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DOE OSTI2022

Artificial Intelligence and Machine Learning for Bioenergy Research: Opportunities and Challenges

The integration of artificial intelligence and machine learning (AI/ML) with automated experimentation, genomics, biosystems design, and bioprocessing technologies is poised to revolutionize scientific investigation and, particularly, bioenergy research. To identify the opportunities and challenges in this emerging research area, the U.S. Department of Energy’s (DOE) Biological and Environmental Research program (BER) and Bioenergy Technologies Office (BETO) held a joint virtual workshop on AI/ML for Bioenergy Research (AMBER) on August 23–25, 2022. These interests have since been amplified in a September 2022 Executive Order, “Advancing Biotechnology and Biomanufacturing Innovation for a Sustainable, Safe, and Secure U.S. Bioeconomy,” to promote a whole-of government approach to biotechnology development (White House 2022). Approximately 50 scientists with various backgrounds and expertise from academia, industry, and DOE national laboratories met to discuss the opportunities and challenges of AI/ML for bioenergy research. Workshop participants were tasked with assessing the potential for AI/ML and laboratory automation to advance biological understanding and engineering in general. They particularly examined how integrating AI/ML tools with laboratory automation could accelerate biosystems design and optimize biomanufacturing. Discussions included the data and computational infrastructure needed to augment biosystems design applications and the expertise and workforce development efforts urgently required to shift integrated systems toward bioenergy research more broadly. Participants discussed many existing and future applications of AI/ML for biosystems design ranging from enzymes to plants and microbes, microbiomes, and bioprocess development. They also identified three key categories of scientific and technical opportunities and challenges: high-quality data, AI/ML algorithms, and laboratory automation. Several main takeaways emerged from the workshop: 1. Numerous AI/ML and automated experimentation applications exist for a variety of DOE mission needs in energy and the environment; 2. Exemplary research grand challenges for which AI/ML could provide solutions include: building microbes and microbial communities to specifications, developing closed-loop autonomous design and control for biosystems design, and advancing scale-up and automation; 3. Lack of sufficient high-quality, annotated data hinders the development of AI/ML applications; 4. New and improved AI/ML tools are needed, particularly those meeting the specific needs of the BER and BETO research communities; 5. Trade-offs in performance, cost, and reliability exist between deploying commercially available versus building custom-developed instrumentation and software for automated or autonomous experimentation; translation of manual to automated or autonomous methods is often a nontrivial endeavor; 6. Training a new generation of young scientists who can develop and apply AI/ML tools is needed to solve long-standing scientific challenges in bioenergy research. The integration of AI/ML tools and automated experimentation represents a new data-driven research paradigm complementary to the traditional hypothesis-driven research paradigm. This paradigm accelerates design and optimization of biological systems and processes for a variety of DOE mission needs in energy and the environment. The AMBER workshop broadly explored the potential of this new paradigm for bioenergy research, of particular interest to BER and BETO, and identified key challenges and opportunities that DOE can address in the coming years by leveraging its unique capabilities and resources.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Physical optics simulations with PHASE for SwissFEL beamlines

PHASE is a software tool for physical optics simulation based on the stationary phase approximation method. The code is under continuous development since about 20 years and has been used for instance for fundamental studies and ray tracing of various beamlines at the Swiss Light Source. Along with the planning for SwissFEL a new hard X-ray free electron laser under construction, new features have been added to permit practical performance predictions including diffraction effects which emerge with the fully coherent source. We present the application of the package on the example of the ARAMIS 1 beamline at SwissFEL. The X-ray pulse calculated with GENESIS and given as an electrical field distribution has been propagated through the beamline to the sample position. We demonstrate the new features of PHASE like the treatment of measured figure errors, apertures and coatings of the mirrors and the application of Fourier optics propagators for free space propagation.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

High-resolution climate model datasets for energy infrastructure planning in a renewable-dependent future

Electrification and renewables deployment efforts are amplifying the interdependence of the climate and energy systems. Increases in climate model resolution, which is now approaching that of reanalysis datasets and operational weather forecast models, present a unique opportunity to use future climate projections for energy infrastructure planning. In this Perspective, we review recent developments in high-resolution climate modeling, which have been driven by increased computing power and advanced software tools. We then look ahead to discuss how high-resolution climate data can be used to plan for a renewable-dependent future, and envision a unified climate-energy model framework that captures the two-way feedbacks between these interdependent systems.

climate change↗

DOE OSTI2021

VARS Framework

The Verification and Validation Assuring Reliability and Security (VARS) project team has developed the proof-of-concept VARS framework which will be implemented in the form of a software tool called Risk-Informed Verification and Validation Recommendation (RIVVR). The framework will provide Energy Delivery System (EDS) stakeholders with cybersecurity focused verification and validation (V&V) approach which includes list of potentially relevant vulnerabilities to test or address, pre-procurement guidance, and separate lists of relevant standards, tools, and techniques (ST2) to be considered by utilities and vendors

Pal, Seemita↗

DOE OSTI2019

Benchmarking Algorithm for Radio Nuclide Identification (BARNI) Literature Review

This is a literature review of published radioisotope identification (ID) methods, and an attempt at systematic organization of the approaches for solving this problem. In addition, there is an overview of the related open and closed source software, and patents related to radioisotope identification. This document is also part of the development plan for BARNI (Benchmarking Algorithm for RadioNuclide Identification) software, since it is meant to be a comparison tool, a summary of radiation ID performance evaluations is also included.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Detecting Data-Races in High-Performance Computing

High-performance computing is susceptible to data-race bugs. Data races occur when sequences of computed events do not happen in the intended order, a significant barrier to the integrity of parallel programs using shared-memory architectures. Many approaches to data-race detection are based on traditional static-analysis techniques that typically execute on a program’s source code or control-flow graph (the graphical representation of all possible orders of events in the execution of a program). Similar to classical data-flow analyses, such tools can produce false alarms that report spurious race conditions on error free programs. We have developed a software verification technique that requires as input only a program’s source code and can automatically detect a data-race bug which definitely exists, determine that a program is definitely data-race free, or report that it cannot determine either of the two cases.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Cloud-Based Model Calibration Using OpenStudio: Preprint

OpenStudio is a free, open source Software Development Kit (SDK) and application suite for performing building energy modeling and analysis. The OpenStudio Parametric Analysis Tool has been extended to allow cloud-based simulation of multiple OpenStudio models parametrically related to a baseline model. This paper describes the new cloud-based simulation functionality and presents a model cali-bration case study. Calibration is initiated by entering actual monthly utility bill data into the baseline model. Multiple parameters are then varied over multiple iterations to reduce the difference between actual energy consumption and model simulation results, as calculated and visualized by billing period and by fuel type. Simulations are per-formed in parallel using the Amazon Elastic Cloud service. This paper highlights model parameterizations (measures) used for calibration, but the same multi-nodal computing architecture is available for other purposes, for example, recommending combinations of retrofit energy saving measures using the calibrated model as the new baseline.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

MFANS 2024 - Formally Proving Characteristics of Cyber-Physical Systems

Cyber-physical systems (CPS) are engineered systems that rely on the smooth integration of computational algorithms and physical elements. This integration presents new challenges for verifying that systems will behave as expected. The goal of this presentation is to present current challenges and potential solutions for the formal verification of cyber-physical systems. For cyber systems, formal methods refer to systematically rigorous mathematical techniques employed in the specification, development, analysis, and verification of both software and hardware systems. Recent advancements in computer science have yielded sophisticated tools specifically designed to address challenges associated with formal methods in complex systems. These tools leverage various foundational concepts such as logic, formal languages, program semantics, type systems, type theory, and automata theory. A notable achievement in the application of formal methods is the seL4 microkernel, claimed to be the first general-purpose operating-system kernel to be verified. Its proof implies the absence of bugs and guarantees that the kernel meets specifications. For physical systems, dynamic and control theory has a history of using rigorous analytic techniques to prove functional correctness. Lyapunov, optimal, classical, modern, and robust control theories all provide rigorous mathematical methods both to analyze system performance and to design controller that can be guaranteed to meet certain objectives. Recent computational techniques like level set theory and reachability analysis provide assertions that a system's state will avoid unsafe regions. Even though success has been independently achieved for cyber systems and physical systems, the integration of such systems creates new challenges. In particular, there is an obvious discrepancy between finite-state machines and infinite-state systems, resulting in different approaches for modeling and analyzing these system. While it is possible to simulate hybrid systems, this provides only a demonstration of a performance and not proof. For hybrid systems, current formal methods and system analysis approaches typically require a workarounds to work on hybrid systems like CPS. This paper will outline the state of the art and limits of current practice for formally verifying CPS and will identify possible research directions that require attention.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Software-Based Challenges of Developing the Future Distribution Grid

The software that the utility industry currently uses may be insufficient to analyze the distribution grid as it rapidly modernizes to include active resources such as distributed generation, switch and voltage control, automation, and increasingly complex loads. Although planners and operators have traditionally viewed the distribution grid as a passive load, utilities and consultants increasingly need enhanced analysis that incorporates active distribution grid loads in order to ensure grid reliability. Numerous commercial and open-source tools are available for analyzing distribution grid systems. These tools vary in complexity from providing basic load-flow and capacity analysis under steady-state conditions to time-series analysis and even geographical representations of dynamic and transient events. The need for each type of analysis is not well understood in the industry, nor are the reasons that distribution analysis requires different techniques and tools both from those now available and from those used for transmission analysis. In addition, there is limited understanding of basic capability of the tools and how they should be practically applied to the evolving distribution system. The study reviews the features and state of the art capability of current tools, including usability and visualization, basic analysis functionality, advanced analysis including inverters, and renewable generation and load modeling. We also discuss the need for each type of distribution grid system analysis. In addition to reviewing basic functionality current models, we discuss dynamics and transient simulation in detail and draw conclusions about existing software?s ability to address the needs of the future distribution grid as well as the barriers to modernization of the distribution grid that are posed by the current state of software and model development. Among our conclusions are that accuracy, data transfer, and data processing abilities are key to future distribution grid modeling, and measured data sources are a key missing element . Modeling tools need to be calibrated based on measured grid data to validate their output in varied conditions such as high renewables penetration and rapidly changing topology. In addition, establishing a standardized data modeling format would enable users to transfer data among tools to take advantage of different analysis features. ?

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2016

Global Solutions Through Simulation For Better Decommissioning - 16457

Each nuclear facility is different due to their history and there is no rule for choosing a decommissioning strategy. There are three major decommissioning strategies. First, 'immediate dismantling', which means the decommissioning begins immediately after the transfer of waste and nuclear material. Second, 'deferred dismantling strategy', meaning the facility is maintained into a containment zone from thirty to one hundred years before being decommissioned. Finally, 'entombment', referring to the placement of the facility into a reinforced containment until the radionuclides decay and reach a level allowing the site release. When a strategy is decided many factors have to be taken into account. Into a major project such as a reactor decommissioning, there are many smaller projects and the decommissioning strategy can be different among these smaller projects. Very often, some entry data are not perfectly known, for example, the dosimetric activity has not been updated through time or after specific events. Because of uncertainties and/or hypothesis existing around projects and their high level of interdependency, global solutions are a good way to choose the best decommissioning strategy. Especially since each entry data has consequences on output results whether it is on costs, cumulated dose, waste or delays. Also the dose, delays or waste management, all have impact on costs. To obtain an optimal scenario into a special environment, it is necessary to deal with all these items together. This global solution can be implemented thanks to simulation in dedicated software which helps define the global strategy, optimize the scenario, and prevent contingencies. For a specific environment, when many scenarios have been developed and simulated, sensitivity studies are really important to choose the optimal decommissioning strategy. Sensitivity studies can be done with simulation tools by comparing results of scenarios directly into the software. This comparison helps to choose the optimal scenario according to which output data is considered as key determinant. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Microgrid Design Analysis Using Technology Management Optimization and the Performance Reliability Model

Microgrids are a focus of localized energy production that support resiliency, security, local con- trol, and increased access to renewable resources (among other potential benefits). The Smart Power Infrastructure Demonstration for Energy Reliability and Security (SPIDERS) Joint Capa- bility Technology Demonstration (JCTD) program between the Department of Defense (DOD), Department of Energy (DOE), and Department of Homeland Security (DHS) resulted in the pre- liminary design and deployment of three microgrids at military installations. This paper is focused on the analysis process and supporting software used to determine optimal designs for energy surety microgrids (ESMs) in the SPIDERS project. There are two key pieces of software, an ex- isting software application developed by Sandia National Laboratories (SNL) called Technology Management Optimization (TMO) and a new simulation developed for SPIDERS called the per- formance reliability model (PRM). TMO is a decision support tool that performs multi-objective optimization over a mixed discrete/continuous search space for which the performance measures are unrestricted in form. The PRM is able to statistically quantify the performance and reliability of a microgrid operating in islanded mode (disconnected from any utility power source). Together, these two software applications were used as part of the ESM process to generate the preliminary designs presented by SNL-led DOE team to the DOD. Acknowledgements Sandia National Laboratories and the SPIDERS technical team would like to acknowledge the following for help in the project: * Mike Hightower, who has been the key driving force for Energy Surety Microgrids * Juan Torres and Abbas Akhil, who developed the concept of microgrids for military instal- lations * Merrill Smith, U.S. Department of Energy SPIDERS Program Manager * Ross Roley and Rich Trundy from U.S. Pacific Command * Bill Waugaman and Bill Beary from U.S. Northern Command * Tarek Abdallah, Melanie Johnson, and Harold Sanborn of the U.S. Army Corps of Engineers Construction Engineering Research Laboratory * Colleagues from Sandia National Laboratories (SNL) for their reviews, suggestions, and participation in the work.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2019

NIST Infiltration Tools for Commercial Buildings

The Department of Energy estimates that infiltration through building envelopes accounted for 6 % of the total energy consumed by commercial buildings and 21 % of the heating and cooling energy. Air barrier requirements are now being included in ASHRAE Standards 90.1 and 189.1 and other construction requirements. The energy impacts of unintended infiltration on building energy use can be significant, but current energy simulation software and design methods are generally not able to accurately account for envelope infiltration and the impacts of improved airtightness. NIST has been developing tools to better account for infiltration in building energy models. The tools that will be discussed in this paper include: CONTAM Results Export Tool; weather-correlated infiltration inputs for prototype commercial buildings and the associated Open Studio Measures; and a web-based tool to evaluate the energy savings of building envelope airtightening, which was developed with the Oak Ridge National Laboratory and the Air Barrier Association of America. This paper briefly describes each tool, their applications, and the benefits of using each. All of the tools are publicly available at no cost.

Ng, Lisa↗

DOE OSTI2018

Modernising ATLAS Software Build Infrastructure

In the last year ATLAS has radically updated its software development infrastructure hugely reducing the complexity of building releases and greatly improving build speed, flexibility and code testing. The first step in this transition was the adoption of CMake as the software build system over the older CMT. This required the development of an automated translation from the old system to the new, followed by extensive testing and improvements. This resulted in a far more standard build process that was married to the method of building ATLAS software as a series of 12 separate projects from Subversion. We then proceeded with a migration of the code base from Subversion to Git. As the Subversion repository had been structured to manage each package more or less independently there was no simple mapping that could be used to manage the migration into Git. Instead a specialist set of scripts that captured the software changes across official software releases was developed. With some clean up of the repository and the policy of only migrating packages in production releases, we managed to reduce the repository size from 62 GiB to 220 MiB. After moving to Git we took the opportunity to introduce continuous integration so that now each code change from developers is built and tested before being approved. With both CMake and Git in place we also dramatically simplified the build management of ATLAS software. Many heavyweight homegrown tools were dropped and the build procedure was reduced to a single bootstrap of some external packages, followed by a full build of the rest of the stack. This has reduced the time for a build by a factor of 2. It is now easy to build ATLAS software, freeing developers to test compile intrusive changes or new platform ports with ease. We have also developed a system to build lightweight ATLAS releases, for simulation, analysis or physics derivations which can be built from the same branch.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Binary-level Software Compatibility Tool Agreement

Application Binary Interface (ABI) compatibility is essential for system or software updates to ensure that libraries continue to function. Tools that can assess a binary or library ABI can thus be used to make predictions about compatibility, and predict downstream bugs by informing developers and users about issues. In this work, we are interested in describing a set of well-known tools for assessing ABI, and testing them in a controlled set experiments to assess tool agreement. We run 7660 smaller experiments across tools (N=30,640 total results) to evaluate not only predictions, but also each tool’s ability to provide detail about underlying issues. In this paper, along with highlighting the problem of assessing ABI compatibility and critiquing the pros and cons of currently available tools, we provide guidance to developers interested to test ABI based on our empirical results and suggestions for future work.

ABI↗

DOE OSTI2023

Simulations and analysis tools for charge-exchange (d, 2 He) reactions in inverse kinematics with the AT-TPC

Charge-exchange (d, 2 He) reactions in inverse kinematics at intermediate energies are a very promising method to investigate the Gamow–Teller transition strength in unstable nuclei. A simulation and analysis software based on the attpcroot package was developed to study this type of reactions with the active-target time projection chamber (AT-TPC). The simulation routines provide a realistic detector response that can be used to understand and benchmark experimental data. Analysis tools and correction routines can be developed and tested from simulations in ATTPCROOT , because they are processed in the same way as the real data. In particular, we study the feasibility of using coincidences with beam-like particles to unambiguously identify the (d, 2 He) reaction channel, and to develop a kinematic fitting routine for future applications. More technically, the impact of space-charge effects in the track reconstruction, and a possible correction method are investigated in detail. Finally, this analysis and simulation package constitutes an essential part of the software development for the fast-beams program with the AT-TPC.

(d,2He)↗

DOE OSTI2024

Privacy Preserving Federated Learning for Advanced Scientific Ecosystems

We present a framework to provide privacy preserving (PP) federating learning (FL) across multiple computational and experimental facilities. This work joins the compute capabilities of National Energy Research Scientific Computing Center (NERSC) and Oak Ridge National Laboratory Research Cloud (ORC) with simulated experimental data, such as those produced at the SLAC National Accelerator Laboratory and Spallation Neutron Source (SNS). We describe the software infrastructure developed to provide privacy for computational and experimental networks. We developed algorithmic privacy across the federated system by embedding database security, computation, and communication into the federation architecture, utilizing scientific tools developed by the experimental community.

Archibald, Rick [ORNL] (ORCID:0000000245389780)↗

DOE OSTI2020

SpackDev: Multi-Package Development with Spack

High Energy Physics (HEP) software environments often involve ~ hundreds of external packages and libraries, and similar numbers of experiment-specific, science-critical packages—many under continuous development. Managing coherent releases of the external software stack is challenging enough, but managing the highly-collaborative—and distributed—development of a large body of code against such a stack adds even more complexity and room for error. Spack is a popular Python-based package management tool with a specific focus on the needs of High Performance Computing (HPC) systems and system administrators whose strength is orchestrating the discrete download, build, testing, and installation of pre-packaged or tagged third-party software against similarly stable dependencies. As such it is becoming increasingly popular within HEP as that community makes increasing use of HPC facilities, and as efforts to develop future HPC systems utilize Spack to provide scientific software on those platforms. SpackDev is a system to facilitate the simultaneous development of interconnected sets of packages. Intended to handle packages without restriction to one internal build system, SpackDev is integrated with Spack as a command extension in order to leverage features such as dependency calculations and build system configuration, and is generally applicable outside HEP. We describe SpackDev’s features and development over the last two years, initial experience using SpackDev in the context of the LArSoft liquid argon detector toolkit, and work remaining before it can be considered a fully-functional multi-package build system for HEP experiments utilizing Spack.

Green, Chris↗

DOE OSTI2013

The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities in Assessing the Degradation of Cementitious Barriers - 13487

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in K{sub d}/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software tools. Modification of the existing tools can provide many opportunities to bring defense in depth in prediction of the performance of cementitious barriers over time. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗