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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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DOE OSTI2026

Report of the 2026 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science

Scientific computing is undergoing rapid transformation as advances in artificial intelligence, heterogeneous computing, automation, and data-intensive research reshape not only computational tools but also the institutions, workforce models, and collaborative practices that support scientific discovery. This report synthesizes insights from the 2026 Workshop on Next-Generation Ecosystems for Scientific Computing, the second in a three-year series focused on strengthening scientific computing ecosystems through socio-technical co-design. Workshop discussions identified four interdependent strategic themes: software ecosystems for AI-enabled scientific discovery; trust, validation, and traceability; human-AI teaming and paradigm shifts; and workforce, pedagogy, and governance. The report translates these themes into eight priorities for community action spanning shared research infrastructure, trust and traceability, user experience, human-AI teaming, workforce development, cross-sector coordination, stewardship and sustainability, and evaluation of scientific value. Together, these priorities outline directions for building scientific computing ecosystems that remain trustworthy, sustainable, innovative, and resilient as AI assumes a growing role in scientific work.

AI↗
DOE OSTI2024

A Refined Method to Translate Solar Data Quality Assessment Flags to Estimated Measurement Uncertainty

Integrating solar resource uncertainties due to radiometer measurement performance and operational data quality assessment can provide improved estimates of economic bankability, system design performance, and compliance of solar energy conversion systems. Estimating radiometer measurement uncertainty is an established procedure consistent with recognized best practices and international guidelines. SERI QC is a robust solar data quality assessment software tool that has been in continuous use for more than three decades. This report, the fourth of six for the Data Quality and Uncertainty Integration Project, presents a refined algorithm description for software to translate solar resource data quality assessment results into estimated uncertainty values in a Solar Resource Operational Uncertainty Integrator (SROUI) application. This algorithm requires three-component solar irradiance measurements - global horizontal irradiance, direct normal irradiance, and diffuse horizontal irradiance - collected at 1- to 60-minute intervals, as described in the previous deliverables. The development of this report as Deliverable 6.4 was an iterative process that included reviews and feedback from the project team on initial drafts designed to refine how the new software could best support determining solar resource data uncertainty. The results of this effort will contribute to the final software system development by National Renewable Energy Laboratory staff.

14 SOLAR ENERGY↗
DOE OSTI2023

Verification of a Modeling Toolkit for the Design of Building Electrical Distribution Systems

DC electrical distribution systems offer many potential advantages over their AC counterparts. They can facilitate easier integration with distributed energy resources, improve system energy efficiency by eliminating AC/DC converters at end-use devices (e.g., laptop chargers), and reduce installation material, time, and cost. However, DC electrical distribution systems present additional design considerations, largely resulting from potentially greater magnitude and variation in cable losses. Modeling and simulation are rarely used to design such systems. However, the greater dependency of DC system energy efficiency on design choices such as distribution voltages, architecture, and integration of PV and BESS suggests that modeling and simulation may be required. Such system performance analysis is currently not a standard practice, in part due to limited availability and validation of capable software tools. This paper characterizes the accuracy of a Modelica-based Building Electrical Efficiency Analysis Model (BEEAM) toolkit, as a precursor for validating its use to perform system performance analysis and inform design decisions. The study builds upon previous verification research by characterizing complete systems comprised of commercially available equipment, and providing a more detailed analysis of simulation results. Five lighting systems with varying electrical distribution architectures were designed using market-available equipment, installed in a laboratory environment, modeled using BEEAM, and simulated using three Modelica integrated development environments (IDEs). Simulated and measured results were compared to characterize toolkit accuracy. Initial results revealed that simulated performance was mostly within ±5% of measured system-level and device-level performance. While simulation results were not found to be dependent on the IDE, some Modelica compiler interoperability issues were identified. Although the BEEAM toolkit showed promise for the targeted use case, further work is needed to determine whether the demonstrated 5% accuracy is sufficient for making real-world design decisions, and for BEEAM to advance from an interesting research tool to one that can impact real-world building projects.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Radiation Simulation using Wi-Fi Signal Strength and Frequency

For routine radiological operations, lost radioactive sources, decommissioning and cleanup of nuclear facilities, and radiological terrorist events such as Radioactive Dispersive Devices (RDDs) or Radiological Exposure Devices (REDs), individuals are tasked with accurately locating both point and distributed sources of radiation. Radiation workers must often practice these tasks, whether part of initial training or periodically as part of formal or informal exercises or drills. In such circumstances, it is desirable to have an accurate recreation of a radioactive source, including a method of detecting it, which does not include dangerous amounts of radiation. The goal of this research was to develop a radiation simulation technology that uses IEEE 802.11x W-LAN protocol, i.e. Wi-Fi sources and detectors for these, as an inexpensive, precise and accurate method of replicating sources of gamma radiation. For this work, existing 802.11x sources were used. Software was developed for use with an Android smartphone to detect the presence of these sources. The measurements followed the expected behavior as a function of distance from the sources, mimicking that of gamma radiation, thus demonstrating the fundamental principle of operation. The ultimate system will be used in an outreach program to interest students in the radiation protection field.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2022

tapir: A tool for topologies, amplitudes, partial fraction decomposition and input for reductions

The demand for precision predictions in the field of high energy physics has dramatically increased over recent years. Experiments conducted at the LHC, as well as precision measurements at the intensity frontier such as Belle II require equally precise theoretical predictions to make full use of the acquired data. To match the experimental precision, second-, third- and, for certain quantities, even higher-order calculations in perturbative quantum field theory are required. To facilitate such calculations, computer software automating as many steps as possible is required. Yet, each calculation poses different challenges and thus, a high level of configurability is required. In this context we present tapir: a tool for identification, manipulation and minimization of Feynman integral families. It is designed to integrate in toolchains based on the computer algebra system FORM, the use of which is common practice in the field. tapir can be used to reduce the complexity of multi-loop problems with cut-filters, topology mapping, partial fraction decomposition and alike. Program Title:tapir CPC Library link to program files:https://doi.org/10.17632/ptc9t46xyn.1 Developer's repository link:https://gitlab.com/tapir-devs/tapir Licensing provisions: GPLv3 Programming language:python 3, C++ Nature of problem: Multi-loop computations require the automatization of a large number of different tasks related to Feynman integral topologies. Among them are the identification and minimization of integral topologies, partial fraction decomposition of topologies in the case of linearly dependent propagators as well as mapping scalar products of loop momenta to scalar functions. Solution method: The minimization of topologies is performed by comparison of their respective Nickel indices [1], even further minimization utilizes Pak's algorithm [2]. To efficiently map scalar products of loop momenta to scalar functions FORM [3] code is generated. Additional comments including restrictions and unusual features: Minimization based on Pak's algorithm slows down for many lines and scales. A coarser minimization using the Nickel indices, however, is still possible. [1]B. Nickel, D. Meiron, G.A.J. Baker, Compilation of 2-pt and 4-pt graphs for continuous spin model, Report, University of Guelph, 1977.[2]A. Pak, J. Phys. Conf. Ser. 368 (2012) 012049, https://doi.org/10.1088/1742-6596/368/1/012049, arXiv:1111.0868.[3]B. Ruijl, T. Ueda, J. Vermaseren, FORM version 4.2, arXiv:1707.06453, 7 2017.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2026

Multi-Artifact Analysis of Self-Admitted Technical Debt in Scientific Software

Context: Self-admitted technical debt (SATD) occurs when developers acknowledge shortcuts in code. In scientific software (SSW), such debt poses unique risks to the validity and reproducibility of results. Objective: This study aims to identify, categorize, and evaluate scientific debt, a specialized form of SATD in SSW, and assess the extent to which traditional SATD categories capture these domain-specific issues. Method: We conduct a multi-artifact analysis across code comments, commit messages, pull requests, and issue trackers from 23 open-source SSW projects. We construct and validate a curated dataset of scientific debt, develop a multi-source SATD classifier to guide SATD management, and conduct a practitioner validation to assess the practical relevance of scientific debt. Results: Our classifier performs strongly across 900,358 artifacts from 23 SSW projects. SATD is most prevalent in pull requests and issue trackers, underscoring the value of multi-artifact analysis. Models trained on traditional SATD often miss scientific debt, emphasizing the need for its explicit detection in SSW. Practitioner validation confirmed that scientific debt is both recognizable and useful in practice. Conclusions: Scientific debt represents a unique form of SATD in SSW that that is not adequately captured by traditional categories and requires specialized identification and management. Our dataset, classification analysis, and practitioner validation results provide the first formal multi-artifact perspective on scientific debt, highlighting the need for tailored SATD detection approaches in SSW.

Melin, Eric [Boise State University]↗
DOE OSTI2022

Radiation-Hardened GaN-Based Wireless Communications Architectures for Terrestrial Nuclear Reactor Sensing and Instrumentation

Wireless technologies have become increasingly common in applications, ranging from close proximity inductive communication links in medical devices to short-range Bluetooth and WiFi communications and longer-range cellular communications. Nonetheless, these technologies are unsuitable for use in or around nuclear reactors due to the extreme radiation and temperatures inherent in these environments and their associated significant degradative effects on electronics hardware. However, recent work in wide bandgap– based electronics has shown promise for gallium nitride (GaN) as an emerging technology for the realization of practical wireless communications systems for use in harsh environments. This report presents initial progress on the development of wireless communications architectures designed specifically for nuclear reactor application, based on inherently radiation-hardened (rad-hard) GaN technology. Prior work on rad-hard analog communications topologies is reviewed, and several digital modulation and encoding schemes that utilize GaN-based electronics devices are newly proposed for application in reactor environments. Continuous-time and discrete-time system simulations were performed, and results are presented for the preliminary transmitter and receiver designs, respectively. In addition, an overview of a software-defined radio testbed, designed for communications protocol development, is provided. Future work will focus on implementing candidate radiation-resistant wireless architectures using a research AlGaN/GaN high electron mobility transistor (HEMT) integrated circuit process, which is available at the Ohio State University, and irradiation studies will be carried out to assess the true potential of this technology for reactor application.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Methodology and Tool for the Physical Security Analysis of Micro and Advanced Reactors

This work proposes a dynamic evaluation methodology to relax the conservatism in physical security evaluation, by leveraging an ongoing work in the Light Water Reactor Sustainability pathway. This methodology is implemented in a dynamic risk assessment tool named Event Modeling Risk Assessment using Linked Diagrams (EMRALD). The work extends EMRALD’s capability to support a sandbox feature where analysts can easily create attack scenarios and modify advanced/small modular reactor (A/SMR) security and safety features using templates. This approach saves time and cost since the analysis does not require creating detailed computer-aided design models, as is commonly required in commercial force-on-force software tools. EMRALD is completely free to use at https://emraldapp.inl.gov. We have developed basic templates including physical barriers, intrusion sensors, physical areas, and safety actions, that can be downloaded from EMRALD’s GitHub site: https://github.com/idaholab/EMRALD. These templates use generic data commonly used for training purposes, which do not reflect any actual operating nuclear reactor. Users may adjust the data in the templates with their own dataset and/or create new templates in EMRALD. The proposed methodology combines security and safety by assessing sabotage effects up to the radiological consequence to the public instead of merely the core damage state. This practice follows the industry standard for advanced non-light-water reactors currently proposed for endorsement by the Nuclear Regulatory Commission. The combination of security and safety is expressed in an achievability-consequence chart. EMRALD can be used to generate data for this chart. A hypothetical case study using a representative sodium-cooled fast reactor (SFR) facility is presented in this report to demonstrate this methodology. This case study does not contain any actual nuclear plant information. This work will benefit A/SMR vendors and utilities to implement security by design during the reactor design iteration phase, such that they do not have to perform upgrades and retrofits to the reactor after it is installed to improve its physical protection system. The tool may also be used to analyze domestic or foreign reactor designs to support the International Nuclear Security Techniques for Advanced Reactors (INSTAR) bilateral missions. Future works are planned to implement the methodology on a reference SFR reactor and a reference high-temperature gas-cooled reactor to obtain insights and lessons-learned for the A/SMR community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-xHA NEON Harvard Forest (HARV)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xHA NEON Harvard Forest (HARV). This is the FLUXNET version of the carbon flux data for the site US-xHA NEON Harvard Forest (HARV) produced by applying the standard ONEFlux (1F) software. Site Description - The Harvard Forest site is comprised of 3,750 acres of land and multiple research facilities; it is the core NEON site for the Northeast region. Harvard Forest is a department of the Faculty of Arts and Sciences of Harvard University. Representative habitats at Harvard Forest include northern, transition, and central forests; marshes, swamps, and conifer-dominated bogs; and forest plantations. Since its inception in 1907, research and education have been the focus of Harvard Forest: the original purpose was to develop a field laboratory for students, a research center in forestry and related disciplines, and a demonstration of practical sustained forestry. Since 1988, Harvard Forest has been a Long-Term Ecological Research site, funded by the National Science Foundation to conduct integrated, long-term studies of forest dynamics.

Network), NEON (National Ecological Observatory↗
DOE OSTI2025

FAIR Ecosystems for Science at Scale

High Performance Computing (HPC) centers provide resources to users who require greater scale to “get science done”. They deploy infrastructure with singular hardware architectures, cutting-edge software environments, and stricter security measures as compared with users’ own resources. As a result, users often create and configure digital artifacts in ways that are specialized for the unique infrastructure at a given HPC center. Each user of that center will face similar challenges as they develop specialized solutions to take full advantages of the center’s resources, potentially resulting in significant duplication of effort. Much duplicated effort could be avoided, however, if users of these centers found it easier to discover others’ solutions and artifacts as well as share their own. The FAIR principles address this problem by presenting guidelines focused around metadata practices to be implemented by vaguely defined “communities”; in practice, these tend to gather by domain (e.g. bioinformatics, geosciences, agriculture). Domain-based communities can unfortunately end up functioning as silos that tend both to inhibit sharing of solutions and best practices as well as to encourage fragile and unsustainable improvised solutions in the absence of best-practice guidance. We propose that these communities pursuing “science at scale” be nurtured both individually and collectively by HPC centers so that users can take advantage of shared challenges across disciplines and potentially across HPC centers. We describe an architecture based on the EOSC-Life FAIR Workflows Collaboratory, specialized for use with and inside HPC centers such as the Oak Ridge Leadership Computing Facility (OLCF), and we speculate on user incentives to encourage adoption. We note that a focus on FAIR workflow components rather than FAIR workflows is more likely to benefit the users of HPC centers.

Wilkinson, Sean [ORNL] (ORCID:0000000214437479)↗
DOE OSTI2023

Organizational and psychological measures for data center energy efficiency: barriers and mitigation strategies

Abstract It was last estimated that in 2020, data centers comprised approximately 2% of total US electricity consumption, with an estimated annual growth rate of 4%. As our country increasingly relies on information technology (IT), our data centers (DCs) will need to increase their energy efficiency (EE) to stabilize their energy consumption. The task of studying EE in DCs is complicated by the interconnected nature of humans and mission-critical technical systems. Moreover, the literature tends to focus on technology solutions such as improvements to IT equipment, cooling infrastructure, and software, without addressing organizational and psychological drivers. Our research demystifies the complex interactions between humans and DCs, by asking What non-technical barriers impede EE investment decision-making and/or implementing energy management strategies? To begin to answer this question, we perform a literature review of 86 resources, ranging from peer-reviewed journal publications to handbooks. We also consider related fields such as organizational behavioral management and energy intensive buildings. We develop a public Zotero library, perform content coding, and complete a rudimentary network analysis. Our findings from the literature review suggest that (1) technological solutions are abundant in the literature but fall short of providing practical guidance on the pitfalls of implementation, (2) making energy efficiency a priority at the executive level of organizations will be largely ineffective if the IT and facilities staff are not directly incentivized to increase EE, and (3) there is minimal current understanding of how the individual psychologies of IT and facilities staff affect EE implementation in DCs. In the next phase of our research, we plan to interview data center operators/experts to ground-truth our literature findings and collaboratively design decarbonization policy solutions that target organizational structure, empower individual staff, and foster a supportive external market.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Classical combinatorial optimization scaling for random Ising models on 2D heavy-hex graphs

Motivated by near term quantum computing hardware limitations, combinatorial optimization problems that can be addressed by current quantum algorithms and noisy hardware with little or no overhead are used to probe capabilities of quantum algorithms such as the quantum approximate optimization algorithm. In this study, a specific class of near term quantum computing hardware defined combinatorial optimization problems, Ising models on heavy-hex graphs both with and without geometrically local cubic terms, are examined for their classical computational hardness via empirical computation time scaling quantification. Specifically the time-to-solution (TTS) metric using the classical heuristic simulated annealing is measured for finding optimal variable assignments (ground states), as well as the time required for the optimization software Gurobi to find an optimal variable assignment. Because of the sparsity of these Ising models, the classical algorithms are able to find optimal solutions efficiently even for large instances (i.e. 100 000 spin variables). The Ising models both with and without geometrically local cubic terms exhibit average-case linear-time or weakly quadratic scaling when solved exactly using Gurobi, and the Ising models with no cubic terms show evidence of exponential-time TTS scaling when sampled using simulated annealing. These findings point to the necessity of developing and testing more complex, namely more densely connected, optimization problems in order for quantum computing to ever have a practical advantage over classical computing. Our results are another illustration that different classical algorithms can indeed have exponentially different running times, thus making the identification of the best practical classical technique important in any quantum computing vs. classical computing comparison.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Illinois Express Quantum Network (IEQNET): metropolitan-scale experimental quantum networking over deployed optical fiber

The Illinois Express Quantum Network (IEQNET) is a program to realize metro-scale quantum networking over deployed optical fiber using currently available technology. IEQNET consists of multiple sites that are geographically dispersed in the Chicago metropolitan area. Each site has one or more quantum nodes (Qnodes) representing the communication parties in a quantum network. Q-nodes generate or measure quantum signals such as entangled photons and communicate the results via standard, classical, means. The entangled photons in IEQNET nodes are generated at multiple wavelengths, and are selectively distributed to the desired users via optical switches. Here we describe the network architecture of IEQNET, including the Internet-inspired layered hierarchy that leverages software-defined-networking (SDN) technology to perform traditional wavelength routing and assignment between the Q-nodes. Specifically, SDN decouples the control and data planes, with the control plane being entirely classical. Issues associated with synchronization, calibration, network monitoring, and scheduling will be discussed. An important goal of IEQNET is demonstrating the extent to which the control plane can coexist with the data plane using the same fiber lines. This goal is furthered by the use of tunable narrow-band optical filtering at the receivers and, at least in some cases, a wide wavelength separation between the quantum and classical channels. We envision IEQNET to aid in developing robust and practical quantum networks by demonstrating metro-scale quantum communication tasks such as entanglement distribution and quantum-state teleportation.

Chung, Joaquin↗
DOE OSTI2023

Demonstration of INCC6 for advanced list-mode data acquisition and analysis using ALMM

The International Neutron Coincidence Counting (INCC) software plays an important role in nuclear safeguards and nuclear material control and accounting (NMC&A) measurements. While the current version, INCC5, represents the traditional standard utilized by inspectorates as well as facilities and practitioners alongside shift register hardware, LANL has recently developed an upgraded version of the software, INCC6. INCC6 offers the same analysis tools as INCC5 while adding new capabilities including acquisition and analysis of list-mode data, recording and storage of list-mode data files, and an expanded set of advanced analysis tools that make use of the additional information available from list-mode data. Here, this paper presents the first demonstration of data acquisition and analysis using INCC6 and the Advanced List Mode Multiplicity Module (ALMM). The capability of INCC6 to perform live list-mode data acquisition and analysis is demonstrated for a variety of neutron sources with a range of neutron emission rates relevant for practical applications and validated against the results obtained with INCC5 and traditional shift register hardware. Advanced list-mode analysis tools introduced by INCC6, such as time-interval and coincidence matrix analysis, are also demonstrated. Finally, the capability of INCC6 to analyze list-mode data files is tested and validated against traditional shift register results using INCC5.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

The Energy and Operational Impacts of Using 0-10V Control for LED Streetlights

LED lighting is becoming widely adopted and displacing most traditional lighting technologies. However, the traditional methods used to control light sources have not seen similar displacement. Lighting systems have historically utilized either a proprietary control method, or one of a handful of standardized methods (e.g., 0-10V, DALI, DMX512). The utility and market success of the standardized methods has been limited for a variety of reasons. Analog 0-10V methods have long been popular due to their simplicity and low cost of implementation and are presently the most commonly available control interface for indoor and outdoor LED products in North America. The emergence of “connected lighting systems” with more modern network interfaces and luminaire-level sensors and intelligence was anticipated by many to mark the beginning of the end of analog control. However, 0-10V interfaces continue to be prevalent with these more “digital” systems. The use of 0-10V methods has significant tradeoffs. 0-10V standards have historically not explicitly defined the relationship between the luminaire input control signal and output luminous flux for the full control signal range. As a result, it is difficult to predict relative luminaire light output and input power at any particular control voltage, and in practice the performance across LED drivers and the luminaires power is inconsistent. While this inconsistency has long been acknowledged by experts in the field, it is not accounted for in standard practice deployment, and end-users continue to regularly see unexpected and undesirable performance. It is hoped that the results from this study will help the lighting industry and standards developing organizations better understand and possibly resolve the shortcomings of 0-10V products, and consider what is best for the industry – additional incremental improvements to this fundamentally limited analog technology, or fully moving on to existing digital approaches, such as DALI D4i, that deliver accurate and consistent dimming performance across all luminaires in the system and thus guarantee the delivery of expected light levels, and energy and cost savings. Recommendations consistent with these goals are made to lighting and driver manufacturers, lighting software developers, standard developing organizations, and system designers and specifiers.

0-10V↗
DOE OSTI2025

A Beginner's Guide to Power and Energy Measurement and Estimation for Computing and Machine Learning

Concerns about the environmental footprint of machine learning are increasing. While studies of energy use and emissions of ML models are a growing subfield, most ML researchers and developers still do not incorporate energy measurement as part of their work practices. While measuring energy is a crucial step towards reducing carbon footprint, it is also not straightforward. This paper introduces the main considerations necessary for making sound use of energy measurement tools and interpreting energy estimates, including the use of at-the-wall versus on-device measurements, sampling strategies and best practices, common sources of error, and proxy measures. It also contains practical tips and real-world scenarios that illustrate how these considerations come into play. It concludes with a call to action for improving the state of the art of measurement methods and standards for facilitating robust comparisons between diverse hardware and software environments.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗