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At least 163 records · Page 9

Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly—present and future challenges

Abstract The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design–build–test–learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.

36 MATERIALS SCIENCE↗

Characterization of muon and electron beams in the Paul Scherrer Institute PiM1 channel for the MUSE experiment

The MUon Scattering Experiment, MUSE, at the Paul Scherrer Institute, Switzerland, investigates the proton charge radius puzzle, lepton universality, and two-photon exchange, via simultaneous measurements of elastic muon-proton and electron-proton scattering. The experiment uses the PiM1 secondary beam channel, which was designed for high precision pion scattering measurements. We review the properties of the beam line established for pions. We discuss the production processes that generate the electron and muon beams, and the simulations of these processes. Simulations of the π/μ/e beams through the channel using TURTLE and G4beamline are compared. The G4beamline simulation is then compared to several experimental measurements of the channel, including the momentum dispersion at the intermediate focal plane and target, the shape of the beam spot at the target, and timing measurements that allow the beam momenta to be determined. Finally, we conclude that the PiM1 channel can be used for high precision π, μ, and e scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental Benchmarking for High-Reproducibility, Cross-Institutional Evaluation of Iron Redox Electrochemistry

We present a practical case study standardizing experimental protocols between collaborators with the goal of understanding ferrous iron (Fe 2+ ) chemistry and improving the iron deposition reaction for energy-efficient, electrochemical iron production. The study of iron reactions can be difficult, as aqueous iron electrolytes exhibit complex behaviors that can lead to differing interpretation of ostensibly similar experiments. The question we want to answer: are we studying the same chemistry? Our protocols address inherent challenges such as the tendency for Fe 2+ to spontaneously oxidize to ferric iron (Fe 3+ ) and the production of hydrogen at the potentials of interest. Our standardized protocol, executed by four collaborators in different labs and institutions, yields high-reproducibility results, and identified glassy carbon electrode surface quality and Fe 3+ impurities in the salt as key factors with outsized effects on cyclic voltammetry measurements. The process of developing the protocols helped to troubleshoot underlying issues that created poorer reversibility and reproducibility. This study highlights the fact that even nominally straightforward electrochemical systems can yield vastly different outcomes due to small differences in experimental preparation and serves as a useful example for creating transparent and achievable standards for the generation of reliable datasets that can be widely used and shared.

Ketter, Benjamin [Argonne National Laboratory (ANL↗

Joint Genome Institute Analysis Workflow Service (JAWS) v2.7

The U.S. Department of Energy Joint Genome Institute (JGI) has developed the JGI Analysis Workflow Service (JAWS) as a distributed framework to run computational workflows across diverse high-performance computing (HPC) and cloud environments. JAWS enhances the reusability, scalability, and robustness of scientific workflows by orchestrating data movement, code execution, and results retrieval across multiple DOE facilities. At its core, JAWS integrates the Cromwell workflow engine to run workflows expressed in the Workflow Description Language (WDL), ensuring portability and interoperability. To provide consistent runtime environments, JAWS employs container technologies such as Shifter, Apptainer, and Docker. Workflow tasks are managed via HTCondor on HPC backends, while Globus ensures secure and efficient data transfer between sites. JAWS is deployed as a multi-site workflow manager across national laboratory computing facilities, with dedicated instances supporting community projects such as the National Microbiome Data Collaborative (NMDC) and KBase. This distributed, service-oriented architecture enables users to "write once, run anywhere," providing scalable, production-quality workflow execution.

Kirton, Edward↗

Two new SciDAC institutes promote mathematical tools and software technology for high-performance computing

Bigger is often said to be better, and the newest extreme-scale computers certainly are bigger, with millions of processing units. Moreover, the breadth of science performed on the U.S. Department of Energy (DOE) computing facilities is expanding, with new technology such as artificial intelligence emerging. These advances are exciting, creating new opportunities for scientific discovery; however, they also raise new questions for scientists who want to exploit these advances for tackling more complex problems. Will my simulation code be able to utilize the accelerators in extreme-scale computing systems? Can I take advantage of the deepening memory hierarchy in heterogeneous processors? Is there a way around bottlenecks caused by the widening ratio of peak floating-point operations per second to I/0 bandwidth? How can I manage my huge amounts of data effectively? Can I analyze data in situ, or must I transfer it to offline storage for later analysis? To address such questions, DOE announced that it is providing $57.5 million over the next five years for two multidisciplinary teams — FASTMath and RAPIDS2 — to develop new tools and techniques to harness supercomputers for scientific discovery. The teams, called SciDAC Institutes, are part of the Scientific Discovery through Advanced Computing program.

97 MATHEMATICS AND COMPUTING↗

Evaluation of the Lawrence Livermore Microbal Detection Array at the Statens Serum Institut

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Statens Serum Institut to evaluate and transition the Lawrence Livermore Microarray Detection Array (LLMDA) analysis software package, the Composite Likelihood Maximization method (CLiMax) to the SSI. The SSI is a public enterprise under the Danish Ministry of Health that operates a microbiology reference laboratory for the Danish population and analyzes tens to thousands of human clinical samples annually. SSI has been collaborating with the LLNL team for several years to use the LLMDA to analyze viral and bacterial infections from human clinical samples. The collaboration has resulted in two joint publications thus far, describing improvements to LLMDA sample preparation, and the utility of the LLMDA for detecting emerging viruses in clinical samples.

59 BASIC BIOLOGICAL SCIENCES↗

Validation of the Public Radiation Exposure Calculation for the Incident at the National Institute of Standards and Technology Center for Neutron Research on February 3, 2021

The Department of Energy/National Nuclear Security Administration Consequence Management Program was contacted by the Health Physics Chief of the National Institute of Standards and Technology Center for Neutron Research (NCNR) to review public radiation exposure calculations for an event that occurred on its Gaithersburg, Maryland, campus on February 3, 2021. Subject matter experts from the Nuclear Emergency Support Team (NEST) assets, specifically the Consequence Management Home Team (CMHT) and the National Atmospheric Release Advisory Center (NARAC), were selected to provide support. CMHT used three separate modeling codes to validate the results the scientists at NCNR calculated using the HotSpot model. The analyses were performed using NARAC’s in-house Lagrangian dispersion codes known as LODI and Aeolus, as well as the Turbo FRMAC software from Sandia National Laboratories. The team used parameters provided by the NCNR scientists regarding the site, applicable observable meteorological data, and environmental survey and sampling data to estimate public exposure. Each model estimated public dose at much less than 0.5 mrem. CMHT concurs with the NCNR public radiation exposure calculations which state that members of the public at the 400-meter boundary would have received a radiological dose of less than 0.5 mrem.

61 RADIATION PROTECTION AND DOSIMETRY↗

Massachusetts Institute of Technology Reactor LEU Fuel Element Flow Test Conceptual Design – Hydraulic Reactor Design Parameters

The Massachusetts Institute of Technology Reactor (MITR-II, also referred to as MITR) is one of six U.S. high performance research reactors (USHPRR), including one critical facility, that is actively collaborating with the U.S. National Nuclear Security Administration (NNSA) Material Management and Minimization (M 3 ) Reactor Conversion Program to convert to the use of low-enriched uranium (LEU, < 20 wt% 235 U) fuel. The MIT Nuclear Reactor Laboratory has been working with the USHPRR Reactor Conversion (RC) Pillar at Argonne National Laboratory to perform fuel element design and fuel cycle performance analyses, steady-state thermal hydraulics safety analyses, and accident safety analyses in preparation for the conversion of MITR and support a preliminary Safety Analysis Report (SAR) for conversion to LEU fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Cooperative Research and Development Agreement among National Energy Technology Laboratory, The Board of Regents of the University System of Georgia by and on behalf of Georgia Institute of Technology, and University of Texas at El Paso [Abstract]

Georgia Institute of Technology (GIT), University of Texas at El Paso (UTEP), and the National Energy Technology Laboratory (NETL) will collaborate and develop cyber-physical systems for advanced power systems. GIT will test virtual models on hybrid power system hardware and cyber physical components. UTEP will test novel actuators on hybrid power system hardware. NETL will access GIT’s expertise in the engineering and real time simulation of power system processes for cyber-physical systems and simulations to control hardware. NETL will establish a relationship to promote UTEP’s capabilities in additive manufacturing and high-temperature piezo-electric devices with the potential for controlling high-temperature flows with a light and inexpensive device at high response rates. This project is the result of an EERE Advanced Manufacturing Office open Multi-Topic awarded proposal led by GIT titled, “Robust Combined Heat and Hybrid Power (CHHP) for High Electrical Efficiency Cogeneration”.

42 ENGINEERING↗

NNSA Minority Serving Institute Partnership Program (MSIPP)--Indigenous Mutual Partnership to Advanced Cybersecurity Technology (ASPIRE, IMPACT and PAMER); FY22 Q2 Progress Report

The following report summarizes the status update during this quarter for the National Nuclear Security Agency (NNSA) initiated Minority Serving Institution Partnership Plan's (MSIPP) projects titled, Indigenous Mutual Partnership to Advanced Cybersecurity Technology (ASPIRE), Indigenous Mutual Partnership to Advanced Cybersecurity Technology (IMPACT) and Partnership for Advanced Manufacturing Education and Research (PAMER).

42 ENGINEERING↗

Abstract for CRADA among National Energy Technology Laboratory, Research Triangle Institute, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory (AGMT-0921)

Through the Carbon Capture Simulation for Industry Impact (CCSI 2 ) project, the National Energy Technology Laboratory (NETL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL) (herein collectively “the CCSI 2 team”) will collaborate through a CRADA with the Research Triangle Institute (RTI). This collaboration will develop a modeling framework of RTI’s Non-Aqueous Solvent (NAS) process using physical and thermodynamic data and models previously developed by RTI. RTI will provide existing models and data on its NAS system to inform the model construction effort by the CCSI 2 team.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Looking back at 50 years of cutting-edge capabilities: LANSCE ‘underpins Los Alamos as a world-class scientific institution’

What started with an idea and a memo has since grown into a one-of-a-kind, world-renowned facility that contributes to the nation’s advancement of science and technology. First known as LAMPF (Los Alamos Meson Physics Facility) until the 1990s when it became LANSCE (Los Alamos Neutron Science Center), the facility is celebrating the 50th anniversary of its first full-capacity proton beam on June 9, 1972. Since then, LANSCE has contributed to a range of national security goals, such as supporting the Lab’s stockpile stewardship program, helping to advance the science of medical radioisotopes, improving the understanding of hydrodynamics, and more. “LANSCE has served the nation through its near-unique capabilities,” said Alan Carr, Senior Historian at the National Security Research Center, which houses the facility’s evolution through decades of documents, photos and other materials. “Since 1972, LANSCE has been the Lab’s major experimental science facility and underpins Los Alamos as a world-class scientific institution. This was true 50 years ago and is still true today.” In commemoration of this anniversary, we’re taking a look back at LANSCE’s historic five decades, including its first director, earliest milestones and important contributions to national security.

43 PARTICLE ACCELERATORS↗

Neutron Source Facility of the National Science Center “Kharkiv Institute of Physics and Technology” at Kharkiv, Ukraine

Argonne National Laboratory developed, designed, and supported the construction of a state-of-the-art Neutron Source Facility (NSF) at the Kharkov Institute of Physics and Technology (KIPT) in Kharkov Ukraine, under the U.S. DOE NNSA Russian Research Reactor Fuel Return (RRRFR) program. Ukraine approved the return of all highly enriched uranium in the country to Russia prior to the 2012 Nuclear Security Summit in return for the RRRFR program to fund the development, the design, and the construction of the NSF. The facility is designed to produce medical isotopes, train nuclear professionals, support the Ukrainian nuclear industry, and provide experimental capabilities for performing reactor physics, materials, and basic science research. The NSF was successfully started and operated in August 2021. The NSF is the first facility of this type in the world, and it will be used to understand the physics of driven systems for energy production and the disposal of spent nuclear fuels. The NSF consists of a subcritical assembly using low enriched uranium (LEU) fuel driven with an electron accelerator. The NSF target design utilizes tungsten or natural uranium for producing neutrons through photonuclear reactions using 100-MeV electrons. The accelerator power is 100 KW, which produces 3x10 14 neutrons per second from the uranium target. The subcritical assembly is designed to obtain the highest possible neutron flux intensity with an effective neutron multiplication factor of less than 0.98. Passive safety, reliability, and environmental considerations were included in the NSF design. The NSF utilization study shows that this neutron source has the capability of producing different medical isotopes. Several horizontal neutron channels are incorporated for performing applied and basic research. The NSF is configured to accommodate future design upgrades and new missions. The facility design was approved by the Ukraine Academy of Sciences before starting the NSF construction. The construction, the equipment installation, and the operation of the different systems of the NSF were completed and approved by the Ukrainian regulators. In July 2020, the State Nuclear Regulatory Inspectorate of Ukraine (SNRIU) issued a license for the physical startup of the NSF. The construction of facility was completed in early 2021.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Operational Energy Life Cycle Data Development for the National Institute of Standards And Technology (NIST) Building Industry Reporting and Design for Sustainability (BIRDS) Neutral Environmental Software Tool (NEST)

For this analysis, regionalized life cycle assessment (LCA) results for environmental impacts (using the Tool for Reduction and Assessment of Chemicals and Other Environmental Impacts [TRACI] 2.1) and cumulative energy demand (using the Federal Life Cycle Analysis Commons Elementary Flow List [FEDEFL] Inventory Methods v1.0.0) were evaluated for the production and utilization of electricity, natural gas, fuel oil, and propane as commodities within residential and commercial buildings. These results can used as a framework for future research into net zero, high-performance buildings, such as done here for the Building Industry Reporting and Design for Sustainability (BIRDS) database by the National Institute of Standards and Technology (NIST) Engineering Laboratory. The geographical results were assigned to each United States (U.S.) Zone Improvement Plan (ZIP) code based on the ZIP code location and corresponding Balancing Authority Area, natural gas basin, and Petroleum Administration for Defense Districts (PADDs). Additionally, previously developed models were utilized to develop future life cycle profiles. Projections were based on data available from the U.S. Energy Information Administration Annual Energy Outlook 2022 through 2050 (AEO 2022). Electricity LCA models were updated based on AEO 2022 projected annual generation mixes, while the natural gas baseline model was updated based on projected shares of natural gas types (conventional, shale, tight, and coalbed methane). Projections of crude oil production rates and export rates were applied to the petroleum baseline model in five-year increments to investigate their effects on the life cycle profile of fuel oil and propane. While only 100-year Global Warming Potential (GWP-100) with climate carbon feedback (CC-FB) and Cumulative Energy Demand are shown in Section 4: Results, the complete results, including Acidification Potential, Eutrophication Potential, Freshwater Ecotoxicity Potential, GWP-100 without inclusion of CC-FB, Human Health Impacts Potentials (Cancer, Non-Cancer), Ozone Depletion Potential, Particulate Matter Formation Potential, and Photochemical Smog Formation Potential, are tabulated for each ZIP code in the Excel worksheets that accompany this analysis. For the Excel spreadsheet tools associated with this report, please go to https://www.netl.doe.gov/energy-analysis/details?id=f8890fac-be55-44ac-aaa9-e2888bfabe93

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

RAPIDS2 SciDAC Institute: Rutgers Final Report (as of 06/21)

The Rutgers team transitioned to the University of Utah in 2021 and is continuing to be part of and to contribute to the RAPIDS2 SciDAC Institute. This final report is for the contributions of the Rutgers team to the project at Rutgers as of 06/21. The 01/22 annual report of the project is also included in this report to demonstrate the continued contributions and to put these contributions in the context of the overall project.

97 MATHEMATICS AND COMPUTING↗

The Demonstration of Power over Ethernet (PoE) Technologies in Commercial and Institutional Buildings

Power over Ethernet (PoE) technologies are currently ubiquitous in offices in the form of phones, access points, and IP security cameras. They are systems that are familiar to and managed by on-site IT staff. As low voltage DC-power capabilities have increased with the advancement of IT network switches within offices, PoE devices are now being integrated across additional building systems, including lighting, computers, and HVAC controls. The connection of PoE devices to network switches offers the opportunity for energy monitoring and management to be performed through IT network management software. Data and results from technology validations of PoE equipment remain very limited. This lack of information hinders expansion of PoE as an energy management strategy as its benefits and challenges have been insufficiently quantified in real-world scenarios. This final report presents the findings of a DOE/State of Minnesota-funded project that demonstrated and assessed the energy and non-energy benefits of Power over Ethernet (PoE) technologies at six sites: two offices, three schools, and a hotel. The goals of the demonstrations were to: (1) assess the receptiveness of commercial and institutional markets to these new technologies, (2) demonstrate the feasibility of PoE technologies within standard design/construction practices and commercial codes, (3) assess the energy and cost savings opportunities of these technologies, (4) provide energy management opportunities where not typically available, and (5) formulate approaches to spur adoption of these technologies in the marketplace.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

National Institute of Standards and Technology Requirements (Analysis Report)

EPOC uses the Deep Dive process to discuss and analyze current and planned science, research, or education activities and the anticipated data output of a particular use case, site, or project to help inform the strategic planning of a campus or regional networking environment. This includes understanding future needs related to network operations, network capacity upgrades, and other technological service investments. A Deep Dive comprehensively surveys major research stakeholders’ plans and processes in order to investigate data management requirements over the next 5–10 years. In October of 2022, staff members from the Engagement and Performance Operations Center (EPOC) met with researchers and staff from the National Institute of Standards and Technology (NIST) for the purpose of a Deep Dive into scientific and research drivers. The goal of this activity was to help characterize the requirements for a number of campus use cases, and to enable cyberinfrastructure support staff to better understand the needs of the researchers within the community. Material for this event included the written documentation from each of the profiled research areas, documentation about the current state of technology support, and a write-up of the discussion that took place via e-mail and video conferencing. The case studies highlighted the ongoing challenges and opportunities that NIST has in supporting a cross-section of established and emerging research use cases. Each case study mentioned unique challenges which were summarized into common needs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗