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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records

Cryo-EM Visualization of Intermolecular π-Electron Interactions within π-Conjugated Peptidic Supramolecular Polymers

The self-assembly of “π-peptides” – molecules with π-electron cores substituted with two or more oligopeptide chains – brings organic electronic function into biologically relevant nanomaterials. π-Peptides assemble into fibrillar nanomaterials as driven by enthalpic peptide-based hydrogen bonding networks and pi-core-based quadrupolar interactions. A large body of spectroscopic, morphological and computational studies informs on the nature of the self-assembly process and the resulting nanostructures, but detailed structural information has remained elusive. Here, inspired by the recent use of cryogenic electron microscopy (cryo-EM) to provide high-resolution structures for synthetic peptide nanomaterials, we present here the use of cryo-EM to offer ca. 3 Å resolution of π-peptide nanomaterial assemblies, visualizing for the first time the nature of the intermolecular π-core electronic interactions responsible for energy transport through these supramolecular materials.

Group theory↗

Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model

As cryo-electron microscopy (cryo-EM) enters mainstream structural biology, the demand for fitting methods is high. Here, we review existing flexible fitting methods for cryo-EM. We discuss their importance, potential concerns and assessment strategies. We aim to give readers concrete descriptions of cryo-EM flexible fitting methods with corresponding examples.

59 BASIC BIOLOGICAL SCIENCES↗

EMS and DMS Integration of the Coordinative Real-time Sub-Transmission Volt-Var Control Tool under High DER Penetration

This paper proposes an applicable approach to deploy the Coordinative Real-time Sub-Transmission Volt-Var Control Tool (CReST-VCT), and a holistic system integration framework considering both the energy management system (EMS) and distribution system management system (DMS). This provides an architectural basis and can serve as the implementation guideline of CReST-VCT and other advanced grid support tools, to co-optimize the operation benefits of DERs and assets in both transmission and distribution networks. Potential communication protocols for different physical domains of a real application is included. Performance and security issues are also discussed, along with specific considerations for field deployment. Finally, the paper presents a viable pathway for CReST-VCT and other advanced grid support tools, which could be integrated in an open-source standardized-based platform that supports distribution utilities.

Nguyen, Quan H.↗

Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the subångström- resolution structure of a protofibril formed by a wild-type segment from the β2–α2 loop of the bank vole prion protein. In this work, the structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named ‘polar clasps’.

59 BASIC BIOLOGICAL SCIENCES↗

Cryo-EM structure of the human neutral amino acid transporter ASCT2

Human ASCT2 belongs to the SLC1 family of secondary transporters and is specific for the transport of small neutral amino acids. ASCT2 is upregulated in cancer cells and serves as the receptor for many retroviruses; hence, it has importance as a potential drug target. Here we used single-particle cryo-EM to determine a structure of the functional and unmodified human ASCT2 at 3.85-Å resolution. ASCT2 forms a homotrimeric complex in which each subunit contains a transport and a scaffold domain. Prominent extracellular extensions on the scaffold domain form the predicted docking site for retroviruses. Relative to structures of other SLC1 members, ASCT2 is in the most extreme inward-oriented state, with the transport domain largely detached from the central scaffold domain on the cytoplasmic side. In conclusion, this domain detachment may be required for substrate binding and release on the intracellular side of the membrane.

59 BASIC BIOLOGICAL SCIENCES↗

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗

Novel features and GPU performance analysis for EM particle transport in the Celeritas code

Celeritas is a new computational transport code designed for high-performance simulation of high-energy physics detectors. This work describes some of its current capabilities and the design choices that enable the rapid development of efficient on-device physics. The abstractions that underpin the code design facilitate low-level performance tweaks that require no changes to the higher-level physics code. We evaluate a set of independent changes that together yield an almost 40% speedup over the original GPU code for a net performance increase of 220× for a single GPU over a single CPU running 8.4M tracks on a small demonstration physics app.

Johnson, Seth R.↗

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗

Barotrauma em peixes em usinas hidrelétricas: ferramentas para o estudo

The main source of electric power generation in Brazil comes from hydropower plants, nevertheless, the installed power is expected to raise 56.8%, reaching a total of 116,000 MW at the year 2020. The increase at the hydroelectric sector will be responsible for a series of fish community impacts. One of the impacts over the fish community is related to fish kills due to downstream passage through turbines or fish entrance at the draft tube from the tailrace. Usually when there is a maneuver and the turbine stops, fish get attracted and enter the draft tube and, just as the downstream passage through a turbine, when the turbine starts, a rapid decompression occurs and can cause barotrauma. When such events happen, according to Boyle’s law (P1V1=P2V2), swim bladder volume expands at the same rate that the pressure decreases, which can lead to the organ’s rupture.

barotrauma↗

The U.S. DOE-EM International Program - 17411

The U.S. Department of Energy (DOE) Office of Environmental Management (EM) has a mission to complete the safe clean-up of the environmental legacy resulting from six decades of weapons production and energy research. This effort is recognized as one of the largest and most diverse and technically complex environmental clean-up operations in the world. The overall strategy to address this challenge includes several components, one of which involves leveraging the expertise within the International community, when applicable. The opportunities related to international collaborations are an important component of the DOE EM strategy for the clean-up mission, providing excellent forums for EM to stay beneficially engaged with the international community and our global partners. EM has been supporting the clean-up mission of the Department through international collaborations for almost 20 years. The EM International Program is sponsored by the DOE EM Office of the Chief of Staff (EM-2.1), which directly supports the DOE-EM Office of Assistant Secretary (EM-1), in coordination with the entire EM organization. The primary objective of the EM International Program is to provide benefit to the Department in successful completion of the EM clean-up mission, through establishing strategic approaches for specific international collaboration initiatives that are focused on appropriate strategic program goals. The EM International Program strategy to support the EM mission includes many facets, but they can generally be grouped into two primary areas. First, the EM International Program maintains, establishes, and/or participates in international agreements such that appropriate mechanisms are available for conducting international collaborations with foreign government organizations, educational institutions and private industry to leverage resources and link international experience and expertise, in support of the EM mission and compliant with US foreign policy. Second, through coordination with the EM Office of Technology Development (EM-3.2), the EM International Program leverages these agreements to identify mutually beneficial opportunities to evaluate, test, and adapt technologies, capabilities, and expertise for application to EM mission needs. These activities directly support goals within the current DOE Strategic Plan 2014 - 2018, issued in April 2014. Working with the Office of Technology Development, the EM International Program is developing a process for identifying and selecting collaborative international technology projects for Fiscal Year 2017 (FY17) that have high potential impact to the EM mission. The technical scope of these activities is expected to span the entire EM mission, including tank waste and nuclear materials management; groundwater and soil remediation; deactivation and decommissioning; and radioactive waste disposal operations. Depending on budget availability, these collaborative activities are expected to be awarded by mid-FY17. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Use of Historical EM Practices and Policies for Management of Cleanup Program and Address GAO Concerns - 20222

As Department of Energy (DOE) Environmental Management (EM) program policies and management practices are revised over time, it might be useful to periodically reflect on the DOE EM program's past to identify practices that have worked and those that might be appropriate for possible reuse in the future. An added impetus to examine alternative approaches is the recent Government Accountability Office (GAO) report entitled 'Nuclear Waste Cleanup - DOE Could Improve Program and Project Management by Better Classifying Work and Following Leading Practices.' The February 2019 GAO report states that EM categorizes most of its work in a way that does not adequately involve independent experts and DOE senior leadership. It also noted that EM has not followed leading practices for program and project management that could help keep the cleanup efforts on schedule and control costs. The GAO report recommended that EM, working with DOE Office of Project Management (PM): - Establish requirements and then assess EM's ongoing operations activities to determine if some activities should be reclassified as capital asset projects based on these newly established requirements. - Review and revise EM's 2017 cleanup policy to include program management leading practices related to scope, cost, schedule performance, and independent reviews. - Update the cleanup policy to require that earned value management (EVM) systems be maintained and used in a way that follows EVM best practices. - Develop a policy to ensure that work is categorized as level of effort (LOE) only in appropriate, specified circumstances, such as when work is not measurable or when measurement is impractical. - Integrate EVM data into EM's performance metrics for operations activities. To assist with improving program performance and implementing audit recommendations, this paper reviewed past successful cleanups such as Weldon Springs, Rocky Flats, Fernald, Ashtabula, Battelle Columbus (abs, and other historical resources and people with experience during the early years of EM program. As such, there are several past practices which may well be suited for reuse today. Some of these practices include: - In 1990's, as the DOE EM cleanup program, known as Environmental Restoration came into effect, the known cleanup scope at each geographic location or site was organized into four levels ranging from overall site-wide cleanup effort to the individual 'release sites', providing high granularity to the program. - The cleanup program was organized by geography (Northwest, Southwest, Eastern Area Programs, etc.). These 'sub-program' managers provided a degree of Headquarters oversight and management allowing upper management (EM-1, 2, and 3) to focus on major decisions and issues. - Budget levels at selected cleanup sites were funded above 'minimum-safety' levels to accelerate actual cleanup work. - Past practice utilized EVM techniques and uniform EM oversight over all discrete project-like activities, providing for a coordinated cleanup effort. - EM managed LOE activities using benchmarking and best in class management practice techniques to help manage costs. - EM managed and reviewed entire site cleanup baselines, not only individual projects, focusing on a successful overall outcome. - Sites had a 'Road map' or 'Management Action Plan' that provided the overall strategy or plan for that site's cleanup - this helped with understanding and coordination of efforts. - EM had a robust lessons-learned program and database to capture and transmit worthy ideas. - EM had well-structured cleanup baseline change control policies to control cost and schedule changes, at the contractor and higher Headquarters levels. Finally, some of the GAO observations may be valid, however it is not clear as to their extent. For example, for some operation types of work, the use of the Level of Effort (LOE) earned value method to track progress may be appropriate. Also, to ensure independence of thought, and to obtain useful insight on past practices, it may be suitable to have former EM employees to assist with understanding past practices or to verify that activities have been properly identified. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Panel Session 2: 30 Year Anniversary of US DOE-Environmental Management-EM Update

This panel focused on Senior US DOE Managers from Washington, D.C. speaking on the pressing issues facing US DOE EM sites and the 30 year anniversary of DOE - EM. The panel was moderated by Martin Schneider, Longenecker and Associates. Presentations proposed include: 1 - DOE Environmental Management Update From EM-2 (Mark Gilbertson, US DOE EM (USA)); 2 - DOE Environmental Management Update From EM-3 (Jeffrey Griffin, US DOE EM (USA)); 3 - DOE Environmental Management Update From EM-4 (Betsy Connell, US DOE EM (USA)); 4 - DOE Environmental Management Update From EM-5 (Steve Trischman, US DOE EM (USA))

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗