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ATDM AD projects to ECP Report (Q3 FY2020)

The SPARC team has completed much of the workflow development needed for the coupled and uncoupled analyses needed to support our flight test validation work. The SPARC team has continued to make progress on development activities to support unsteady, full reentry vehicle aero analysis, which have focused on turbulence modeling, uniform mesh refinement, in-situ visualization (with the Paraview/Catalyst team), and performance analysis. The SPARC team is making solid progress towards our Q4 goal of demonstrating an improved Wall Modeled Large Eddy Simulation (WMLES) capability for standard geometries using high-order finite difference, discontinuous Galerkin, and low-dissipation finite volume methods. The SPARC team has met the minimum completion criteria for parts of the L1, including documenting performance and scaling of SPARC on Trinity, Sierra and Astra, and performing runs for the flight test validation case.

97 MATHEMATICS AND COMPUTING↗

gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes

High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).

59 BASIC BIOLOGICAL SCIENCES↗

Biocene 2018 - Welcome to the Period of New Life

Biocene is the period of new life. When our descendants look back at this period in time, they will see evidence, in the geologic and electronic record, of anthropic climate change, growing population, and scarcity of resources. But they will also see the rebirth of human ingenuity as we overcame the challenges that faced us through nature-inspired exploration. The Periodic Table of Life (PeTaL) is a proposed tool and open source framework that uses artificial intelligence to aid in the systematic inquiry of biology for its application to human systems. This presentation defines the PeTaL concept and workflow. Biomimicry, biophysics, biomimetics, bionics and numerous other terms refer to the use of biology and biological principles to inform practices in other disciplines. For the most part, the domain of inquiry in these fields have been confined to extant biological models with the proponents of biomimicry often citing the evolutionary success of extant organisms relative to extinct ones. The primary objective of this paper is to expand the domain of inquiry for human processes that seek to model those that are, were or could be found in nature with examples that relate to the field of aerospace and to spur development of tools that can work together to accelerate the use of artificial intelligence in problem solving. Specifically specialized fields such as paleomimesis, anthropomimesis and physioteleology are proposed in conjunction with artificial evolution. Blockchain technology may be vital in allowing open source design tools such as PeTaL to democratize design and yet protect intellectual property. The overarching philosophy outlined here can be thought of as physiomimetics, a holistic and systematic way of learning from natural history. The backbone of PeTaL integrates an unstructured database with an ontological model consisting of function, morphology, environment, state of matter and ecosystem. Tools include text classification, thesaurus, data visualization, and analysis. Applications of PeTaL include guiding human space exploration, understanding human and geological history, and discovering new or extinct life.

Biocene↗

Machine Learning-Driven Solvent Screening for Biobased 2,3-Butanediol Extraction

Biobased 2,3-butanediol (2,3-BDO) is a valuable biomass-derived chemical due to its versatility in being transformed into a wide variety of products. However, the separation and purification of 2,3-BDO from fermentation broth remain a significant challenge owing to its high boiling point and hydrophilic nature. Herein, we developed a machine learning (ML)-based screening workflow that uses molecular calculations as training data and requires only a small number of experimental measurements for validation to identify alternative solvent candidates for the liquid–liquid extraction (LLE) of 2,3-BDO from aqueous solution. In particular, 130 density functional theory (DFT) calculations with the implicit solvation method not only built a correlation between the computational partition coefficient and the experimental distribution coefficient of 2,3-BDO but also parameterized an Extra-Trees ML model to screen the distribution coefficient for a wider range of 6717 organic solvents. The experimental measurements of only 24 solvents were needed to validate the computational results. A list of 50 prioritized solvents was proposed for 2,3-BDO LLE, and seven additional experimental measurements were conducted to further verify our selected solvents. The impact of the extraction temperature and solvent-to-feed ratio was also investigated for selected solvents in experiments. Furthermore, this work suggested alternative solvents for 2,3-BDO LLE and proposed a versatile workflow that requires fewer experiments and can be applied to a broader range of LLE studies.

Extraction↗

BOPTest As a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

BOPTEST as a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

Energy transport analysis of NSTX plasmas with the TGLF turbulent and NEO neoclassical transport models

This work presents a study of plasma transport at low aspect ratio on the National Spherical Torus Experiment tokamak, where the turbulent and neoclassical energy fluxes calculated by the quasilinear Trapped Gyro Landau Fluid (TGLF) model and the multi species drift-kinetic Neoclassical solver (NEO) are validated against experimental data. The turbulent energy transport of two plasma discharges, one in the L-mode confinement regime and another in the H-mode regime, is dominated by electrostatic drift-wave instabilities, while the ion heat transport has a significant neoclassical contribution. The data analysis workflow is described in detail to understand how the variations of mapping and fitting of experimental data affect the power balance solution and subsequent flux-matching plasma profile predictions with the TGYRO solver. On average, the predicted plasma profiles are consistent with experimental data. However, the solutions are sensitive to various input parameters, including boundary conditions, and the electron-ion coupling. Linear gyrokinetic stability analysis demonstrates close agreement of the real frequencies of unstable modes between TGLF and CGYRO gyrokinetic simulations, but higher growth rates are predicted by TGLF, especially for the H-mode case. Estimates of the low-k modes' contributions to the total flux are consistent with linear stability analysis and the E × B suppression of turbulence in TGLF simulations with the SAT1 saturation model, while the SAT2 saturation model over-predicts the low-k modes' contribution in the H-mode case. Moreover, the results with SAT1 model are consistent with power balance analysis, which indicates only neoclassical ion energy fluxes inside ρ < 0.4 in the L-mode case and $\rho \unicode{x2A7D} 0.7$ in the H-mode case. The presence of multi-scale turbulence and ion-scale driven zonal flow mixing effects are also observed in TGLF scans of the electron turbulent heat flux over a range of temperature gradients and the electron-ion temperature ratio, which could explain the strong model sensitivity to variations of input parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Generation and representation of synthetic smart meter data

Advanced energy algorithms running at big-data scale will be necessary to identify, realize, and verify energy savings to meet government and utility goals of building energy efficiency. Any algorithm must be well characterized and validated before it is trusted to run at these scales. Smart meter data from real buildings will ultimately be required for the development, testing, and validation of these energy algorithms and processes. However, for initial development and testing, smart meter data are difficult to work with due to privacy restrictions, noise from unknown sources, data accessibility, and other concerns which can complicate algorithm development and validation. This paper describes a new methodology to generate synthetic smart meter data of electricity use in buildings using detailed building energy modeling, which aims to capture the variability and stochastics of real energy use in buildings. The methodology can create datasets tailored to represent specific scenarios with known truth and controllable amounts of synthetic noise. Knowledge of ground truth also allows the development and validation of enhanced processes which leverage building metadata, such as building type or size (floor area), in addition to smart meter data. The methodology described in this paper includes the key influencing factors of real-world building energy use including weather data, occupant-driven loads, building operation and maintenance practices, and special events. Data formats to support workflows leveraging both synthetic meter data and associated metadata are proposed and discussed. Finally, example use cases of the synthetic meter data are described to illustrate potential applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Integrating CVMix into GOTM (v6.0): a consistent framework for testing, comparing, and applying ocean mixing schemes

Abstract. The General Ocean Turbulence Model (GOTM) is a one-dimensional water column model, including a set of state-of-the-art turbulence closure models, and has widely been used in various applications in the ocean modeling community. Here, we extend GOTM to include a set of newly developed ocean surface vertical mixing parameterizations of Langmuir turbulence via coupling with the Community Vertical Mixing Project (CVMix). A Stokes drift module is also implemented in GOTM to provide the necessary ocean surface waves information to the Langmuir turbulence parameterizations, as well as to facilitate future development and evaluation of new Langmuir turbulence parameterizations. In addition, a streamlined workflow with Python and Jupyter notebooks is also described, enabled by the newly developed and more flexible configuration capability of GOTM. The newly implemented Langmuir turbulence parameterizations are evaluated against theoretical scalings and available observations in four test cases, including an idealized wind-driven entrainment case and three realistic cases at Ocean Station Papa, the northern North Sea, and the central Baltic Sea, and compared with the existing general length scale scheme in GOTM. The results are consistent with previous studies. This development extends the capability of GOTM towards including the effects of ocean surface waves and provides useful toolsets for the ocean modeling community to further study the effects of Langmuir turbulence in a broader scope.

58 GEOSCIENCES↗

Developing Ultrahigh-Resolution E3SM Land Model for GPU Systems

Designing and refactoring complex scientific code, such as the E3SM land model (ELM), for new computing architectures is challenging. This paper presents design strategies and technical approaches to develop a data-oriented, GPU-ready ELM model using compiler directives (OpenACC/OpenMP). We first analyze the datatypes and processes in the original ELM code. Then we present design considerations for ultrahigh-resolution ELM (uELM) development for massive GPU systems. These techniques include the global data-oriented simulation workflow, domain partition, code porting and data copy, memory reduction, parallel loop restructure and flattening, and race condition detection. We implemented the first version of uELM using OpenACC targeting the NVidia GPUs in the Summit supercomputer at Oak Ridge National Laboratory. During the implementation, we developed a software tool (named SPEL) to facilitate code generation, verification, and performance tuning using these techniques. The first uELM implementation for Nvidia GPUs on Summit delivered promising results: 1) over 98% of the ELM code was automatically generated and tuned by scripts. Most ELM modules had better computational performances than the original ELM code for CPUs. The GPU-ready uELM is more scalable than the CPU code on fully-loaded Summit nodes. Example profiling results from several modules are also presented to illustrate the performance improvements and race condition detection. The lessons learned and toolkit developed in the study are also suitable for further uELM deployment using OpenMP on the first US exascale computer, Frontier, equipped with AMD CPUs and GPUs.

Schwartz, Peter↗

Enhancing occupant behavior representation for interoperability between building information modeling and building energy modeling

Building Performance Simulation (BPS) has been adopted as an essential tool for designing, operating, and retrofitting buildings to optimize energy efficiency throughout the building life cycle. The Green Building XML (gbXML) schema facilitates seamless data exchange between Building Information Modeling (BIM) and Building Energy Modeling (BEM) software tools. However, limited occupant behavior (OB) representation in BIM often leads to inconsistent and inaccurate energy simulation in BEM software. This paper presents 154 systematic enhancements to the existing occupant behavior XML (obXML) schema v1.3.4, initially developed for standardizing OB representation for BEM, to address existing limitations and improve interoperability with BIM models. The enhancements encompass improved integration with BIM models through extended building representations and system operations, expanded support for advanced OB models with additional environmental parameters and mathematical capabilities, and implementation of a standardized model documentation framework. To facilitate seamless data transformation between gbXML and obXML schemas, we developed a publicly available gb-obXML Schema Converter. Three case studies demonstrate the enhanced schema’s capabilities: representation of building information using a two-story office building model, documentation of a window operation behavior model, and validation of the schema converter’s functionality. The enhanced obXML schema v1.4 enables sophisticated modeling of occupant-building interactions while maintaining consistency with industry-standard BIM schemas. The standardized documentation framework facilitates reproducibility and knowledge sharing in the OB research community, while the schema converter automates the integration of building information into OB simulation workflows. These enhancements establish a foundation for more accurate building performance simulation by supporting sophisticated representation of occupant behavior within the BIM-to-BEM simulation workflows.

Chung, Jihoon↗

Machine learning-based real-time monitoring system for smart connected worker to improve energy efficiency

Recent advances in machine learning and computer vision brought to light technologies and algorithms that serve as new opportunities for creating intelligent and efficient manufacturing systems. In this study, the real-time monitoring system of manufacturing workflow for the Smart Connected Worker (SCW) is developed for the small and medium-sized manufacturers (SMMs), which integrates state-of-the-art machine learning techniques with the workplace scenarios of advanced manufacturing systems. Specifically, object detection and text recognition models are investigated and adopted to ameliorate the labor-intensive machine state monitoring process, while artificial neural networks are introduced to enable real-time energy disaggregation for further optimization. The developed system achieved efficient supervision and accurate information analysis in real-time for prolonged working conditions, which could effectively reduce the cost related to human labor, as well as provide an affordable solution for SMMs. The competent experiment results also demonstrated the feasibility and effectiveness of integrating machine learning technologies into the realm of advanced manufacturing systems.

42 ENGINEERING↗

Optimization performance, fidelity, and cost: SIAM VQE

This dataset contains files storing results from classically-simulated quantum subroutines within a dynamical mean-field theory workflow, and jupyter notebooks processing the data in these files to generate plots. The files store: (1) Results from variational quantum eigensolver (VQE) simulations searching for optimal parameters allowing parametrized quantum circuits to prepare approximations to ground states of different Anderson impurity models (AIMs) (2) Results from simulations of a quantum Lanczos algorithm (QLA) estimating the Lanczos coefficients defining the continued-fraction representation of an (AIM) Green’s function Description: Any file named vqe_gs_results* stores approximations to the ground state and energy of a given AIM estimated using three different methods: (1) Numerical diagonalization (2) Ideal VQE simulation (3) VQE simulation with sampling noise For each VQE simulations metadata about the optimization (optimization results plus number of quantum circuits that would have been executed on real hardware) is also stored. Any file named qla_dos_results* estimations for the Lanczos coefficients defining the Green’s function of an AIM. The stored estimations are achieved using different methods: (1) Numerical Lanczos algorithm from initial states obtained from numerical diagonalization (2) Simulated quantum Lanczos algorithm from initial states prepared from parametrized quantum circuits yielded by corresponding ideal and noisy VQE subroutines. The dataset is used and described in M. Karabin et al., "Quantum solver for single-impurity Anderson models with particle-hole symmetry", Phys. Rev. Research 8, 033066 (2026). DOI: https://doi.org/10.1103/7ys3-tl4l

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

L-SCIE and SUPCRTNE model and database development

This progress report (Level 3 Milestone Number M3SF-25LL010301052) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Argillite Host Rock Properties & Processes Work Package SF-25LL01030105. The focus of this milestone is to create an initial SUPCRTNE database and extensively test the SUPCRTNE code. We prepared a draft manuscript describing our workflow and approach for developing a next-generation thermodynamic database for the Spent Fuel and High Level Waste Disposition campaign. The goal is to ease any future formal software qualification effort as was done on the Yucca Mountain Project for codes including SUPCRT92 and EQ3/6. We are attempting to extend the SUPCRTNE database to include more species, mainly from the NEA volumes. We can also take advantage of thermodynamic database activities that are ongoing at Thermochimie and as part of the EURADII program. However, our effort is limited by the funds available and the changes to program scope that was initiated in mid-FY25.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County

The dataset contains hourly Anthropogenic heat (AH) from buildings in Los Angeles County, based on weather data from 2018. The hourly AH is aggregated at three spatial resolutions: 450m x 450m grid, 12km x 12km grid, and census tract. The AH is broken down into three components: building envelope surface convection, heating, ventilation, and air conditioning (HVAC) system heat release, and zone exfiltration and exhaust air heat loss. The dataset is created with the physics-based EnergyPlus building energy models to calculate individual buildings' AH considering WRF-UCM simulated microclimate conditions. Please refer to the paper "A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County" for more information about the data generation workflow and the data validation procedure. The data set contains two folders: the "output_data" folder holds the simulation results (EP_output and EP_output_csv), building metadata (building_metadata.geojson and building_metadata.csv), aggregated heat emission and energy consumption time-series data (hourly_heat_energy), and geographical data (geo_data) associated with the GEOID referenced in heat and energy consumption data. The "input_data" folder contains the raw data used to generate files in the "output_data" folder as well as data sets used in the validation. The code repository (https://github.com/IMMM-SFA/xu_etal_2022_sdata) holds the processing scripts for data curation, validation, and visualization.

Energy↗

Methodology to determine printability criteria of highly concentrated pastes through rheological characterization

Material extrusion is an additive manufacturing technique that enables the creation of reproducible and complex hardware by depositing a viscous, shear-thinning ink onto a substrate in a custom-pattern via extrusion through a syringe. Here, the ability of an ink to be extruded onto a substrate in many layers, and maintain the desired shape is what defines the printability. Printability is often investigated by formulating, printing, and postmortem analysis of final parts in an iterative manner. Investigations of printability through rheological characterization have often been concerned with inks that straddle the line between printable and too thin, leaving out an entire class of inks that are highly-filled pastes, where extrudability is the limiting factor. Highly-filled pastes continue to pose issues for researchers as the effect of filler morphology, size, loading, and packing fraction on the ink rheology and corresponding printability is not understood. While traditional rheological characterizations may be useful for some inks, we show that protocols utilizing steady-shear, or large-amplitude oscillatory shear are difficult and unreliable for highly-filled pastes. Through transient rheology paired with real-time images we show that each traditional protocol produces inhomogeneous deformations that violate the assumptions that underly common rheological definitions. Instead, we demonstrate metrics measured with small-amplitude oscillatory shear that are correlated to the printability of various ink formulations ranging in loading. The rheological measures that accurately predict the printability of the inks are the axial stress measured at small amplitudes, and the critical stress amplitude above which rheological characterizations become impossible. In addition, we estimate the maximum packing fraction for each filler, based on the exponent common to hard sphere models, and show that the printability of each ink can be predicted by the ratio of the packing fraction to the theoretical maximum. We show how small-amplitude oscillatory shear allows users to develop printability criteria for any ink to enhance the workflow in the development of new inks, increase the performance of material extrusion printing, and improve the stability of printed parts, with less wasted time and materials.

36 MATERIALS SCIENCE↗

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a “user guide” for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure–property relationships in soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

59 BASIC BIOLOGICAL SCIENCES↗