Disease Control and Prevention’s (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel and the Applied Biosystems 7500 Fast Dx system; Limits of detection for positive clinical specimen using the Centers for Disease Control and Prevention’s (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel and the Applied Biosystems 7500 Fast Dx system; Ability of the lysis buffers in each kit to inactivate the virus as measured by a cell-based infectivity assay.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Agent-based Disease Surveillance and Transmission Model

The SARS-CoV-2 pandemic has driven a need for models that can predict transmission among populations and test the effectiveness of proposed interventions to control it such as testing, quarantining, vaccinations, and nonpharmaceutical interventions. Some questions of interest include:1. How rapidly will the virus spread if no action is taken? 2. How frequently should people be tested and quarantined if necessary? 3. Should unvaccinated persons be tested more frequently than the vaccinated? 4. If test results are delayed, how will that affect the spread? 5. How do test false negative rates affect the overall efficacy of testing programs? 6. How do constraints on testing resources impact the overall efficacy of testing programs? 7. How does the patient’s failure to recognize COVID symptoms and quarantine affect the spread? 8. What level of vaccination coverage is needed to suppress the epidemic? 9. What is the risk of a large outbreak (probability exceeding x infections)? 10. What is the cost effectiveness of interventions (dollars per avoided infection)? This report describes the structure of a discrete event simulation model that provides actionable information to address these questions. Parameter inputs and results of analyses have been reported in briefings provided to LLNL management and are not discussed here.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Large Scale MD to Predict Epitope Regions in HIV Env [Slides]

Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Non-Equilibrium Plasma Interactions with Biomaterials, Biological Solutions and Tissues

Cold atmospheric pressure plasma discharges offer an abundant source of reactive oxygen and nitrogen species (RONS) at room temperature enabling unique interactions with biomaterials, biological solutions and tissues. These interactions particularly with living matter are presently an important intellectual frontier in plasma science with promising potential applications ranging from human health care to advanced biomaterial processing. Exciting case studies have been reported that illustrate the huge potential of cold atmospheric plasma technology in wound healing and cancer treatment. The interaction of plasma with conducting and dielectric biomaterials such as tissue strongly influences the plasma properties. In turn this changes the impact of the plasma on the biomaterial. Particularly in the case of living matter, liquid based solutions are ubiquitous which complicates interfacial processes. The lack of insight into the underlying mechanisms of the interaction of plasma with wounds and tumors is currently a bottleneck for the further development of the technology and gives rise to many interesting scientific questions. This project was focused on plasma properties and kinetics during plasma-biomaterial interactions. Both DC pulsed and RF driven atmospheric pressure plasma jets, extensively used by the plasma community were studied. The bio-interfaces included hydrogel as a tissue model, (saline) solutions, bacteria and virus. Plasma diagnostics used include Thomson scattering, Rayleigh scattering, Raman scattering, (two-photon absorption) laser induced fluorescence, optical emission spectroscopy, absorption spectroscopy, molecular beam mass spectrometry and fast imaging allowing to determine electron densities and temperatures, ionic species, reactive species including radicals, gas temperatures, gas composition, electric fields and solution components transferred to the gas phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

SuiteGoo [Slides]

SuiteGoo is a liquid product used to detect "undetectable" material traces. It is used when you need to improve detection limits, anywhere where cotton swiping is used, and anywhere where cotton swiping fails. It is also used by law enforcement to find DNA from fingerprints, used by health care to detect the presence of viruses and bacteria, used by emergency response to detect explosive traces, and used by environmental management to detect pollutant traces.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

CSRI Summer Proceedings 2021

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

HIV Env assembling is tightly modulated by lipid composition and cytoplasmic tail integrity

HIV envelope glycoprotein (Env) is a homotrimeric transmembrane protein which binds to receptors CD4, CCR5- CXCR4, leading to a cascade of conformational changes ultimately resulting in the entrance of the virus into the host cell. Its whole structure comprises an extracellular region, a transmembrane domain and a cytoplasmic region. While many efforts are carried in order to develop an effective vaccine specifically targeting the extracellular domain, less efforts are focus into regions close to the transmembrane region; mostly limited by the lack of structural knowledge within this domain. Thus, it is desirable to have a molecular description of the trimeric association of the transmembrane domain, as well as the membrane properties affecting their structure. We have carried molecular dynamic (MD) simulations of HIV transmembrane region in different lipid environments, mimicking the complex viral membrane. Our results indicate that the lipid environment heavily affects the dynamics and association of the transmembrane helices, modulating its structure. In addition, we have investigated the effect of the cytoplasmic tail (CT). Unexpectedly, this region has a tremendous effect on the lateral organization of the transmembrane. These results clearly highlights the importance of this region in the overall structure of the Env protein and point towards its key role for the in-silico design of effective vaccines towards this domain.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Expanding the Scope of Genomic Security: Targeted Genome Editing within Microbiomes through Designer Bacteriophage Vectors

The ability to engineer the genome of a bacterial strain, not as an isolate, but while present among other microbes in a microbiome, would open new technological possibilities in the areas of medicine, energy and biomanufacturing. Our approach is to develop sets of phages (bacterial viruses) active on the target strain and themselves engineered to act not as killers but as vectors for gene delivery. This approach is rooted in our bioinformatic tools that map prophages accurately within bacterial genomes. We present new bioinformatic results in cross-contig search, design of phage genome assemblies, satellites that embed within prophages, alignment of large numbers of biological sequences, and improvement of reference databases for prophage discovery. We targeted a Pseudomonas putida strain within a lignin-degrading microbiome, but were unable to obtain active phages, and turned toward a defined microbiome of the mouse gut.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

SARS-CoV-2 transmission control in California correctional facilities

LBNL provided technical assistance to the CalPROTECT project, which is a collaboration between the University of California, Berkeley and the University of California, San Francisco. The CalPORTECT team provided support and guidance to the California Department of Corrections and Rehabilitation (CDCR) and the California Correctional Health Care Services (CCHCS) in their response to the COVID-19 pandemic. The CalPROTECT team provided recommendations to mitigate the risk posed to the residents and staff who live and work in CDCR prisons through considering scientific knowledge of the virus, analyzing anonymized resident and staff level data from CCHCS, evaluation of statewide and institution-level policies, and data collection during site visits to CDCR prisons during the pandemic.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Development and Demonstration of a Fuel-Efficient, Class 8 Tractor & Trailer Engine System (SuperTruck II)

Navistar presents the SuperTruck II (ST II) Final Report to the Unites States Department of Energy (US DOE), which covers the five Budget Periods (BPs) from 10-1-2016 through 6-30-2022. For ST II, Navistar built on the achievements of the SuperTruck I (ST I) Program as a catalyst to continue critical research, design and development, testing, and operations to reach the ambitious goals of the ST II project. This approach allowed Navistar to continue contributing to the essential needs of our nation for safe, efficient, and cost-effective delivery of goods and services, as we reduced negative environmental effects and improved operational productivity. This document contains information specified in DOE F 4600.2, Final Scientific/Technical Report DOE F 241.3, B. SCIENTIFIC/TECHNICAL REPORTS, explaining how we met and exceeded program requirements. Throughout this Final Report, Navistar extracted information from documents prepared during the project that represent our management, design and development, building, and testing efforts to meet and exceed SuperTruck II project goals. Navistar followed Plan requirements to achieve / exceed Project Objectives: a) >100% improvement in vehicle freight efficiency (FE) (on ton-MPG basis) relative to 2009 baseline with stretch goal of 140% improvement [actual: 170%); b) >55% engine brake thermal efficiency (BTE) demonstrated in operational engine at a 65-mph cruise point on a dynamometer – ≥31% increase from 2009 baseline [actual: 55.20% of combined BTE) ; and c) development and implementation of commercially cost effective technologies (in terms of a simple payback). Technology selection / development path focused on developing technologies applicable for production within 3-year approach, while ensuring technology readiness and cost of ownership for end users. The Program was organized into five budget periods: Requirements / Technology Assessment and Initial Hardware Testing; Technology Development and Concept Readiness Demonstration; Technology Finalization and Validation Tractor / Trailer Fabrication, Integration and Commissioning Demonstration; and Fuel Economy (FE) and Brake Thermal Efficiency (BTE) and Program Completion. Leadership was provided by DOE, with tasks performed by laboratories (Argonne National Laboratory, Lawrence Livermore National Laboratory); partners at Bosch, TPI, Dana, and J.B. Hunt; , and support from University of Michigan and Clemson University. Navistar lead this team with Principal Investigator / Contracting Officer; Project Manager (PM); Vehicle, Engine, and Aftertreatment Engineers; Finance Manager, Technical Program Leads, and Legal/IP; and other key personnel. Work also included personnel in risk management; funding / budget / finance. Work involved analysis, development, testing, and down selection of individual/system engine, aftertreatment, and vehicle technologies, with integration of selected technologies into a prototype vehicle for demonstration of fuel-efficiency gain. Work also included component/integrated system level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. As ST II progressed, Navistar performed computer-based modeling / simulations of technologies focused on the primary operational areas: Engine, Aftertreatment, and Vehicle. During the ST II Program, the COVID Virus outbreak unexpectedly challenged by the effects of, which affected staffing, scheduling, design, supplies, availability of materials, production procedures, and testing. The DOE responded by extending the program by three quarters to ensure that project tasks were completed for this vital project. Focus continued on analyzing, developing, testing, and down selecting individual-/system-level engine and vehicle technologies for integration of the final selected technologies into a prototype vehicle that would demonstrate fuel-efficiency gains made possible through these technologies. This included component/integrated system-level development of truck and trailer aerodynamics, base engine efficiency, advanced aftertreatment, combustion efficiency, waste heat recovery, solar power, distributed and intelligent vehicle power, hybrid powertrain, reduced rolling resistance, weight reduction, idle reduction, and driver feedback. Throughout the program, function, reliability, and performance at all levels were ensured through testing. Proof of this approach was demonstrated in multiple, on-road demonstrations: Scenario A (Flatland) Fuel Economy, Scenario B (Hilly) Fuel Economy, and City Cycle Tests. Other benefits derived from ST II included new/improved products, publications, patents, and next-step capabilities related to electric/hydrogen vehicles and autonomous driving.

Zukouski, Russ↗

DOE OSTI2023

New signature method for identifying organic material in atmosphere and water samples

The levels of plastic contamination in the earth’s oceans have steadily increased over the past century, creating a threat to marine life and increasing climate change. Several methods have been developed over the past decade to try to determine the amount and accumulation rate of plastic impurities in the ecosystem. These methods have proven promising but suffer from long measurement times, bulky non-mobile systems, and sample degradation. We propose a smaller, faster system that employs an electron beam to examine seawater samples for polyethylene contamination levels. This process generates a full electron and photon energy spectrum analyses based on the subatomic particles generated from electron interactions. Our simulations have already been developed based on the known molecular composition of seawater and polyethylene, showing the possibility of discerning molecular plastics from microorganisms. With a system the size of a suitcase, this system would be easily deployable to remote locations around the world or installed as a monitoring system for manufacturing facilities. This concept could lead to a new methodology for the science of signatures and be applied to other biological hazard investigations, such as general virus detection.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Defining Lipidomic Responses to Coronavirus Infection

Highly pathogenic human coronavirus infection can cause a severe atypical, rapid onset pneumonia with a mortality rate of up to 10% for severe acute respiratory syndrome coronavirus 1 (SARS-CoV 1), 35% for Middle East respiratory syndrome coronavirus (MERS-CoV), or 1% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2 causative agent of COVID 19). While medical countermeasures successfully controlled the worldwide SARS-CoV epidemic, the MERS-CoV epidemic is still ongoing and continues to be a concern for travelers in the Middle East and the multi-year SARS-CoV 2 pandemic underscore the importance of defining biomarkers that are diagnostic and/or predictive of severe disease outcomes for respiratory viruses. Systems biology approaches provide global snapshots of infection induced changes in host cells/tissues and provide extremely rich datasets for understanding host pathogen interactions. Metabolites, especially lipids, are critical for viral replication but less is understood about infection induced changes to lipids due to limits in lipid species detection and identification. To characterize how individual lipid species and proteins with lipid associated functions contribute to highly pathogenic human coronavirus replication and disease severity, existing datasets were probed to determine cell type specific lipid responses to MERS-CoV infection and verification studies were performed to determine if modification of the host lipid signature (by inhibiting enzymatic functions that produce specific lipid species) can perturb CoV replication in human lung cells. MERS-CoV infects human lung epithelial, endothelial and fibroblast cells. All three cell types were infected with MERS-CoV and samples collected to analyze lipids, proteins, metabolites, and transcripts from 12 to 48 hours post infection. Time matched mock-infected cells were collected in parallel for each cell type. Following sample and statistical analysis, functional enrichment and bioinformatic analysis was performed to identify differentially expressed lipids and proteins. Two lipid species were found to be significantly upregulated following MERS-CoV infection, ceramides, and triacylglycerol both of which are indicative of cells undergoing apoptotic cell death. In contrast, sphingomyelins (lipid molecules that can serve as a precursor for one pathway for ceramide synthesis) had significantly decreased expression in MERS-CoV infected cells. An inhibitor of acid sphingomyelinase (that converts sphingomyelin to ceramides and phosphorylcholine) reduced MERS-CoV replication suggesting that production of ceramides is key for successful viral replication and transmission. Acyl-CoA-synthetase 3 (ACSL3), the only protein whose function is lipid associated and had increased differential expression in our dataset, regulates the synthesis of triacylglycerol (increased expression). Inhibitors that directly block ACSL3 (Triacsin C) but not steps later in the triacylglycerol synthesis pathway (Etomoxir) inhibit MERS-CoV replication suggesting that triacylglycerol production and/or ACSL3 activity is also key for viral replication. ACSL3 expression is also upregulated in lung cancer cells and is predicted to promote continued cell viability which would also enhance viral replication. The differentially expressed lipid and lipid-associated protein species identified in our studies suggest that MERS-CoV infection is activating cellular death pathways to limit the number of cells that become infected but also stimulating the production of lipid-associated enzymes that can prolong host cell viability and the amount of time progeny virions can be produced and released. As the inhibitors that worked against MERS-CoV infection were also efficacious against SARS-CoV 2 infection, countermeasures that target these host pathways may provide novel ways to block highly pathogenic human coronavirus infection and/or prevent severe disease outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

COVID-19 Lead Time: Evaluating the timeliness and reliability of reported COVID-19 cases and hospitalizations as leading indicators of hospitalizations and death in the US

The COVID-19 pandemic prompted a reliance on real-time data sources to understand the global spread and impact of the SARS-CoV-2 virus. Reported cases were presumed leading indicators for hospitalizations, while hospitalizations were considered predictive of deaths. However, studies have questioned the consistency of reported cases as leading indicators. This study systematically assesses the reliability of United States (US) reported cases and hospitalizations as leading indicators for hospitalizations and deaths respectively, examining the first 2.5 years of the pandemic (January 2020 - June 2022) across different phases of the pandemic and states. Using correlation analysis, population data, and forecasting accuracy measures, we investigate the temporal relationships and identify possible determinants of lead time variability. Notably, we found that the average lead time between reported cases and hospitalizations across US states is relatively short at 1.76 days, implying that reported cases might not be as effective a leading indicator for hospitalizations as previously believed. Populations with higher comorbidity burdens, such as proportion of smokers, are expected on average to have shorter lead times, possibly due to shorter time to hospitalization among these vulnerable populations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Affordable Realtime Viral Detection: Demonstrated with SARS COV-2

The near real-time detection of airborne particles-of-interest is needed for avoiding current/future threats. The incorporation of imprinted particles into a micelle-based electrochemical cell produced a signal when brought into contact with particle analytes (such as SARS-COV-2), previously imprinted onto the structure. Nanoamp scales of signals were generated from what may’ve been individual virus-micelle interactions. The system showed selectivity when tested against similar size and morphology particles. The technology was compatible with airborne aerosol sampling techniques. Overall, the application of imprinted micelle technology could provide near real-time detection methods to a host of possible analytes of interest in the field.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Threat Agnostic Virulence Assessment of Pathogens

Virulence assessment of new, emerging, and engineered pathogens is critical to mounting an appropriate response to a biothreat agent. The capacity of the pathogen to colonize human and harm tissues must be characterized to understand pathogenicity pathways and optimize diagnosis and treatment of resulting disease. Respiratory pathogens are of interest because they can have high transmissibility rates, as observed with the SARS-CoV-2 virus, the causative agent of Covid-19. Current technologies are insufficient to assess threats due to their reliance on systems with only one cell type and on sequencing the pathogen. However, it is known that sequence is not an accurate predictor of function, and sequencing can be unreliable for newly emerged or engineered pathogens. An ideal system would consist of relevant epithelial cell types and an assay sensitive enough to detect changes in host responses that do not rely on DNA sequencing. We chose a system consisting of host lung epithelial cells that can be used to assess the virulence of unknown respiratory pathogens. We interrogated pathogens using this model and assess features of pathogenicity. Our objective is to leverage PNNLs strengths in tissue engineering and proteomics capabilities to build a multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) liquid chromatography-tandem mass spectrometry assay for human host cell proteins whose abundance is influenced by infection. These responses can were then assessed for relative virulence using pathogen agnostic signatures. When confronted with a pathogen, cells activate dedicated signaling pathways, typically through phosphorylation of regulatory proteins and downstream activation of host cell networks.

59 BASIC BIOLOGICAL SCIENCES↗