Protein Structural Alignments From Sequence
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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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A Program Analysis Tool to Query Static and Dynamic Characteristics of HPC Applications
Emerging HPC platforms are becoming extraordinarily difficult to program as a result of complex, deep and heterogeneous memory hierarchies, heterogeneous cores, and the need to divide work and data among them. New programming models and libraries are being developed to aid in porting efforts of application developers, but substantial code restructuring is still necessary to fully make use of these new technologies. To do this effectively, these developers need information about their source code characteristics, including static and dynamic (e.g. performance) information to direct their optimisation efforts and make key decisions. On the other hand, system administrators need to understand how users are using the software stack and resources on their systems to understand what software they need to provide to improve the productivity of the users on a platform.In this paper we describe a tool that combines compiler and profiler information to query performance characteristics within an application or across multiple applications on a given platform. Static and dynamic data about applications are collected and stored together in an SQL database that can be queried by either a developer or a system administrator. We will demonstrate the capabilities of this tool via a real-world example from application-driven case studies that aims at understanding the use of scientific libraries on a routine from the molecular simulation application CP2K.
Welch, Aaron↗
Manipulating and Probing Ultrafast Atomic and Molecular Dynamics (Final Report)
This program has focused on the exploration and control of dynamics in atoms, small molecules, clusters, and micro- or nano-structures following ultrafast excitation and/or driven by strong oscillating fields. In our principal experiments, gas phase atoms and molecules were exposed to short pulses of electromagnetic radiation with frequencies ranging from THz into the XUV spectral regions, and with durations from picoseconds to attoseconds. The pulses coherently induce and/or probe dynamics in the electronic, vibrational, and rotational degrees of freedom of the targets. The overarching goal of the various projects has been to exploit strong-field processes and/or implement novel ultrafast techniques for manipulating and probing coherent electronic and nuclear motion. Typically, the relevant system evolution occurs over attosecond to picosecond timescales. In doing so, we have gained a more complete picture of correlated multi-particle dynamics in atoms, molecules, and other complex systems and expanded the toolbox of useful techniques for manipulating and probing those dynamics. Grant funds were primarily used to: (i) pay salaries and fringe benefits for the PI and postdocs and stipends, tuition, and health care costs for graduate students; (ii) cover travel expenses for the PI, postdocs, and students to attend and participate in professional meetings, conferences, and workshops; and (iii) purchase research materials, supplies, and equipment required for experiments. The research resulted in the publication of 24 peer reviewed articles (including 1 in Nature Physics, 2 in Nature Communications, 7 in Physical Review Letters, and 12 in Physical Review A), and 4 PhD dissertations. The specific results from different funding periods are summarized separately in the main report.
74 ATOMIC AND MOLECULAR PHYSICS↗
High Energy Physics Network Requirements Review: Final Report, July 2024–December 2024
The world-class research infrastructure at the US Department of Energy (DOE) Office of Science (SC) provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance the core DOE mission in science and technology for its SC program to stimulate rich scientific discoveries and enhance its innovation ecosystem. Research communities gather and flourish around each user facility, bringing together new and enhanced perspectives. The continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by the SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high-performance data, networking, and computing solutions. The ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements review methodology. Between July and December 2024, the Energy Sciences Network (ESnet) and the Office of High Energy Physics (HEP) of the DOE-SC organized an ESnet requirements review of HEP-supported program activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about its relationship to the HEP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Burst buffer dynamic logical volume sizing in high performance computing environment
A method, data processing system and program product utilize dynamic logical storage volume sizing for burst buffers or other local storage for computing nodes to optimize job stage in, execution and/or stage out.
97 MATHEMATICS AND COMPUTING↗
A Multi-Model, Multi-Scale Research Program in Stressors, Responses, and Coupled Systems Dynamics at the Energy-Water-Land Nexus and for Concentrated, Interdependent Infrastructures: Toward Next Generation Capabilities in Integrated Impacts, Adaptation, and Vulnerability (I-IAV) Modeling and a Community of Practice
The goal of this research program was to build a next generation integrated suite of science-driven modeling and analytic capabilities, and a more expanded and connected community of practice, for analyses of the stressors, impacts, adaptations and vulnerabilities of global and regional change. The emphasis was on understanding energy-water-land interactions and feedbacks and interdependent infrastructures at appropriate regional and temporal scales. Although the scope spans many complex facets of data, modeling, and analysis, as well as scales appropriate for integrated impacts and adaptation research, the focus of this effort was the development of multi-model, multi-scale capabilities spanning the domains of Multi-Sector Dynamics (MSD) models; Impact, Adaptation, and Vulnerability (IAV) models; and Earth System Models (ESMs).
54 ENVIRONMENTAL SCIENCES↗
Cluster Dynamics Modeling Needs for the Advanced Materials and Manufacturing Technologies Program
This milestone report aims to identify and assess the cluster dynamics (CD) modeling requirements within the Department of Energy's Office of Nuclear Energy (DOE-NE) Advanced Materials and Manufacturing Technologies (AMMT) program and to communicate these needs to the DOE-NE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. The goal is to ensure NEAMS is well-informed about the CD modeling requirements to support AMMT's mission of accelerating the development, qualification, demonstration, and deployment of advanced structural materials and manufacturing for nuclear energy applications. CD modeling is an essential tool for predicting the degradation of structural materials under irradiation, which is a key component of AMMT's accelerated qualification process. The AMMT program focuses on both additively manufactured and wrought structural alloys, such as laser powder-bed fusion 316H austenitic stainless steel, alloy 709, Haynes 244, and alloy 617. These materials require a generalized CD modeling framework to facilitate rapid model development and computational simulation. A flexible, generalized CD software, similar to the Multiphysics Object-Oriented Simulation Environment (MOOSE) finite element framework, would enable modeling of various cluster types, including defect clusters, defect-solute clusters, and multicomponent clusters, incorporating thermodynamics and kinetics parameters. Radiation effects, microstructural feature evolution, and multi-dimensional modeling are critical considerations for the CD model. The usability of the CD code should allow for easy modification and coupling with MOOSE-based simulations. Additionally, the software should adhere to Nuclear Quality Assurance-1 standards, include a testing suite for verification and validation, and be version-controlled within a national laboratory-managed Git repository. Benchmark problems are needed to assess code predictions and performance.
11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Finite Element Analysis of the TRUST Nonlinear Dynamics Testbed
This paper builds on prior work conducted within the Los Alamos National Laboratory (LANL) Testbeds to Reduce Uncertainty in Simulations and Tests (TRUST) program. Specifically, it builds on finite element (FE) modeling efforts for the TRUST program’s Nonlinear Dynamics (ND) testbed. Historically, the FE model for the ND testbed has exclusively utilized a Lanczos eigensolver that linearly extracts the system’s natural frequencies. This paper investigates the Abaqus 2024’s explicit dynamic solver, which implements a central difference explicit solver. The central difference method used in Abaqus can capture nonlinear material responses in structural dynamic simulations making it suitable for the ND FE model.
42 ENGINEERING↗
Software classification using phylogenetic techniques
Software, such as malware, may be classified using phylogenetic techniques. An evolutionary history of a representative set of software programs may be reconstructed to generate a reference phylogeny. Dynamic traces of the representative software programs may be obtained. The dynamic traces may include time-ordered sequences of execution commands extracted from running software binaries. Metrics may be developed using the dynamic traces. One or more unknown software programs may then be classified against the reference phylogeny using the metrics developed using the dynamic traces of the representative set of software programs.
97 MATHEMATICS AND COMPUTING↗
An Atlas of Current Customer-Facing Utility Program Designs and Pricing
The National Renewable Energy Laboratory (NREL) and Kevala conducted a targeted literature review and leveraged extensive expertise, including team members with four decades of experience in the utility sector, to characterize utility programs and rate designs. This analysis delves into the motivations behind these programs and the various hurdles they face. Through this in-depth study, the team provides critical insights into the operational dynamics of utility programs, identifying key drivers and barriers that influence their effectiveness and implementation.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Applying Quantum Computing to Simulate Power System Dynamics
Power system dynamics are generally modeled by high dimensional nonlinear differential-algebraic equations due to a large number of generators, loads, and transmission lines. Thus, its computational complexity grows exponentially with the system size. This paper demonstrates the potential use of quantum computing algorithms to model the power system dynamics. Leveraging a symbolic programming framework, we equivalently convert the power system dynamics’ differential algebraic equations (DAEs) into ordinary differential equations (ODEs), where the data of the state vector can be encoded into quantum computers via amplitude encoding. The system's nonlinearity is captured by Taylor polynomial expansion, the quantum state tensor, and Hamiltonian simulation, whereas state variables can be updated by a quantum linear equation solver. Our results show that quantum computing can simulate the dynamics of the power system with high accuracy, whereas its complexity is polynomial in the logarithm of the system dimension. Our work also illustrates the use of scientific machine learning tools for implementing scientific computing concepts, e.g., Taylor expansion, DAEs/ODEs transform, and quantum computing solver, in the field of power engineering.
Tran, Huynh↗
Dynamically morphing microchannels in liquid crystal elastomer coatings containing disclinations
Liquid crystal elastomers (LCEs) hold a major promise as a versatile material platform for smart soft coatings, since their orientational order can be predesigned to program a desired dynamic profile. In this work, we introduce temperature-responsive dynamic coatings based on LCEs with arrays of singular defects-disclinations that run parallel to the surface. The disclinations form in response to antagonistic patterns of the molecular orientation at the top and bottom surfaces, imposed by the plasmonic mask photoalignment. Upon heating, an initially flat LCE coating develops linear microchannels located above each disclination. The stimulus that causes a non-flat profile of LCE coatings upon heating is the activation force induced by the gradients of molecular orientation around disclinations. To describe the formation of microchannels and their thermal response, we adopt a Frank-Oseen model of disclinations in patterned director field and propose a linear elasticity theory to connect the complex spatially-varying molecular orientation to the displacements of the LCE. The thermo-responsive surface profiles predicted by the theory and by the finite element modeling are in good agreement with the experimental data; in particular, higher gradients of molecular orientation produce a stronger modulation of the coating profile. The elastic theory and the finite element simulations allow us to estimate the material parameter that characterizes the elastomer coating’s response to the thermal activation. The disclinations containing LCEs show potential as soft dynamic coatings with a predesigned responsive surface profile.
36 MATERIALS SCIENCE↗
Dynamic Risk-Aware Patch Scheduling
A program that defines and assesses the dynamic risk of software vulnerabilities and considers the dynamic risks into patch scheduling to reduce security risks posed by vulnerabilities and provide formal guidance to security operations at various organizations.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Community Solar for All: Key Findings for State Energy Offices and State LIHEAP Agencies from the Inclusive Shared Solar Initiative
Despite the significant potential for community solar to reduce energy burdens and costs, it has largely remained out of reach for low-income households. While the U.S. community solar market has grown considerably over the last decade, as of December 2022 low to moderate-income (LMI) community solar represented just 2% of the overall market. Effective community solar policies and program decisions can help address this dynamic. State laws, policies, and program rules are critical to the development of community solar programs and projects that are affordable for and cater to the needs of LMI utility customers, who often face disproportionately high energy costs relative to their incomes. This report explores how two sets of state agencies in particular — State and Territory Energy Offices and State Low Income Home Energy Assistance Program (LIHEAP) Agencies —can help to streamline and prioritize the delivery of affordable and accessible shared solar. State Energy Offices are often involved in community solar policy and program design from inception, whether by supporting the enactment of enabling legislation or informing the development of program rules and regulations. State Energy Offices may also be charged with administering or overseeing the implementation of statewide community solar programs and, through the U.S. State Energy Program and other sources of funding, can provide resources and loans that enhance community, developer, and utility confidence and capacity to build, host, and derive value from projects. Relatedly, as implementers of federal LIHEAP block grants, State LIHEAP Agencies have a deep understanding of the needs of lower-income households and can help inform the design and delivery of community solar programs.
14 SOLAR ENERGY↗
ESnet Requirements Review Program Through the IRI Lens: A Meta-Analysis of Workflow Patterns Across DOE Office of Science Programs (Final Report)
The Department of Energy (DOE) ensures America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The DOE’s Office of Science (SC) delivers groundbreaking scientific discoveries and major scientific tools that transform our understanding of nature and advance the energy, economic, and national security of the United States. The SC’s programs advance DOE mission science across a wide range of disciplines and have developed the research infrastructure needed to remain at the forefront of scientific discovery. The DOE SC’s world-class research infrastructure — exemplified by the 28 SC scientific user facilities — provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance core DOE mission science for its sponsor SC program and to stimulate a rich discovery and innovation ecosystem. Research communities gather and flourish around each user facility, bringing together diverse perspectives. A hallmark of many facilities is the large population of students, postdoctoral researchers, and early-career scientists who contribute as full-fledged users. These facility staff and users collaborate over years to devise new approaches to utilizing the user facility’s core capabilities. The history of the SC user facilities has many examples of wildly inventive researchers challenging operational orthodoxy to pioneer new vistas of discovery; for example, the use of the synchrotron X-ray light sources for study of proteins and other large biological molecules. This continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high performance data, networking, and computing solutions. The DOE SC’s three HPC user facilities and the Energy Sciences Network (ESnet) high-performance research network serve all of the SC’s programs as well as the global research community. Argonne Leadership Computing Facility (ALCF), the National Energy Research Scientific Computing Center (NERSC), and Oak Ridge Leadership Computing Facility (OLCF) conceive, build, and provide access to a range of supercomputing, advanced computing, and large-scale data-infrastructure platforms, while ESnet interconnects DOE SC research infrastructure and enables seamless exchange of scientific data. All four facilities operate testbeds to expand the frontiers of computing and networking research. Together, the ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements reviews (RRs) methodology. In recent years, the research communities around the SC user facilities have begun experimenting with and demanding solutions integrated with HPC and data infrastructure. This rise of integrated-science approaches is documented in many community and high-level government reports. At the dawn of the era of exascale science and the acceleration of artificial intelligence (AI) innovation, there is a broad need for integrated computational, data, and networking solutions. In response to these drivers, DOE has developed a vision for an Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation.
42 ENGINEERING↗
Improving Dose Modeling With Dynamic Modeling Tools [Slides]
Utilities aiming for higher fuel enrichment for power uprates or extended operation times before refueling must conduct a new dose analysis. Current conservative dose estimation standards may cause utilities to exceed regulatory limits for proposed increased fuel enrichment. A more accurate modeling of doses from reactor accidents can lower these conservative assumptions. Prescott et al. (2022) demonstrated that the Event Modeling Risk Assessment using Linked Diagrams (EMRALD) software tool, developed at Idaho National Laboratory (INL), can be coupled with the Modular Accident Analysis Program (MAAP5) for dynamic accident analysis in reactor plants. EMRALD forms models of potential accident scenarios, while MAAP5 simulates the accident progression and dose consequences. By integrating these software tools with utility-specific data, a more precise estimation of dose consequences from plant accidents can be achieved. Preliminary findings indicate that EMRALD provides accurate mean core damage frequencies for generalized accident scenarios. Future work includes expanding the model to account for plant-specific data and mitigation factors.
97 - MATHEMATICS AND COMPUTING↗
Ushering in the New Age of Laboratories: Smart Labs in Practice; Preprint
Ventilation is the first line of defense against airborne hazards produced during research activities in laboratories. A vital component to maintaining healthy, safe, indoor air quality, laboratory ventilation systems are often victim to ineffective operation, posing a risk to an organization's most important asset - the researchers. Furthermore, system inefficiencies can lead to up to 50% wasted energy. By providing a framework to improve the safety and energy efficiency through optimized ventilation and operations, the Smart Labs Toolkit guides laboratory stakeholders through a straight-forward, holistic approach to achieving a dynamic Smart Labs program. A Smart Labs program employs a combination of physical, administrative, and management techniques to plan, assess, optimize, and manage high-performance laboratories. Grounded in the Smart Labs methodology, the National Renewable Energy Laboratory (NREL) implemented a successful Smart Labs program to oversee the design, construction, maintenance, and operations of its laboratories. To accomplish this effort, NREL's key stakeholders created an internal partnership to align NREL's existing laboratories with Smart Labs principles and solidify organizational roles for the safe and efficient operation of laboratory assets. The program provides the groundwork for decarbonization strategies centered around building operation. This paper outlines best practices employed by NREL to develop a cross-cutting Smart Labs team, garner managerial support, and effectively communicate of goals around safety and energy. Strategies include specific Smart Labs best practices, such as implementing a Laboratory Ventilation Risk Assessment - a systematic process for identifying risk due to airborne hazards and informing dynamic, demand-based ventilation to optimize safety and efficiency.
decarbonization↗