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At least 127 records · Page 7

Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid

Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide. Structure-guided drug discovery by Pfizer, Inc (facilitated by PDB structures), initiated in the 2000s in response to SARS-CoV-1 and resumed in 2020, yielded nirmatrelvir (the active ingredient of Paxlovid) -- a potent, orally-bioavailable inhibitor of the SARS-CoV-2 main protease. You've got to love the Protein Data Bank!

Burley, Stephen K.↗

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools

Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. In this paper, we have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. Finally, the herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

59 BASIC BIOLOGICAL SCIENCES↗

Cataloging Legacy Data from the Tritium Systems Test Assembly Program

The Tritium Systems Test Assembly (TSTA) at Los Alamos National Laboratory, operational from 1984 to 2001, was critical in advancing fusion fuel cycle technologies, including tritium storage, gas separation, and pumping. TSTA’s contributions, particularly in safe tritium operations, have influenced subsequent fusion projects. This paper discusses the ongoing effort to digitize and catalog TSTA’s historical data to create a searchable resource for the fusion research community. While the long-term objective is to develop a relational database for structured data management, the project remains in the early phase, with current efforts focused on scanning and indexing physical documents. Initial plans for database implementations are also presented, outlining key considerations for structure, query indexing, and standardization. As digitization progresses, future discussions will refine these implantation details to ensure an efficient and comprehensive system. This initiative aims to preserve critical legacy data, enhance the design of tritium system facilities, and support the next generation of fusion energy research.

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A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

Beneficial symbiotic fungi colonize plant tissues, delivering crucial ecosystem services such as carbon sequestration and plant fertilization. Specifically, trees that form a nutrient-acquiring symbiosis with mutualistic ectomycorrhizal (ECM) fungi gain advantages from these associations by experiencing enhanced growth rates and increased resilience to both biotic and abiotic stresses. Despite the vital role ECM fungi play in the nutrition and well-being of trees, identifying key regulators participating in the molecular communication between plant and fungal cells is still in its early stages. The mutualistic relationship between Laccaria bicolor and Populus spp. has been utilized as a model system for investigating ECM symbiosis at the molecular level. It has been demonstrated that the fungus L. bicolor secretes Mycorrhiza-induced Small Secreted Proteins (MiSSPs) required for ECM development. Meanwhile, we have previously shown that P. trichocarpa small, secreted proteins (PtSSPs) are highly induced during mutualistic symbiosis and some of them can enter, via in-vitro feeding, L. bicolor hyphae affecting their growth and morphology. However, the exact role and mode of action of PtSSPs in mutualistic symbiosis remain unknown. Because previous study showed that PtSSP1 is taking up by fungal cell and then localize in fungal cells, we decide to dig further on its putative role in fungal cells and also by overexpressing it in poplar because it is not technically possible yet to overexpress poplar protein in Laccaria bicolor hyphae. Here, we further characterized the function of PtSSP1(Potri.009G063200) in ectomycorrhization, which accumulates in the nucleus of L. bicolor in an in-vitro feeding experiment. Our results provide new knowledge for the genetic engineering of plants to control associated microbes.

59 BASIC BIOLOGICAL SCIENCES↗

Training package 1 for slitting data analysis

This document and accompanying files are intended as a first training package on how to analyze slitting data. The end goal is to have Idaho National Laboratory (INL) personnel trained to analyze future slitting data taken in the INL Hot Cell on clad, Low-Enriched Uranium (LEU) fuel plates. This first data package will cover data analysis for a monolithic material (as compared to a layered material like the clad fuel plates). The additional issues for layered specimens will be covered in a future training package.

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Sierra Structural Dynamics Code Verification Plan

Verification and validation (V&V) of scientific computing programs are important at San- dia National Laboratories (SNL) due to the expanding role of computational simulation in managing the United States nuclear stockpile. This document presents the verification plan for the Sierra Structural Dynamics application. This verification plan includes code devel- opment practices, structure of test suites, and additional quality assurance practices used by the Sierra/SD team.

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Probabilistic Seismic Hazard Assessment for Georgia

Probabilistic Seismic Hazard Assessments (PSHA) form the basis for most contemporary seismic provisions in building codes around the world. The current building code of Georgia (2009) is not fully compatible with seismic hazard and design concepts of modern codes. The Ministry of Economy and Sustainable Development of Georgia is currently undertaking an update to the building code to align it with EuroCode. In conjunction with EuroCode, a National Annex specific to Georgia is needed, including seismic hazard values for the territory of Georgia. A comprehensive earthquake catalogue is fundamental to a robust PSHA in the region. The Caucasus has had an uneven seismic recording and reporting history both temporally and spatially. Therefore, there has been a strong regional effort to bring together data from all the countries in the Caucasus, to digitize and standardize paper-based data from the Soviet era, and to re-examine magnitude and location calculations. The earthquake catalogue resulting from this effort forms the basis for a reliable seismic hazard assessment. Recognizing these needs, the U.S. Department of Energy through Lawrence Livermore National Laboratory (LLNL) initiated a project in 2015 to engage and train local scientists in the Caucasus to install new equipment, to enhance the quality of seismic monitoring and reporting, and to improve and harmonize the regional earthquake catalogue. In 2016, the project scope was expanded to include the modernization of seismic hazard assessments. To this end, a series of workshops were held in Georgia, the first one of which presented an overview of PSHA and its components to various participants from the universities and other research organizations in the region. This kick-off workshop was followed by numerous hands-on training workshops in 2017 and 2018, covering all aspects of PSHA. In addition to their training goals, the workshops brought together existing and new information relevant to PSHA studies in the region, providing a platform for local scientists/engineers and experts from other parts of the world to interact, cooperate and discuss various pieces of the PSHA input. This report outlines the aspects of the earthquake catalogue development and PSHA project that were specifically undertaken to form the basis for the building code update in Georgia. Georgia straddles the Greater Caucasus and Lesser Caucasus Fold and Thrust belts, where the convergent tectonic setting generates significant earthquake activity. To the east of the country, evidence indicates the possibility of a remnant subducting slab that causes earthquakes deeper than 40km. This study systematically compiles and improves all available data on local seismicity, active faults, and ground motion attenuation characteristics of the region; and builds a framework to enable a contemporary PSHA to be carried out with the engagement of local scientists. To this end, six regional workshops were organized in total over a three-year period of time, with participation from the United States, Canada and Hungary as well as countries in the Caucasus: Georgia, Armenia, Azerbaijan and Turkey. The workshops served multiple purposes such as training, data collection, interactions between local earth scientists and engineers, and brainstorming and knowledge exchange among local and international experts.

Geosciences↗

Fundamental Forces, Lasting Impressions: Historical Documentation of the Sigma Press Building (TA-3-35) Volume 1

The US Department of Energy, National Nuclear Security Administration, Los Alamos Field Office (Field Office) has prepared final documentation for the resolution of adverse effects to Building 35 in Technical Area (TA) 3 at Los Alamos National Laboratory (LANL or the Laboratory). This documentation is being submitted to the New Mexico State Historic Preservation Officer (SHPO). TA-3-35, a Cold War-era press building, was determined eligible for listing in the National Register of Historic Places (Register) in the report Pressing Matters: An Evaluation of the Cold War Buildings at the Sigma Complex (LA-UR-15-28961). This report also identified Building TA-3-35 as excess property to be decontaminated, decommissioned, and demolished by the LANL Footprint Reduction Program in Fiscal Year 2016, an adverse effect requiring mitigation. The SHPO concurred with the both the eligibility determination of, and adverse impact to, Building TA-3-35 on February 29, 2016.

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Library of Advanced Materials for Engineering (LAME) 4.54

Accurate and efficient constitutive modeling remains a cornerstone issue for solid mechanics analysis. Over the years, the LAMÉ advanced material model library has grown to address this challenge by implementing models capable of describing material systems spanning soft polymers to stiff ceramics including both isotropic and anisotropic responses. Inelastic behaviors including (visco)plasticity, damage, and fracture have all incorporated for use in various analyses. This multitude of options and flexibility, however, comes at the cost of many capabilities, features, and responses and the ensuing complexity in the resulting implementation. Therefore, to enhance confidence and enable the utilization of the LAMÉ library in application, this effort seeks to document and verify the various models in the LAMÉ library. Specifically, the broader strategy, organization, and interface of the library itself is first presented. The physical theory, numerical implementation, and user guide for a large set of models is then discussed. Importantly, a number of verification tests are performed with each model to not only have confidence in the model itself but also highlight some important response characteristics and features that may be of interest to end-users. Finally, in looking ahead to the future, approaches to add material models to this library and further expand the capabilities are presented.

36 MATERIALS SCIENCE↗

Future SDN-HPON Control Plane Architecture and Protocol for On-Demand Terabit End-to-End Extreme-Scale Science Applications

The UC Davis team conducted architecture, algorithm and experimental studies for next generation ultra-high-bandwidth optical networks in support of extreme-scale science applications. In particular, over the course of this 3-year project, the UC Davis team achieved the following main accomplishments: Designed a network architecture for automated multi-domain service provisioning: Designed information exchange schemes between autonomous systems (domains) Designed application programming interfaces to orchestrate resource reservation in data centers, high performance computation facilities, and communication networks belonging to different autonomous systems Experimentally assessed the multi-domain network architecture in a distributed field trial set-up connecting premises in three continents Designed a broker-based orchestrated multi-domain optical networking framework supporting observe-analyze-act cycle based cognitive inter-domain service provisioning: Designed an inter-domain operation mechanism, e.g., topology abstraction, for the broker plane and domain managers to collaboratively accomplish inter-domain service provisioning while respecting the autonomy of each administrative domain Designed an alien wavelength monitoring scheme and an artificial neural network based optical signal-to-noise ratio estimator for quality-of-transmission aware inter-domain service provisioning Developed a deep neural network based multi-domain traffic predictor and a cognitive routing and spectrum assignment algorithm to realize knowledge-based autonomous traffic engineering in multi-domain networks Implemented an optical signal-to-noise ratio estimator and traffic predictor with Google’s Tensor flow and assessed their performance using experimental and synthetic data Demonstrated the benefits of the proposed cognitive schemes with experiments ona two-domain elastic optical network testbed and evaluations on a six-domain simulation framework Built a two-domain software-defined networking control plane testbed using the ONOS platform and demonstrated the workflow of broker and domain manager cooperation, including hierarchical performance monitoring, topology abstraction and cognitive resource allocation. Designed self-learning cognitive service provisioning schemes using advanced machine learning technologies: Designed a self-taught anomaly detection framework for optical networks, including an unsupervised data clustering module for pattern recognition, a supervised data regression and classification module for online anomaly detection, and the system operation principle Experimentally validated the effectiveness of the self-taught anomaly detection framework with various failure/anomaly scenarios. Designed a self-learning autonomic routing, modulation and spectrum assignment (RMSA) provisioning framework for elastic optical networks with deep reinforcement learning. Designed effective modeling and training mechanisms for the self-learning RMSA framework Conducted extensive numerical simulations with various traffic patterns and topologies to verify the advantage of the self-learning RMSA framework.

42 ENGINEERING↗

Global Perspective of Energy Storage (2019 Annual Peer Review Report)

This report provides information about the DOE Office of Electricity Energy Storage Peer Review held in 2019 and includes posters reviewed in these categories: postdoctoral, validated reliability and safety performance, equitable regulatory environment and analytics, applied materials (Materials I), power electronics, industry acceptance, partnerships, and Materials I.

13 HYDRO ENERGY↗

TA-16-306: A Plastics Components Development Facility (Volumes 1 & 2)

The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), Los Alamos Field Office (Field Office), has prepared final documentation for the resolution of adverse effects to Building 306 in Technical Area (TA) 16 at Los Alamos National Laboratory (LANL or the Laboratory). This documentation is being submitted to the New Mexico State Historic Preservation Officer (SHPO). TA-16-306 was determined eligible for listing in the National Register of Historic Places (Register) in 1995 in the report, TA-16 Heating System Replacement (LA-CP-95-0180). TA-16- 306 was identified as an excess property to be decontaminated, decommissioned, and demolished by the LANL Footprint Reduction Program in fiscal year 2021, an adverse effect to Register eligible building 16-306 requiring mitigation. To bring a resolution to the adverse effects to Building TA-16-306, the Field Office initiated consultation with the SHPO on December 4, 2017. The New Mexico Historic Preservation Division concurred with the mitigation actions outlined in the Programmatic Agreement among the U.S. Department of Energy, National Nuclear Security Administration, Los Alamos Field Office, the New Mexico State Historic Preservation Office, and the Advisory Council on Historic Preservation Concerning Management of Historic Properties of Los Alamos National Laboratory, Los Alamos, New Mexico (PA) in correspondence dated January 30, 2018. The PA states in Appendix D.2.A that adverse effects to Register-eligible buildings and structures will be resolved according to the procedures defined in A Plan for the Management of the Cultural Heritage at Los Alamos National Laboratory, New Mexico (CRMP) (LA-UR-19-21590, formerly LA-UR-15-27624) and within the PA itself. Volume 2 contains a collection of photos of building TA-16-306 with index.

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Tribal Colleges and Universities/Advanced Manufacturing Network Initiative (Phase II) (Q1 FY2021 Progress Report)

The National Nuclear Security Agency (NNSA) initiated the Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA’s enduring technical workforce at the laboratories and production plants, and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new consortium in early FY17 focused on Tribal Colleges and Universities (TCUs) known as the Advanced Manufacturing Network Initiative (AMNI). This consortium has been extended for FY20 and FY21. The following report summarizes the status update during this quarter.

42 ENGINEERING↗

Installation of Ramps and Utility Cabinet at TA-18-1 Slotin Building (Historic Building Report No. 395)

The information below is presented in response to requests for additional information that resulted from a phone conference on November 12, 2020 between Harvey Kaplan of the New Mexico State Historic Preservation Office, DOE NNSA Los Alamos Field Office Manhattan Project National Historical Park Representative, Vicki Loucks, LANL Program Manager for Manhattan Project National Historical Park, Cheryl Abeyta, and LANL Historic Buildings Program Staff, Jeremy Brunette and J.T. Stark. The DOE NNSA Field Office (Field Office) initiated the call to propose additional work be performed to a previously reviewed project, “Restoration of TA-18-0001 (Slotin Building)” (LA-UR-19-26609) (HPD Log # 111110). Of the six actions discussed on the call, which included (1) exterior paint color, (2) entrance ramps, (3) non-period metal siding removal, (4) interior floor finish, (5) reopening secondary entrance door, and (6) addition of utility cabinet with period doors, additional information for two of the actions was requested for further review. The two actions, the construction of entrance ramps and installation of a utility cabinet are addressed in detail.

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Global Trends of ASME "N-Stamp" Certifications for Nuclear Component Vendors

Historically, nuclear component manufacturing vendors, from small businesses through large conglomerates, have felt compelled to obtain an American Society for Mechanical Engineers (ASME) Nuclear Certification, known colloquially as an "N-stamp", to assure supply chain quality standards that will be acceptable to regulators and safety concerns. Since the N-stamp quality standard is a U.S.-origin code, combined with the apparent decline in the U.S. nuclear industry alongside the growth of the Asian nuclear industry, there is the question of whether the rest of the world, including new entrants to the nuclear industry, also regard N-stamp as a needed certification. This study addresses this question through analysis of the entire N-stamp database of holders, and former holders, of N-stamp certificates of all types and for all regions worldwide from 1989-2020 (the dates available in the database). From this 30 years of data, we find that actually U.S.-based vendors still consistently obtain the largest number of N-stamps worldwide over all time periods, but also find that the countries participating in the N-stamp certification process has broadly expanded beyond just North America, Japan, S. Korea and Western Europe (the primary N-stamp recipients before the mid-2000's). We produced global heats maps and bar charts to illustrate our findings, as well as further investigation into why the data shows changes over time and region. We note that nuclear entities involved with Soviet-type reactors do not participate in the N-stamp process, but instead pursue the Russian version PNAE, which is substantially similar to the ASME code. We conclude that at least from the N-stamp database, the United States nuclear component manufacturing industry is alive and well, although there have been some consolidations, and that the ASME N-stamp appears to still be a valued certificate worldwide, including in China which now ranks second only to the United States in obtaining N-stamp certificates in recent years. We further note that the vendors of new reactor types, in particular High Temperature Gas-Cooled Reactors (HTGRs) and Small Modular Reactors (SMRs), are actively engaged with ASME (and other U.S.-based nuclear standards bodies such as the American Nuclear Society and Nuclear Energy Institute) to coordinate updates to the ASME N-Stamp criteria to ensure applicability of the code for these new designs. Implications of these findings include the following: The global use of the U.S.-origin N-stamp certification supports the view that, despite the decline of the U.S. nuclear industry, the United States remains an esteemed global leader in the area of nuclear safety. As the U.S. Government works to revitalize the U.S. nuclear industry, especially in the area of exports, it may be beneficial to leverage the global standing of the N-stamp certification. The findings indicate that the N-stamp database would be a useful tool for the U.S. Government to use to track the growth of the civil nuclear industry in foreign countries, under certain circumstances. The Excel-format N-stamp database produced as part of this study may be a useful tool for this purpose. N-stamp data may be a useful tool for foreign governments to use to identify nuclear manufacturers within their own country, especially to identify "targets" for outreach on nuclear export control compliance. The U.S. Government could carry this message to foreign partners during bilateral engagements or as part of Nuclear Suppliers Group (NSG) discussions on industry outreach.

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