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DOE OSTI2021

Optimization with the OpenACC-to-FPGA framework on the Arria 10 and Stratix 10 FPGAs

The reconfigurable computing paradigm with field programmable gate arrays (FPGAs) has received renewed interest in the high-performance computing field due to FPGAs’ unique combination of performance and energy efficiency. However, difficulties in programming and optimizing FPGAs have prevented them from being widely accepted as general-purpose computing devices. In accelerator-based heterogeneous computing, portability across diverse heterogeneous devices is also an important issue, but the unique architectural features in FPGAs make this difficult to achieve. To address these issues, a directive-based, high-level FPGA programming and optimization framework was previously developed. In this work, developed optimizations were combined holistically using the directive-based approach to show that each individual benchmark requires a unique set of optimizations to maximize performance. We perform this exploration on Intel Arria 10 and Stratix 10 FPGAs. We also explored the relationships between performance, resource usages, and compilation times, and investigated implications for performance portability. Finally, we present an initial evaluation of a real-world proxy application, LULESH.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

The Durability of Piston Seals in Hydraulic Power Take-off Systems in Wave Energy Converters

Hydraulic cylinder seals are a critical component of hydraulic power take-off (PTO) systems in wave energy converters (WECs). Primary hydraulic piston seal wear is a major concern for the longevity of hydraulic PTOs, especially in the context of the effort and expense associated with seal replacement. Piston seals, made from polymeric elastomers, are used to contain and isolate high pressure fluids within PTO systems. A specific challenge for WEC designers is knowing, with confidence, the relative expected lifetimes of commercially available seals and seal materials for the unique long travel and continuous use case of WEC hydraulic systems. This information is critical to accurately determine operating expense (OPEX) and levelized cost of electricity (LCOE). If failures of seals occur earlier than their designed lifetime, the estimated operations, and maintenance (O&M) and LCOE costs may double based on estimation. Unfortunately, information from seal manufacturers on longevity in these applications is not generally available and quantitative performance comparison between different manufacturers is not available, creating significant uncertainty on use of hydraulic PTO system in wave power generation. In this project, PNNL, with advice from different WEC device and seal manufacturers, has created a framework to address the industry need for available, dependable and comparative data for seals and seals materials for WEC hydraulic applications including piston seals, glide rings, and shaft seals. Commonly used and candidate seal materials were identified and available information on the materials such as mechanical and fatigue performance, chemical (fluid) compatibility, and cost has been compiled. Hardware and strategy for bench scale measurement of key materials and seal performance and pathway for publicly available library of hydraulic seal materials, properties, suppliers, and options have also been identified for future implementation. The results of this project were presented at WPTO Seedling Symposium 2023 and OCEANS 2023. The results of the literature review including identified polymer seals and ideal operating conditions were summaried and compiled to a database WEC-SealsDB hosted locally at PNNL.

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

SALT3: An Improved Type Ia Supernova Model for Measuring Cosmic Distances

Abstract A spectral-energy distribution (SED) model for Type Ia supernovae (SNe Ia) is a critical tool for measuring precise and accurate distances across a large redshift range and constraining cosmological parameters. We present an improved model framework, SALT3, which has several advantages over current models—including the leading SALT2 model (SALT2.4). While SALT3 has a similar philosophy, it differs from SALT2 by having improved estimation of uncertainties, better separation of color and light-curve stretch, and a publicly available training code. We present the application of our training method on a cross-calibrated compilation of 1083 SNe with 1207 spectra. Our compilation is 2.5× larger than the SALT2 training sample and has greatly reduced calibration uncertainties. The resulting trained SALT3.K21 model has an extended wavelength range 2000–11,000 Å (1800 Å redder) and reduced uncertainties compared to SALT2, enabling accurate use of low- z I and iz photometric bands. Including these previously discarded bands, SALT3.K21 reduces the Hubble scatter of the low- z Foundation and CfA3 samples by 15% and 10%, respectively. To check for potential systematic uncertainties, we compare distances of low (0.01 < z < 0.2) and high (0.4 < z < 0.6) redshift SNe in the training compilation, finding an insignificant 3 ± 14 mmag shift between SALT2.4 and SALT3.K21. While the SALT3.K21 model was trained on optical data, our method can be used to build a model for rest-frame NIR samples from the Roman Space Telescope. Our open-source training code, public training data, model, and documentation are available at https://saltshaker.readthedocs.io/en/latest/ , and the model is integrated into the sncosmo and SNANA software packages.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The Worldwide C3S CORDEX Grand Ensemble: A Major Contribution to Assess Regional Climate Change in the IPCC AR6 Atlas

The collaboration between the Coordinated Regional Climate Downscaling Experiment (CORDEX) and the Earth System Grid Federation (ESGF) provides open access to an unprecedented ensemble of regional climate model (RCM) simulations, across the 14 CORDEX continental-scale domains, with global coverage. These simulations have been used as a new line of evidence to assess regional climate projections in the latest contribution of the Working Group I (WGI) to the IPCC Sixth Assessment Report (AR6), particularly in the regional chapters and the Atlas. Here, we present the work done in the framework of the Copernicus Climate Change Service (C3S) to assemble a consistent worldwide CORDEX grand ensemble, aligned with the deadlines and activities of IPCC AR6. This work addressed the uneven and heterogeneous availability of CORDEX ESGF data by supporting publication in CORDEX domains with few archived simulations and performing quality control. It also addressed the lack of comprehensive documentation by compiling information from all contributing regional models, allowing for an informed use of data. In addition to presenting the worldwide CORDEX dataset, we assess here its consistency for precipitation and temperature by comparing climate change signals in regions with overlapping CORDEX domains, obtaining overall coincident regional climate change signals. The C3S CORDEX dataset has been used for the assessment of regional climate change in the IPCC AR6 (and for the interactive Atlas) and is available through the Copernicus Climate Data Store (CDS).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

The soil health assessment protocol and evaluation applied to soil organic carbon

The concept of soil health has evolved over the past several decades, recognizing that dynamic soil property response to management and land use is highly dependent on site-specific factors that must be considered when interpreting soil health measurements. Initially, the Soil Management Assessment Framework (SMAF) and Comprehensive Assessment of Soil Health (CASH) were developed and used globally for scoring soil health indicators. However, both SMAF and CASH frameworks were developed using a relatively small dataset and their interpretation curves were not validated at the nationwide scale. Expanding upon these concepts, we propose the Soil Health Assessment Protocol and Evaluation (SHAPE) tool. The SHAPE was developed using 14,680 soil organic C (SOC) observations from across the United States, and accounts for edaphic and climate factors at the continental scale. Data were compiled from the literature, the Cornell Soil Health Laboratory, and the Kellogg Soil Survey Laboratory. In this approach, scoring curves are Bayesian model-based estimates of the conditional cumulative distribution function (CDF) for defined soil peer groups reflecting five soil texture and five soil suborder classes adjusted for mean annual temperature and precipitation. Specifically, SHAPE produces scores between 0 and 1 (0–100%) for measured SOC values that reflect the quantile or position within the conditional CDF along with measures of uncertainty. Herein, we focus on development of the SHAPE scoring curve for SOC with our case studies. SHAPE is a flexible, quantitative tool that provides a regionally relevant interpretation of this key soil health indicator.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Pulse-level noisy quantum circuits with QuTiP

The study of the impact of noise on quantum circuits is especially relevant to guide the progress of Noisy Intermediate-Scale Quantum (NISQ) computing. In this paper, we address the pulse-level simulation of noisy quantum circuits with the Quantum Toolbox in Python (QuTiP). We introduce new tools in qutip-qip, QuTiP's quantum information processing package. These tools simulate quantum circuits at the pulse level, leveraging QuTiP's quantum dynamics solvers and control optimization features. We show how quantum circuits can be compiled on simulated processors, with control pulses acting on a target Hamiltonian that describes the unitary evolution of the physical qubits. Various types of noise can be introduced based on the physical model, e.g., by simulating the Lindblad density-matrix dynamics or Monte Carlo quantum trajectories. In particular, the user can define environment-induced decoherence at the processor level and include noise simulation at the level of control pulses. We illustrate how the Deutsch-Jozsa algorithm is compiled and executed on a superconducting-qubit-based processor, on a spin-chain-based processor and using control optimization algorithms. We also show how to easily reproduce experimental results on cross-talk noise in an ion-based processor, and how a Ramsey experiment can be modeled with Lindblad dynamics. Finally, we illustrate how to integrate these features with other software frameworks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Robust inference of ecosystem soil water stress from eddy covariance data

Eddy covariance data are invaluable for determining ecosystem water use strategies under soil water stress. However, existing stress inference methods require numerous subjective data processing and model specification assumptions whose effect on the inferred soil water stress signal is rarely quantified. These uncertainties may confound the stress inference and the generalization of ecosystem water use strategies across multiple sites and studies. In this research, we quantify the sensitivity of soil water stress signals inferred from eddy covariance data to the prevailing data and modeling assumptions (i.e., their robustness) to compile a comprehensive list of sites with robust soil water stress signals and assess the performance of current stress inference methods. To accomplish this, we identify the most prevalent assumptions from the literature and perform a digital factorial experiment to extract probability distributions of plausible soil water stress signals and model performance at 151 FLUXNET2015 and AmeriFlux-FLUXNET sites. Here, we develop a new framework that summarizes these probability distributions to classify and rank the robustness of each site’s soil water stress signal, which we display with a user-friendly heat map. We estimate that only 5%–36% of sites exhibit a robust soil water stress signal due to deficient model performance and poorly constrained ecosystem water use parameters. We also find that the lack of robustness is site-specific, which undermines grouping stress signals by broad ecosystem categories or comparing results across studies with differing assumptions. Lastly, existing stress inference methods appear better suited for eddy covariance sites with grass/annual vegetation. Our findings call for more careful and consistent inference of ecosystem water stress from eddy covariance data.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Implementing Ordinary Differential Equation Solvers in Rust Programming Language for Modeling Vehicle Powertrain Systems: Preprint

Efficient and accurate ordinary differential equation (ODE) solvers are necessary for powertrain and vehicle dynamics modeling. However, current commercial ODE solvers can be financially prohibitive, leading to a need for accessible, effective, open-source ODE solvers designed for powertrain modeling. Rust is a compiled programming language that has the potential to be used for fast and easy-to-use powertrain models, given its exceptional computational performance, robust package ecosystem, and short time required for modelers to become proficient. However, of the three commonly used (>3,000 downloads) packages in Rust with ODE solver capabilities, only one has more than four numerical methods implemented, and none are designed specifically for modeling physical systems. Therefore, the goal of the Differential Equation System Solver (DESS) was to implement accurate ODE solvers in Rust designed for the component-based problems often seen in powertrain modeling. DESS is a text-based software package that provides a flexible framework for building and solving systems of ODEs. This allows DESS to be included as a dependency for automotive powertrain models that require a variety of solvers and solver configurations. Seven explicit ODE solver methods have been implemented in DESS: Euler’s, Heun’s, midpoint, Ralston’s, classic Runge-Kutta, Bogacki-Shampine, and Cash-Karp. These represent five fixed-step methods and two adaptive-step methods. This paper shows that the solver implementations increase accuracy and computational efficiency compared to Euler's method when modeling a system of three thermal masses in Rust. DESS also includes features designed for modeling component-based physical systems. Users can define relationships between nodes in their system, which the package then translates into a system of equations, leading to simpler and more intuitive code. In the case of a three-thermal-mass system, the user can specify node thermal properties (e.g., thermal capacitance), how nodes are interconnected, and thermal conductance between nodes rather than providing a system of equations. The core contribution from this work is an open-source, text-based Rust package with ODE solvers for automotive powertrain modeling to support cost-free, fast, and accurate simulation.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2026

PVDeg: Enhancing Usability and AI-Driven Multi-Mechanism Degradation Modeling

PVDeg version 0.7.0, released in December 2025, introduced major enhancements to improve usability and performance. This update reorganized tutorials and tool notebooks to create a more intuitive experience, enabling users to easily follow and adapt workflows for their specific analyses. In addition to structural improvements, both the notebooks and core logic underwent significant optimization for efficiency, robustness, and style. These refinements were supported by new testing frameworks built on nbval and pytest, adherence to PEP8 standards, and extensive code refactoring, which collectively simplify onboarding for new developers. Looking ahead, version 0.8.0 will deliver advanced AI-driven capabilities. The primary focus is to further develop and automate the degradation workflow, designed to analyze PV module degradation across diverse locations and system configurations. By integrating large language models (LLMs) to scan literature and compile a comprehensive database of materials and degradation rates, this feature will enable modeling of multiple materials and mechanisms within a single, streamlined workflow. Users will be able to evaluate degradation impacts on different system architectures under varying environmental conditions, facilitating informed decisions on bill-of-materials optimization for specific deployment scenarios. These advancements position PVDeg as a powerful, user-friendly tool for accelerating PV reliability research and system design.

14 SOLAR ENERGY↗

DOE OSTI2024

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Development of Energy Storage: Cost models

Energy storage technologies offer a promising solution to electric grid stability issues associated with the integration of variable renewable generators. The capability to match the electrical power output to instantaneous fluctuations in grid demand is crucial to ensure continuity of service. Including energy storage capability in an integrated energy system (IES) can provide the flexibility needed to meet variable electric demand and reduce the load following demands place on the reactor. In this report, economic data collected for energy storage (ES) technologies are described to support the objective of assessing the profitability of ES integration within the IES framework. In particular, there is a growing interest in thermal energy storage (TES) given its unique capability for long-duration storage for improving electricity reliability at a low levelized cost. It is common practice to evaluate the total lifetime cost and profitability before commercializing new technologies. In this report we identify and examine the models needed to better understand the economics of thermal energy storage. We extend the TES cost model in RAVEN in the context of a balance of plant (BOP) that incorporates thermal storage. To focus the discussion, following a general overview of the most promising TES technologies, we consider a use case that involves a sensible heat, two-tank, molten-salt system. Structural and operational details are reported to identify the source of construction capital expenditure and operation and maintenance cost. A detailed description of the different cost items is provided as well as the cost scaling with different storage capacity and power ratings for capacity optimization purpose. In addition, the capital expenditure and the recurring cost of representative two-tank, molten salt coupled with concentrated solar plants are provided for readers’ reference. The ES use case is noteworthy as it is in the pilot stage of commercialization. We identify those areas that would benefit from an increased economic focus to obtain a more complete compilation of cost data. We also describe the thermal coupling issues that arise from integration of the two-tank molten salt thermal energy storage system with a BOP, which is the subject of our current research. Some components of costs will need to be evaluated through dedicated technoeconomic analysis in future modeling activities using modeling procedures proposed in this report. With the data presented and the procedures described in this report, sufficiently accurate models can be implemented for the solution of both the power dispatch and the capacity expansion problems within the RAVEN-based HYBRID framework.

25 ENERGY STORAGE↗

DOE OSTI2023

QASMTrans: A QASM Quantum Transpiler Framework for NISQ Devices

In quantum computing, transpilation plays a crucial role in converting high-level, machine-independent quantum circuits into circuits specially for a quantum device, considering factors such as basis gate set, topology, error profile, etc. Yet, the efficiency of transpilation remains a significant bottleneck, particularly when dealing with very large QASM level input files. In this paper, we present QASMTrans, a C++ based high-performance quantum transpiler framework that can demonstrate on average 50-100× speedups compared to the internal transpiler of Qiskit. Particularly, for large dense circuits such as ’uccsd n24’ and ’qft n320’ incorporating millions of gates, QASMTrans can successfully transpile in 69s and 31s, respectively, while Qiskit failed to finish in one hour. Using QASMTrans as the baseline, it becomes more feasible to explore much larger design space and impose more comprehensive compiler optimizations.

Hua, Fei↗

DOE OSTI2022

Energy Exascale Earth System Model v2.0.2

Second patch release of v2.0.0 Changes since v2.0.1 [Important change] Add and update SSP370 and SSP585 cases, add tests, fix use-case files, Change ocean and sea-ice IC for ARRM60to10. [EAM] allow thetaxx as a CAM_TARGET, enable northamericax4v1pg2_WC14to60E2r3 for AMIP, fix ndrop initialization, allow up to 15 history files. [EAMxx] allow use of readnl [EAM-MMF] allow transient SST case for C++ MMF, remove specific task/thread count for ESMT test, modify the variance transport diagnostic, reorg tests, [HOMME] Allow optional sponge layer. [ELM] add 2 land-atm compsets, update FATES to API 17.0.0, allow FATES sp mode, allow ELM harvest to drive FATES harvest, fix memleaks, reduce test build times, modified parameters for miscanthus and switchgrass based on calibration [MPAS-Ocean] turn on ocean BGC in BGC cases, fix interface locations for 60L PHC grid, add mode spec to conservation check streams, allow oRRS18to6v3 grid to run with JRA, update ocean and sea ice ICs for ARRM60to10 (needed for v2), GPU port of thickness tendency, add CMPASO-JRA1p4, [MPAS framework] Add new reproducible global sum module for MPAS components, Add mostRecentAccessTime attribute to streams [MPAS-landice] Update MALI version and Greenland mesh [MPAS-seaice] add single-cell test case, fix BGC restart, Adds omp critical directives for ice warnings seen on cori. [CIME] Fix component namelist creation bugs when NINST>1, add OpenACC, OpenMP and CXX GPU tests, fix nonBFB tests, stop using config_compilers, reduce ELM test build times with shared executable, update OpenMPI on Chrysalis. fix baseline handling, provenance handling with update to cime6.0.33, also use component-specific config_pes files and add the ones from master [Machine updates] cori modules after maint, Chrysalis to OpenMPI-4.1.3 [run_e3sm] replace default case name and group. [Externals] update SCORPIO to 1.3.2

ECP↗

DOE OSTI2024

Embedding Neural Thermal Scattering (NeTS) Modules in SERPENT for Higher Fidelity Advanced Reactor Analysis

When a neutron born in fission thermalizes to the order of $k$ $B$ $T$, it’s de-Broglie wavelength and energy approach the order of inter-atomic spacing and elementary lattice oscillations, respectively. $S$($a,β,t$) or the scattering law, uuantify these temperature-dependent crystallographic contributions to total cross section (or reaction rate). In a Monte Carlo analysis, cumulative distribution functions (CDFs) of $S$($a,β,t$) are loaded to memory from “A Compact ENDF” (ACE) files for stochastically selecting thermal scattered neutron trajectories. In this work, novel neural thermal scattering (NeTS) modules for $S$($a,β,t$) CDFs are designed, trained, serialized and embedded within SERPENT using Python’s limited C-API for on-the-fly deployment of crystalline graphite $S$($a,β,t$) sampling. Torchscript tracing and Numba just-in-time (JIT) compilation streamline neural inference on NVIDIA GPUs with CUDA libraries. Demonstrations of bare sphere thermalization of fast and thermal sources show excellent agreement between embedded NeTS in SERPENT and MCNP. With an explicit model of the reactor, NeTS can predict on-the-fly changes in TREAT neutron spectra as a function of local temperature, which can serve to improve transient and accident predictions in a multiphysics analysis framework. This framework can be further extended to account on-the-fly for changes in local graphitic microstructure to scattering cross sections, and outlines a novel coupling of modern machine learning with state-of-the-art reactor physics methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Refining T c Prediction in Hydrides via Symbolic‐Regression‐Enhanced Electron‐Localization‐Function‐Based Descriptors

Hydrogen‐based materials are able to possess extremely high superconducting critical temperatures, T c s , due to hydrogen's low atomic mass and strong electron–phonon interaction. Recently, a descriptor based on the Electron Localization Function (ELF) has enabled the rapid estimation of the T c of hydrogen‐containing compounds from electronic networking properties, but its applicability has been limited by the small size and homogeneity of the training dataset used. Herein, the model is re‐examined, compiling a publicly available combined dataset of 244 binary and ternary hydride superconductors. The analysis shows that though ELF‐based networking remains a valuable descriptor, its predictive power declines with increasing compositional complexity. However, by introducing the molecularity index, defined as the highest value of the ELF at which two hydrogen atoms connect, and applying symbolic regression, the accuracy of the predictions can be substantially enhanced. These results establish a more robust framework for assessing superconductivity in hydride materials, facilitating accelerated screening of novel candidates through integration with crystal structure prediction methods or high‐throughput searches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A Systematic Evidence Based Performance Approach to Regulation of Nuclear Sites in England and Wales - 20058

The Environment Agency for England has developed a systematic evidence-based approach to pursue our strategic environmental objectives for the regulation of nuclear sites. We use an annual evidence review process to ensure effective and efficient targeting of limited resources to achieve those objectives. Over the last 8 years, we have been developing and refining this approach to ensure risk-based and value driven regulation. The approach comprises nuclear site and nuclear sector review processes known as Site Environment Review (SER) and Nuclear Environment Review (NER). This approach complements our regulation of nuclear site permit holders under the Environmental Permitting Regulations (EPR). We deliver our regulation of nuclear sites in England and Wales alongside the Office for Nuclear Regulation. The SER process involves the lead regulator for each nuclear site assessing the permit holder's environmental performance across 14 themes, set within the context of the site's main activities and associated waste disposals. Our themes include environmental leadership, resources and climate change, radioactive waste management, facility management and decommissioning, groundwater, and environmental radiological protection. We use evidence from site inspections and working within our subject matter groups to grade current and predicted future environmental performance. We are particularly interested in sustainability and the application of Best Available Techniques (BAT) to prevent the creation, and minimise the disposal, of radioactive wastes. We use risk analysis (strengths, weaknesses, threats and opportunities) to examine performance against our strategic environmental objectives, which are set out, in our 5-year Nuclear Delivery Plan (NDP). The output supports the targeting of our resources at each nuclear site. We consult the relevant permit holders on the SER priorities and use their feedback to refine our plans. We expect all permit holders to take account of our priorities when considering their own programmes of work, objectives and plans. The NER process brings together what we learn and achieve through regulation across the sector. It provides input to planning priorities, supported by qualitative and semi-quantitative evidence. It covers the 28 nuclear sites in England and Wales and spans the same 14 environmental themes. During the process we collate, compile and summarise evidence from the SERs and other sources such as inspection reports and evidence from our other nuclear work programmes. The output is the NER annual report. This provides a snapshot of the status of the nuclear sector and gives insights to enable us to regulate more efficiently and effectively. It also takes account of cross-cutting issues and risks such as changes in international standards, domestic policy, regulatory framework, domestic standards and guidance, learning from experience such as incidents, events and good practice, and innovation, research and development. It provides graphics that illustrate the grading of environmental performance for the nuclear sector across the fourteen environmental themes. This analysis allows benchmarking of nuclear site's environmental performance and the visualisation provides a convenient comparison of performance across themes, sites, and over time. We use this intelligence to inform our investment in training and development of our staff, and our cross-cutting engagement on strategic issues with government, the Nuclear Decommissioning Authority (NDA) and other corporate organisations. Adopting this approach can provide benefits with organisational reputation, stakeholder participation and ensuring value from the public investment. This paper describes the history of the SER/NER process, a selection of outputs from the process and ideas for improvement. The paper will be of interest to other regulators and organisations across the world that are interested in supporting continuous improvement. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

TranSyT , an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE’s release, software development for the automatic integration of transport reactions into models has stalled. Here, in this paper, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Caffeine: CoArray Fortran Framework of Efficient Interfaces to Network Environments

This paper provides an introduction to the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine), a parallel runtime library built atop the GASNet-EX exascale networking library. Caffeine leverages several non-parallel Fortran features to write type- and rank-agnostic interfaces and corresponding procedure definitions that support parallel Fortran 2018 features, including communication, collective operations, and related services. One major goal is to develop a runtime library that can eventually be considered for adoption by LLVM Flang, enabling that compiler to support the parallel features of Fortran. The paper describes the motivations behind Caffeine's design and implementation decisions, details the current state of Caffeine's development, and previews future work. We explain how the design and implementation offer benefits related to software sustainability by lowering the barrier to user contributions, reducing complexity through the use of Fortran 2018 C-interoperability features, and high performance through the use of a lightweight communication substrate.

Rouson, Damian↗