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AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.

59 BASIC BIOLOGICAL SCIENCES↗

Differential methods for assessing sensitivity in biological models

Differential sensitivity analysis is indispensable in fitting parameters, understanding uncertainty, and forecasting the results of both thought and lab experiments. Although there are many methods currently available for performing differential sensitivity analysis of biological models, it can be difficult to determine which method is best suited for a particular model. In this paper, we explain a variety of differential sensitivity methods and assess their value in some typical biological models. First, we explain the mathematical basis for three numerical methods: adjoint sensitivity analysis, complex perturbation sensitivity analysis, and forward mode sensitivity analysis. We then carry out four instructive case studies. (a) The CARRGO model for tumor-immune interaction highlights the additional information that differential sensitivity analysis provides beyond traditional naive sensitivity methods, (b) the deterministic SIR model demonstrates the value of using second-order sensitivity in refining model predictions, (c) the stochastic SIR model shows how differential sensitivity can be attacked in stochastic modeling, and (d) a discrete birth-death-migration model illustrates how the complex perturbation method of differential sensitivity can be generalized to a broader range of biological models. Finally, we compare the speed, accuracy, and ease of use of these methods. We find that forward mode automatic differentiation has the quickest computational time, while the complex perturbation method is the simplest to implement and the most generalizable.

59 BASIC BIOLOGICAL SCIENCES↗

Matilda v1.0: An R package for probabilistic climate projections using a reduced complexity climate model

A primary advantage to using reduced complexity climate models (RCMs) has been their ability to quickly conduct probabilistic climate projections, a key component of uncertainty quantification in many impact studies and multisector systems. Providing frameworks for such analyses has been a target of several RCMs used in studies of the future co-evolution of the human and Earth systems. In this paper, we present Matilda, an open-science R software package that facilitates probabilistic climate projection analysis, implemented here using the Hector simple climate model in a seamless and easily applied framework. The primary goal of Matilda is to provide the user with a turn-key method to build parameter sets from literature-based prior distributions, run Hector iteratively to produce perturbed parameter ensembles (PPEs), weight ensembles for realism against observed historical climate data, and compute probabilistic projections for different climate variables. This workflow gives the user the ability to explore viable parameter space and propagate uncertainty to model ensembles with just a few lines of code. The package provides significant freedom to select different scoring criteria and algorithms to weight ensemble members, as well as the flexibility to implement custom criteria. Additionally, the architecture of the package simplifies the process of building and analyzing PPEs without requiring significant programming expertise, to accommodate diverse use cases. We present a case study that provides illustrative results of a probabilistic analysis of mean global surface temperature as an example of the software application.

54 ENVIRONMENTAL SCIENCES↗

A meta-evaluation of the quality of reporting and execution in ecological meta-analyses

Quantitatively summarizing results from a collection of primary studies with meta-analysis can help answer ecological questions and identify knowledge gaps. The accuracy of the answers depends on the quality of the meta-analysis. We reviewed the literature assessing the quality of ecological meta-analyses to evaluate current practices and highlight areas that need improvement. From each of the 18 review papers that evaluated the quality of meta-analyses, we calculated the percentage of meta-analyses that met criteria related to specific steps taken in the meta-analysis process (i.e., execution) and the clarity with which those steps were articulated (i.e., reporting). We also re-evaluated all the meta-analyses available from Pappalardo et al. to extract new information on ten additional criteria and to assess how the meta-analyses recognized and addressed non-independence. In general, we observed better performance for criteria related to reporting than for criteria related to execution; however, there was a wide variation among criteria and meta-analyses. Meta-analyses had low compliance with regard to correcting for phylogenetic non-independence, exploring temporal trends in effect sizes, and conducting a multifactorial analysis of moderators (i.e., explanatory variables). In addition, although most meta-analyses included multiple effect sizes per study, only 66% acknowledged some type of non-independence. The types of non-independence reported were most often related to the design of the original experiment (e.g., the use of a shared control) than to other sources (e.g., phylogeny). We suggest that providing specific training and encouraging authors to follow the PRISMA EcoEvo checklist recently developed by O’Dea et al. can improve the quality of ecological meta-analyses.

59 BASIC BIOLOGICAL SCIENCES↗

DeepBench: A simulation package for physical benchmarking data

We introduce **DeepBench**, a python library that generates simple simulated image data from first principles, such as basic geometric shapes and astronomical objects. These data are highly valuable for developing (calibration, testing, and benchmarking) statistical and machine learning models because they make it possible to connect the final data product to physically interpretable inputs. This software includes tools to curate and store the datasets to maximize reproducibility.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Windfarm Operations and Maintenance cost-Benefit Analysis Tool (WOMBAT)

This report provides technical documentation and background on the newly-developed Wind Operations and Maintenance cost-Benefit Analysis Tool (WOMBAT) software. WOMBAT is an open-source model that can be used to obtain cost estimates for operations and maintenance of land-based or offshore wind power plants. The software was designed to be flexible and modular to allow for implementation of new strategies and technological innovations for wind plant maintenance. WOMBAT uses a process-based simulation approach to model day-to-day operations, repairs, and weather conditions. High-level outputs from WOMBAT, including time-based availability and annual operating costs, are found to agree with published results from other models.

17 WIND ENERGY↗

Dynamic Decarbonization through Autonomous Physics-Centric Deep Learning and Optimization of Building Operations (Abstract only)

This project directly addresses the primary goal of Area of Interest 2 in the CRADA call: to advance optimization-based integrated energy management systems in commercial and residential buildings. Pacific Northwest National Laboratory (PNNL) and its industry partner PassiveLogic aim to accomplish this by reaching three key objectives. First, to ensure a broad impact in the building controls industry, PNNL will extend its open-source library for predictive control synthesis by augmenting its capabilities with data-driven self-learning of building models and auto-calibration of predictive controllers. The effort will focus on building use cases selected in collaboration with PassiveLogic. The team will specifically address the development of methods for data-driven adaptation of building models, investigation of model architectures that best address specific building types, and automated synthesis of differentiable predictive controllers that optimize diverse objectives. Second, PNNL will collaborate with PassiveLogic to integrate the aforementioned methods with PasiveLogic’s advanced controls platform. The collaborative integration effort will inform the developments under the first objective by providing specific data on the attainable performance of model learning on resource-constrained edge computing platforms. This software integration effort will increase the technical maturity of the developed libraries by exploring the use of software integration tools and methods. Third, PNNL and PassiveLogic will work to improve the technology readiness of the developed predictive controllers by testing their performance in relevant test environments, such as high-fidelity simulation, hardware in the loop, and actual test buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The Release of the Simplified Radionuclide Transport (SRT) Code (V.2.1)

Reactor licensing centers on the protection of the public and environment from the inadvertent release of radioactive material. Therefore, mechanistic source term analysis, or the realistic evaluation of radionuclide transport from the source to the environment for specific transient scenarios, is vital to reactor licensing efforts. Developed to resolve a gap in mechanistic source term modeling capabilities for sodium fast reactors (SFRs), the Simplified Radionuclide Transport (SRT) code created by Argonne National Laboratory (Argonne) is now utilized by advanced reactor vendors, universities, and research institutions to support a multitude of design, licensing, and research efforts. Recently, SRT version 2.1 was released, which includes improvements to code models and verification and validation (V&V) suite to support the SRT user community. The following work provides an overview of the improvements made as part of the release of SRT version 2.1. This effort is supported by the U.S. Department of Energy Office of Nuclear Energy (DOE:NE) Advanced Reactor Technologies (ART) Fast Reactor Program (FRP), as part of the program’s support of national laboratory design and safety analysis computer codes utilized by the fast reactor industry. The expansion of SRT code capabilities and improvements to code V&V associated with version 2.1 are in response to user requests and lessons learned from recent source term analyses performed by Argonne and advanced reactor vendors. They also align with the evolving role of SRT, from research and development tool to software utilized for reactor licensing calculations. The report is structured in alignment with the code improvements, as outlined in Figure 1-1. Section 2 provides background information on SRT, including its history, capabilities, and utilization. Section 3 details new code capabilities as part of version 2.1, while Section 4 focuses on the expansion of the code’s V&V suite. Lastly, Section 5 provides a summary and discussion of next steps.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Physics-Informed Learning Machines for Multiscale and Multiphysics Problems (PHILMS) (Technical Report)

The research work at University of California Santa Barbara (UCSB) resulted in several new developments in the areas of scientific machine learning, numerical analysis, and practical methods for data-driven modeling, prediction, reductions, and simulation. Many of the projects were carried out in collaboration with members of the national laboratories at Sandia National Laboratories (SNL), Pacific Northwestern National Laboratories (PNNL), and other institutions. Results included developing new scientific machine learning methods, related theory and mathematical frameworks for analysis and training, data-driven numerical solvers, and related tools and software for scientific computation. During the support period, over 16+ papers were submitted for publication, and 4 open-source software packages were developed and released (available at http://atzberger.org/). In addition, 7+ students and 2 post-docs were mentored in collaboration with the laboratory staff for future careers in academia, government labs, and industry.

97 MATHEMATICS AND COMPUTING↗

Hydropower Biological Evaluation Toolset (HBET) Version 3.0: User Guide

The Hydropower Biological Evaluation Tools (HBET) software package, developed by Pacific Northwest National Laboratory (PNNL), is designed to assemble, organize, and process data collected by Sensor Fish and live fish. HBET enable users to characterize the hydraulic conditions of hydropower structures and estimate fish injury and mortality rates from various stressors. Future updates of the software may support other technologies, such as bead tracking in physical models and computational fluid dynamics. The HBET program can be customized to analyze different hydraulic applications, including turbines, spillways, weirs, pumped storage, and other user-defined functions, and therefore, help researchers, turbine designers, hydropower operators, and regulators better evaluate hydropower structures regarding their environmental sustainability and cost-effectiveness. Added content to the user guide about the new feature for predicting absolute injury rates.

13 HYDRO ENERGY↗

The SAS4A/SASSYS-1 Version 5.8 Safety Analysis Code System

SAS4A/SASSYS-1 is a software simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced nuclear reactors. Detailed, mechanistic models of steady-state and transient thermal, hydraulic, kinetic, and mechanical phenomena are employed to describe the response of the reactor core, the reactor primary and secondary coolant loops, the reactor control and protection systems, and the balance-of-plant to accidents caused by changes in coolant flow, loss of heat rejection, or reactivity insertion. The consequences of single and double-fault accidents can be modeled, including fuel and coolant heating, fuel and cladding mechanical behavior, core reactivity feedbacks, coolant loop performance including natural circulation, and decay heat removal. Analyses are typically terminated upon demonstration of reactor and plant shutdown to permanently coolable conditions, or upon violation of design basis margins. The objective of the analysis is to quantify accident consequences as measured by the transient behavior of system performance parameters, such as fuel and cladding temperatures, reactivity, and cladding strain. Originally developed for analysis of sodium cooled reactors with oxide fuel clad by stainless steel, the models were subsequently extended and specialized to metallic fuel clad with advanced alloys and to several other coolant options, including lead, LBE, and water.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

High-Burnup BWR LOCA Burst Analysis Using High-Fidelity Multiphysics Simulations

The US nuclear industry is looking to improve on the operating economics of the current fleet of light-water reactors (LWRs). One way of achieving this is by operating fuel to higher burnup. In pressurized water reactors (PWRs), relaxing the current burnup limit will allow for cycle length extensions and power uprates; in boiling water reactors (BWRs) it may allow for improved fuel utilization and reduced feed assemblies, as well as more efficient power uprates and increased capacity factors that will support the Administration’s Executive Order to facilitate 5 GW of power uprates at existing nuclear facilities. However, one of the key limitations to operating fuel to higher burnup is the risk of fuel fragmentation, relocation, and dispersal (FFRD). Recognizing the high interest in extending burnup limits, the US Nuclear Regulatory Commission (NRC) has issued Draft Regulatory Guide DG-1434, which defines an approach that would be acceptable to the NRC for addressing FFRD risk. The approach defined will require better understanding of the phenomena leading to FFRD as well as best-estimate simulation methods to understand FFRD risk in high-burnup cores. The Nuclear Energy Advanced Modeling and Simulation program is supporting the FFRD industry challenge problem through development of state-of-the-art, high-fidelity modeling and simulation LWR analysis capabilities; namely, the BISON fuel performance code and the VERA core simulator software. These tools, along with the US NRC TRACE system analysis code, have been utilized for analysis of FFRD risk in both PWR and BWR cores in recent years. The work documented in this report addresses the lack of high-fidelity research for BWRs and builds on a previous activity where the framework has been applied to Cycles 16 through 18 of Limerick Unit 1, a BWR/4, with introduction of 8 high-burnup lead use assemblies (HBLUAs) that were representative of the 8 HBLUAs loaded into Limerick Unit 2 in 2021. VERA was used in this previous activity to model rod-by-rod depletion in these cycles, and its solution was used to initialize a TRACE simulation of a large-break loss-of-coolant accident (LBLOCA) at the end of Cycle 18. In the work documented in this report, the TRACE model was improved by refining the core mesh and utilizing a new feature that allows for capturing the full 3D VERA power distribution in the model. This allows for a more detailed solution for setting BISON boundary conditions. Furthermore, the solutions from VERA and TRACE were used to set up and perform BISON simulations of about 1,000 rods sampled from the core, including all burnup levels. Utilizing two cladding burst models, it was shown that no fuel rods were predicted to burst during the postulated LBLOCA transient. Additionally, a sensitivity study was performed by artificially increasing linear heat rate during the postulated LBLOCA to identify parameters that correlate with rod burst susceptibility. Burnup, fission gas release, and hoop strain were all found to be positively correlated with rod burst susceptibility. Small-break loss-of-coolant accident (SBLOCA) analyses were also performed; these analyses predicted cladding temperature increases that were bounded by the LBLOCA cladding temperatures for all small break sizes studied for this plant. However, future refinements to the plant response assumptions during the SBLOCA could impact the predicted cladding response. Finally, a benchmark study was performed between CTF and TRACE for LOCA conditions to better qualify CTF for BWR LOCA modeling.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

Commercial PV Inverter IEEE 1547.1 Ride-Through Assessments Using an Automated PHIL Test Platform

As more countries seek solutions to their de-carbonization targets using renewable energy (RE) technologies, interconnection standards and national grid codes for distributed energy resources (DER) are being updated to support higher penetrations of RE and improve grid stability. Common grid-code revisions mandate DER devices, such as solar inverters and energy storage systems, ride-through (RT) voltage and frequency disturbances. This is necessary because as the percentage of generation from DER increases, there is a greater risk power system faults will cause many or all DER to trip, triggering a substantial load-generation imbalance and possible cascading blackout. This paper demonstrates for the first time a methodology to verify commercial DER devices are compliant to new voltage, frequency, and rate of change of frequency (ROCOF) RT requirements established in IEEE Std. 1547-2018. The methodology incorporates a software automation tool, called the SunSpec System Validation Platform (SVP), in combination with a hardware-in-the-loop (HIL) system to execute the IEEE Std. 1547.1-2020 RT test protocols. In this paper, the approach is validated with two commercial photovoltaic inverters, the test results are analyzed for compliance, and improvements to the test procedure are suggested.

14 SOLAR ENERGY↗

The Elastic Analysis Facility's (EAF's) Contribution to the Future of Analysis at Multi-Experiment Institutions and Future Colliders

The Elastic Analysis Facility (EAF) hosted at Fermi National Accelerator Laboratory (Fermilab) is a platform being developed with the goal of providing a fast and efficient facility for physics analysis. As high-energy physics moves towards collecting larger datasets, such as those from the High-Luminosity LHC, the EAF strives to provide a powerful and adaptable framework for future colliders and multi-experiment institutions. Currently, the EAF supports several experiments including CMS, NOvA, and DUNE as well as serving accelerator physicists and beam line operations through integrated software and secure connections to Fermilab's computing resources. In addition, the EAF was designed with a user-friendly interface, intended to be more intuitive for emerging generations of physicists, that is still accessible for established styles of analysis. The EAF can also achieve better analysis efficiency due to the modernization of software and tools that can better utilize Fermilab's computing power. Furthermore, its design incorporates industry standards whenever possible, enhancing its sustainability and making it a possible template for other national or international laboratories and research facilities. Overall, the EAF is a forward-looking solution that will meet the evolving needs of particle physics, ensuring readiness for future colliders and multi-experiment research institutions.

Chavez, Elise [Wisconsin U., Madison]↗