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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The International Virus Bioinformatics Meeting 2020

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2

COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Understanding Air Quality Changes after Implementation of Mitigation Measures during a Pandemic: A Scoping Review of Literature in the United States

Traffic-related emissions continue to be a significant source of air pollution in the United States (US) and around the globe. Evidence has shown that previous policies implemented to restrict-traffic flows have affected air pollution levels. Thus, mitigation strategies associated with the COVID-19 pandemic that modified population-level mobility patterns provide a unique opportunity to study air pollution change across the US. For instance, to slow the spread of the pandemic, state and local governments started implementing various mitigation actions, including stay-at-home directives, social distancing measures, school closures, and travel restrictions. This scoping review aimed to summarize the existing evidence about how air quality changed through mitigation practices throughout the pandemic in the US. We found 66 articles that fit our inclusion criteria. Generally, the consolidated results revealed that nitrogen dioxide (NO 2 ) and carbon monoxide (CO) decreased across the country. Studies observed mixed directions and magnitudes of change for fine and coarse particulate matter (PM 2.5 , PM 10 ), ozone (O 3 ), and sulfur dioxide (SO2). Few articles tried to explain this notable heterogeneity in air quality changes by associating contextual factors, such as mobility, traffic flow, and demographic factors. However, all studies agreed that the change in air pollution was nonuniform across the US and even varied within a city.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2020

Remote Support of ISS Payload Operations During the COVID19 Pandemic

As part of the Human Health and Performance Contract (HHPC) with the NASA Johnson Space Center, the Human Research Program’s (HRP) Research Operations and Integration (ROI) element conducts the planning, implementation, and closing of human research operations on-board the International Space Station (ISS). These operations are supported out of the Telescience Support Center (TSC) located in the Mission Control Center at Houston’s Johnson Space Center (MCC-H). HRP ROI has an Emergency Response Plan in place to allow for remote operations to be completed in the case of inclement weather or other natural disaster; however, nominally, the remote support is only expected to last one to two weeks. In response to the COVID-19 global pandemic, HRP ROI was challenged to complete a quick transition to supporting on-orbit operations remotely and distanced for an indefinite amount of time. This shift in ground support required close collaboration with various external groups as well as the implementation or adaptation of various technologies and tools to ensure no loss of science data. Operational adjustments were put into place for ground commanding, telemetry monitoring, personnel staffing and private and public audio and video with the ISS. Adjustments were also put in place for communication and collaboration with MCC-H, the Payload Operation and Integration Center (POIC) at Marshall Space Flight Center (MSFC), as well as between the various HRP ROI console team members spread across Houston, TX. The ability to successfully support a variety of on-orbit operations from any remote location is more in demand as the commercialization of low Earth orbit is expanding.

Operations↗
DOE OSTI2021

Scenarios of a Sustainable Energy Transition: Perspectives from the U.S.

The energy sector has been undergoing a significant transition over the past decade, which was accelerated in 2020 during the COVD-19 pandemic. This presentation provides an overview of energy trends in the U.S., including electricity, oil and gas, coal, and renewables, the impact of the pandemic in 2020, and forecasts for recovery. Scenarios of energy use and future integrated technologies are outlined as near and mid-term approaches. The presentation concludes with potential U.S. policy priorities focused on energy and economic recovery, as well as perspectives on energy planning from the disruptions of 2020. The presentation is part of day-long series of presentations covering post-COVID-19 energy responses in Asia, Australia, Europe, and the United States.

COVID-19↗
DOE OSTI2021

Delivering Effective Virtual Energy-Focused Trainings: Successful Strategies and Lessons Learned from the Virtual Cohort In-Plant Training Pilot

While there are always barriers to energy efficiency efforts, few challenges have been as severe as the global COVID-19 pandemic. Many manufacturers throughout the United States and the world have been trying to determine how to safely open and operate their plants. To minimize the number of people working within facilities and maximize the physical distance between workers, only essential facility engineers are allowed into plants to ensure proper operations. The Department of Energy’s Better Plants Program created In-Plant Trainings (INPLTs) to help partners develop in-house expertise in energy efficiency. Delivering INPLTs in the traditional in-person fashion is infeasible under these circumstances. To continue providing INPLTs during this difficult time, the Better Plants Program piloted Virtual Cohort In-Plant Trainings (VINPLTs) on wastewater treatment and ammonia industrial refrigeration systems from October 27 to November 19, 2020. This paper provides an overview of the pilot, then discusses successful strategies and lessons learned from this pilot for delivering effective virtual energy-focused trainings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Sustainability, Scalability and Resiliency of the Town of Innisfil Mobility-on-Demand Experiment: Preliminary Results, Analyses, and Lessons Learned: Preprint

In 2017, the Town of Innisfil, Ontario launched Innisfil Transit in partnership with Uber, a transportation network company, to provide a subsidized on-demand public mobility service as an alternative to investing in a new fixed-route bus service. The performance of Innisfil Transit is documented in a 2021 Ryerson University report which shows greater cost effectiveness of the mobility provided over the proposed bus alternative (Sweet, Mitra, and Benaroya 2021). This paper expands on those findings by assessing Innisfil Transit with respect to sustainability, scalability, and resiliency. First, we quantify the energy and emissions of this program relative to traditional transit and driving alone across varying powertrains. We then characterize a conservative first-order estimate of the percentage of US communities that fall within a similar spatial-demographic tier as Innisfil. Replicability also hinges on service cost and performance in comparison to average values for low-density transit in the US. Lastly, most transit agencies experienced a significant drop in demand (as much as 90%) with slowly rebounding ridership since the onset of the COVID-19 pandemic. The resiliency of the Innisfil program to the pressures induced by the pandemic is examined in comparison to other transit operations. The lessons learned across these three dimensions complement prior work to better understand the efficiency and sustainability of on-demand public mobility service for low-density communities like Innisfil.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Pulmonary ACE2 expression in neonatal and adult rats

Children show a distinct presentation of COVID‐19, characterized by a lower incidence and mild phenotype, but the reason for this is still unknown. The angiotensin‐converting enzyme 2 (ACE2) functions as the primary cell entry receptor for Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and is thought to cause distinct clinical features between children and old people. The primary purpose of this study was to determine whether differences exist in the level of expression and distribution of ACE2 between neonatal and adult rat lungs. The lung tissues from rats of various ages were used to investigate the expression patterns of ACE2. Western blot, immunohistochemistry, and immunofluorescence were used to quantify or identify the localization of ACE2 in rat lungs. ACE2 was homogenously expressed in fewer alveolar type II (AT2) cells in the neonatal lung, with no polarization to the alveolar space and additional expression in pulmonary endothelium when compared to adult rat lungs. These findings suggest that the patterns of ACE2 distribution and cellular localization in rat lungs change with age.

Zhao, Depeng↗
DOE OSTI2024

RNA oligomers at atomic resolution containing 1‐methylpseudouridine, an essential building block of mRNA vaccines

Abstract All widely used mRNA vaccines against COVID‐19 contain in their sequence 1‐methylpseudouridine ( m1Ψ ) instead of uridine. In this publication, we report two high resolution crystal structures (at up to 1.01 and 1.32 Å, respectively) of one such double‐stranded 12‐mer RNA sequence crystallized in two crystal forms. The structures are compared with similar structures which do not contain this modification. Additionally, the X‐ray structure of 1‐methyl‐pseudouridine itself was determined.

Nievergelt, Philipp↗
DOE OSTI2026

Exploration of Nirmatrelvir Derivatives as Optimized SARS‐CoV‐2 Antivirals

Nirmatrelvir (NMV) is a SARS‐CoV‐2 antiviral component of the approved COVID‐19 therapeutic Paxlovid. It is a reversible covalent inhibitor of SARS‐CoV‐2 main protease (M Pro ) that is effluxed from human cells by P‐glycoprotein (P‐gp). To identify NMV analogs with improved potency and reduced P‐gp efflux, a structure–activity relationship campaign was conducted. Warheads alternative to nitrile for engaging the active site cysteine were tested showing aldehyde and dichloroacetamide with better enzyme inhibition potency. Crystal structure of MPI‐136−M Pro shows its aldehyde warhead forming a thiohemiacetal with active Cys145 of M Pro . Several S4 binders were explored revealing that an O‐to‐S shift at the N ‐terminal amide leads to better enzyme inhibition. By exploring different combinations of S2, S3, and S4 binders, two inhibitors with better enzyme inhibition potency than NMV were found. Crystal structure of MPI‐148, with ( S )‐2‐azaspiro[4,5]decane‐3‐carboxylate as an alternative S2 binder, shows extensive hydrogen‐bond networks for locking the inhibitor in active site, explaining high affinity of NMV analogs. Further characterization of cellular M Pro engagement and antiviral potency against SARS‐CoV‐2 revealed four inhibitors with greater potency than NMV in P‐gp‐expressing cells. Studies with the P‐gp inhibitor CP‐100356 showed that these compounds were less sensitive to P‐gp inhibition than NMV, consistent with reduced P‐gp‐mediated efflux.

Alugubelli, Yugendar R. [Texas A&M Drug Discovery ↗
DOE OSTI2024

Real‐time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis

X‐ray scattering experiments using free electron lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID‐19 viral proteins). XFEL experiments are a challenge to computing in two ways: (i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; (ii) data‐collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min—sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS‐NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis within 10 min is a first for XFEL experiments and an important milestone if we are to keep up with data‐collection trends.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Commercialization of microcavity plasma devices and arrays: Systems for VUV photolithography and nanopatterning, disinfection of drinking water and air, and biofilm deactivation for medical therapeutics

Abstract A little more than two decades after the introduction of the first microcavity plasma devices, a growing body of commercial products based on the remarkable properties of these low‐temperature, atmospheric plasmas is now available. Following a brief review of early microplasma lamp development, this article describes microplasma‐based devices and systems currently being manufactured for applications in photolithography, photopatterning, and other nanofabrication processes, such as atomic layer deposition, spectroscopic identification and analysis of materials (including wide bandgap crystals), the disinfection of drinking water in off‐grid communities, deactivating COVID‐19 and other pathogens in air and on surfaces in public spaces, and vacuum ultraviolet lamps for driving atomic clocks. The microplasma‐based treatment of otitis media in the human ear will also be discussed.

42 ENGINEERING↗
DOE OSTI2025

Bayesian Calibration of Stochastic Agent Based Model via Random Forest

Agent-based models (ABM) provide an excellent framework for modeling outbreaks and interventions in epidemiology by explicitly accounting for diverse individual interactions and environments. However, these models are usually stochastic and highly parametrized, requiring precise calibration for predictive performance. When considering realistic numbers of agents and properly accounting for stochasticity, this high-dimensional calibration can be computationally prohibitive. This paper presents a random forest-based surrogate modeling technique to accelerate the evaluation of ABMs and demonstrates its use to calibrate an epidemiological ABM named CityCOVID via Markov chain Monte Carlo (MCMC). The technique is first outlined in the context of CityCOVID's quantities of interest, namely hospitalizations and deaths, by exploring dimensionality reduction via temporal decomposition with principal component analysis (PCA) and via sensitivity analysis. The calibration problem is then presented, and samples are generated to best match COVID-19 hospitalization and death numbers in Chicago from March to June in 2020. Further, these results are compared with previous approximate Bayesian calibration (IMABC) results, and their predictive performance is analyzed, showing improved performance with a reduction in computation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A review of antimicrobial implications for improving indoor air quality

The frequent outbreak of infectious respiratory diseases, such as the recent COVID-19 epidemic, raised the importance of indoor air quality. Removing microorganisms from indoor air is critical to improve indoor air quality. Numerous studies in recent years have been published on developing antimicrobial materials and technologies for antibacterial and antiviral applications. Further, this study critically reviews the recent antimicrobial advances for improving indoor air quality. This paper provides a comprehensive analysis of the antimicrobial mechanisms, development of materials, and deployment strategies, as well as a performance evaluation of the antimicrobial implication for indoor air quality. Furthermore, the challenges and opportunities of future research directions are also highlighted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Preface to “From Coadsorption and Catalysis at Solid Surfaces to Liquid–Solid Interfaces in Theory and Experiment, Published in Honor of Professor Robert K. Grasselli, Irsee IX Symposium Kloster Irsee, Germany 16–19 June 2022 (Irsee IX)”

The 9th Irsee Symposium entitled “From Coadsorption and Catalysis at Solid Surfaces to Liquid–Solid Interfaces in Theory and Experiment”, sponsored by the Robert Karl Grasselli Foundation, took place at its traditional venue, the Schwäbisches Bildungszentrum in Irsee, Germany, on 16–19 June 2022. In the Irsee Symposium, selected experts gather every few years to discuss recent progress, challenges, new directions, and frontiers in catalysis. Furthermore, after the moratorium imposed on us by Covid-19, all the participants especially enjoyed the lively meeting and face-to-face interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Topography and electrostatic interactions of electret fibres in N95 facemasks

Facemasks have been a critical line of defense in the Covid-19 pandemic and have been used for decades to reduce the inhalation of sub-micron aerosols, including bacteria, viruses and nano-materials. These facemasks leverage electrostatic charge properties of non-woven electret fibre mats to remove sub-micron aerosols. However, the topographical and electrostatic properties of these mats have not been well characterized at the nano-scale. In this study, we use atomic force microscopy (AFM) to examine the surface topography of the electret fibres within a commercial respirator fibre mat, use electrostatic force microscopy to map the electrostatic interactions emanating from these fibres, and use synchrotron X-ray scattering to probe polymer morphology. We find that within these mats the fibres exhibit significant heterogeneity in surface topography, electrostatic interactions and polypropylene phase composition. The surface topographies ranged from nano-smooth surfaces to ordered spherulitic structures. Furthermore, the electrostatic interactions varied across fibre length and circumference and are only weakly correlated with surface topographical features. Finally, we use AFM to characterize fibres after filtering a NaCl aerosol and find that the deposited particles are heterogeneous in size and distributed over the fibre surfaces.

36 MATERIALS SCIENCE↗