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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Simulating water dynamics related to pedogenesis across space and time: Implications for four-dimensional digital soil mapping

Digital soil mapping (DSM) relies on machine-learning and geostatistics to represent soil property observations across space. DSM techniques are powerful but often empirical, being limited to the quality and density of point samples. Water dynamics are closely related to soil variability, and the physics that govern water movement are well known. Hydrological properties can hence be simulated by physical models through space and time, unveiling key characteristics about soils. We propose the use of hydrologic models to map soils across the surface (2D), depth (1D), and time (1D)–which provides a 4D approach to digital soil mapping (4DSM). The Distributed Hydrology Soil Vegetation Model (DHSVM) was applied to a watershed currently under pasture. Moisture sensors and wells were installed at different depths in the watershed on summit, sideslope and toeslope positions to validate the model. DHSVM simulations of soil moisture distribution and depth to saturation were performed during the hydrological year (October 2008-September 2009). Clusters of similar pixels based on soil moisture values were determined using Dynamic Time Warping (DTW) to align temporal data and K-means. Clustering was performed both seasonally and for the entire year. Temporal patterns simulated by DHSVM matched measurements given by moisture sensors and wells. Seasonal clusters differed from the annual cluster. Distinct clusters were observed for each season and with depth, showing that spatiotemporal soil variability is lost when statically assessing soils. Spatiotemporal clusters corroborated field observations of fragipan occurrence not explicitly spatially mapped by Soil Survey Geographic Database (SSURGO). If a connection can be made between water and soils, static and dynamic soil variability can be predicted using physically based hydrologic models. Hydrologic models can benefit soil mapping by enabling reliable 4D simulation of water dynamics, which are fundamental to soil variability and soil classification and directly relate to biological, physical and chemical soil processes not captured by typical soil sampling protocols.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Molecular simulation and artificial intelligence for the circular economy of bioenergy and bioproducts

The concept of the circular bioeconomy is a carbon neutral, sustainable system with zero waste. One vision for such an economy is based upon lignocellulosic biomass. This lignocellulosic circular bioeconomy requires CO 2 absorption from biomass growth and the efficient deconstruction of recalcitrant biomass into solubilized and fractionated biopolymers, which are then used as precursors for the sustainable production of high-quality liquid fuels, chemical bioproducts, and bio-based materials. Here, in this study, we summarize the roles that molecular dynamics (MD) simulations and machine learning (ML) are playing in overcoming several fundamental challenges hindering the adoption of a circular bioeconomy. Specifically, we discuss the role of MD and ML/AI in overcoming lignocellulose recalcitrance by designing biomass pretreatment methods to efficiently produce solubilized cellulose/lignin/hemicellulose and of that in improving energy-intensive manufacturing of biomass-based materials and their structural and mechanical properties. Quantum mechanical methods and MD simulations, in addition to offering a mechanistic understanding of biomass deconstruction and biomaterials design, can provide meaningful structural, energetics, and physiochemical properties as inputs to train AI/ML models. The ML models can guide the experimental prioritization of materials/solvents and process parameters that significantly accelerate the development of biofuel and biomaterial components of the circular bioeconomy.

Smith, Jeremy C. [Oak Ridge National Laboratory (O↗

DOE OSTI2026

SMR safety through HTTF modeling and benchmark efforts for code validation for gas-cooled reactor applications

Accurate modeling and simulation tools for thermal-hydraulics calculations are a key element needed to design and license new advanced reactors including Small Modular Reactors (SMR) and Microreactors. Uncertainties in modeling and simulation can have significant safety and economic implications. The High Temperature Test Facility (HTTF) at Oregon State University (OSU) is a scaled integral effects experiment designed to investigate transient behavior in high-temperature gas-cooled prismatic-block nuclear reactors. High-quality measurement data is available from the HTTF that is suitable for a thermal-hydraulics code validation benchmark for gas-cooled reactor simulations. Here, this paper summarizes individual HTTF modeling efforts to date for tool validation at Idaho National Laboratory (INL), Argonne National Laboratory (ANL), Oregon State University (OSU) and Canadian Nuclear Laboratories (CNL) using system thermal-hydraulics codes, Computational Fluid Dynamics (CFD) codes and system-CFD code couplings. Also, the paper introduces the ongoing OECD Nuclear Energy Agency (NEA) High Temperature Gas Reactor Thermal-Hydraulics (HTGR T/H) benchmark that allows for better comparisons of results between different international modeling teams. The benchmark provides well defined computational problems that include code-to-code comparisons and comparisons to measured data. These problems provide an avenue for quantifying accuracy and identifying sources of uncertainty in thermal-hydraulics calculations, including in measured thermophysical properties, as part of validation for gas-cooled reactor simulation tools.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

DOE OSTI2024

Simulation of shot noise effects in the EIC strong hadron cooling accelerator using real number of electrons

In the electron ion collider design, in order to achieve the peak luminosity 10 34 /cm 2 /s with a reasonable lifetime, an efficient coherent electron cooling scheme was proposed to reduce the hadron beam emittance growth. Such a cooling scheme requires a good electron beam quality with a small energy spread. However, the shot noise in the electron beam through the accelerator might be amplified due to the microbunching instability and degrades the electron beam quality in the modulator section of the strong hadron cooling channel and correspondingly cooling rate. In this study, we report on self-consistent simulations of these effects using a real number of electrons to capture the details of shot noise and analysis of the shot noise growth through the accelerator.

Qiang, Ji↗

DOE OSTI2024

A data-driven framework for predicting machining stability: employing simulated data, operational modal analysis, and enhanced transfer learning

Chatter, a self-excited vibration phenomenon, presents a significant challenge in machining operations, particularly in high-speed milling, where it can degrade tool life, reduce material removal efficiency, and compromise workpiece quality. Addressing this challenge requires a reliable predictive model that can accommodate the complex dynamics of various machining scenarios. This study introduces a novel, data-driven approach to predicting machining stability, leveraging over 140,000 simulated datasets and employing advanced techniques such as operational modal analysis (OMA), enhanced transfer learning (TL), and receptance coupling substructure analysis (RCSA). By integrating these methodologies, the framework effectively classifies and predicts chatter across diverse operational modes, achieving robust and accurate outcomes. Our model utilizes a Random Forest (RF) classifier trained with the comprehensive dataset, which demonstrates substantial improvements in both predictive accuracy and robustness. Specifically, the RF model achieved an accuracy rate of 85%, an area under the curve (AUC) of 0.90, and an F1 score of 0.88, underscoring its capability to adapt to varying machining configurations. These results highlight the framework’s potential to enhance operational efficiency and machining quality by providing reliable chatter predictions across a broad range of machining parameters. In conclusion, this research thus offers a significant advancement in predictive maintenance for machining processes, enabling more stable and efficient manufacturing operations.

42 ENGINEERING↗

DOE OSTI2022

Accelerating Optimal Integration of Energy Efficiency Strategies with Industrialized Modular Construction: Preprint

The National Renewable Energy Laboratory's (NREL's) Industrialized Construction Innovation team first introduced the Industrialized Construction Assessment Framework to achieve affordable, net-zero energy (NZE) modular multifamily buildings in the 2020 ACEEE paper "Integrating Energy Efficiency Strategies with Industrialized Construction for our Clean Energy Future." Since then, NREL has continued to drive the ambitious plan to accelerate optimal integration of energy efficiency strategies during industrialized construction with little or no additional cost, labor, and production time. This follow-on paper introduces the Energy in Modular (EMOD) buildings method and presents NREL's research efforts over the last two years in collaboration with industry, including affordable housing partners. NREL has developed an idealized NZE modular multifamily building design that incorporates five energy efficiency strategies well suited for industrialized construction in factories: (1) envelope thermal control, (2) envelope infiltration control, (3) mechanical, electrical, and plumbing systems, (4) smart controls, and (5) solar plus storage. This paper highlights results from leveraging design for manufacturing and assembly principles, testing, and validation pilots with factory partners; demonstrating pod prototypes in test stand at NREL; and performing simulations. Overall, these research efforts address barriers to whole-building system integration, such as poor installation quality of thermal and air barriers; lack of unitized systems for space conditioning, energy recovery and ventilation, and water heating; problematic on-site installation, commissioning, and configuration of controls; and lack of cost-effective integration for grid-friendly design and emerging technologies. Conclusively, the paper delineates next steps for future work with NREL's partners toward developing a transformational pathway for our clean energy future.

affordable housing↗

DOE OSTI2025

Uniform field in microwave cavities through the use of effective magnetic walls

Wire medium (WM) resonators have emerged as a promising realization for plasma haloscopes—devices designed to detect axions, a potential component of dark matter. Key factors influencing the detection probability include cavity volume, resonance quality factor, and form factor. While the form factor has been explored for resonant frequency tuning, its optimization for axion detection remains unexplored. Here, in this work, we present an approach to significantly enhancing the form factor of WM plasma haloscopes. By shifting the metal walls of the resonator by a quarter wavelength, we effectively convert an electric wall boundary condition into a magnetic wall one, allowing for an almost uniform mode. Theoretical analysis and numerical simulations confirm that this modification improves the electric field profile and boosts the form factor, while also slightly enhancing the quality factor. We validate these findings through experimental results from two prototype resonators: one with a standard geometry and another with a quarter-wave air gap between the WM and the walls. Additionally, our method provides a simple way to control the field profile within WM cavities, which can be explored for further applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Joint ptycho-tomography with deep generative priors

Abstract Joint ptycho-tomography is a powerful computational imaging framework to recover the refractive properties of a 3D object while relaxing the requirements for probe overlap that is common in conventional phase retrieval. We use an augmented Lagrangian scheme for formulating the constrained optimization problem and employ an alternating direction method of multipliers (ADMM) for the joint solution. ADMM allows the problem to be split into smaller and computationally more efficient subproblems: ptychographic phase retrieval, tomographic reconstruction, and regularization of the solution. We extend our ADMM framework with plug-and-play (PnP) denoisers by replacing the regularization subproblem with a general denoising operator based on machine learning. While the PnP framework enables integrating such learned priors as denoising operators, tuning of the denoiser prior remains challenging. To overcome this challenge, we propose a denoiser parameter to control the effect of the denoiser and to accelerate the solution. In our simulations, we demonstrate that our proposed framework with parameter tuning and learned priors generates high-quality reconstructions under limited and noisy measurement data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Load Shedding for Voltage Regulation With Probabilistic Agent Compliance

With the increased observability and controllability of distribution systems, the share of behind-the-meter systems is trending upwards rapidly. As a consequence, the impact of human behaviors on system performance can no longer be ignored and should be reflected in the energy management system models. In this paper, we discuss the problem of distribution system voltage control by active power curtailment where the agent compliance of the load curtailment signal is probabilistic. We discuss the modeling of the optimal voltage control problem with probabilistic agent compliance as a chance-constrained optimization problem, its tractable safe approximation using convex restriction, and a scenario-based mixed-integer reformulation as well as the associated solution method based on augmented Lagrangian method. The numerical simulation on IEEE test system validates the effectiveness of the proposed approach in obtaining high-quality feasible load curtailment signal with low computational cost, which makes it a viable tool for real time decision making.

augmented Lagrangian method↗

DOE OSTI2020

Materials response under hypersonic flow conditions probed by multi-modal diagnostics in a benchtop wind tunnel

In this LDRD “Materials response under hypersonic flow conditions probed by multi-modal diagnostics in a benchtop wind tunnel” a peer-reviewed lab-scale hypersonic wind tunnel (WT) was planned to be assembled in-house, along with time and space resolved and related flow and materials diagnostics to derive high quality measurements and the science that is able to inform the development of our modeling and simulation codes for the hypersonic regime. The baseline capability to achieve Mach 3 flow was scheduled to be completed in Q4 2020, in the first year of the LDRD. However due to the COVID-19 delays and travel restrictions starting in March, 2020 this task could not be completed to carry out the materials response studies in-house, or those planned with external partners that were engaged during this LDRD (NASA Langley, NASA Ames, Texas A&M university, and Virginia Tech). Still, using our hypersonic computational fluid simulation codes, many of the hypersonic components have been designed (for Mach 3, 5, and 7) and procured (or in procurement phase), and a new dedicated hypersonic laboratory was facilitized, 2 WT test sections have been manufactured, and a Mach 3 nozzle was 3D printed for prototyping. In parallel, unique materials diagnostics have been tested under static conditions and fully specified and awaiting validation in our partner facilities. Due to the new hypersonic initiative announced in January, 2020 we proposed a related scope increase in hypersonics research requiring energy interactions and new diagnostics well beyond what could be supported by an LDRD ER. A decision was made to end the current LDRD ER and formally propose a new LDRD SI that leverages the current effort, which will be starting in FY21. As a result of the uniqueness of this LDRD work, our early efforts have been encouraged and well received in the hypersonic research community, and is now part of multiple unsolicited internal and external project proposals expected to be funded in the coming years, which is encouraging to make LLNL a leader in experimentally probing extreme physics of local energetics critical to hypersonics.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Exploration of Domain Aware Machine Learning for Grid Analytics: Transfer-Learnt Energy Models to Assist Buildings Control with Sparse Field Data

Buildings are a primary consumer of energy in the United States and are also increasingly being perceived as providers of grid services such as load shifting, shedding and modulation. High fidelity models of building energy consumption are needed to set appropriate baselines for measurement and verification (M&V) of controllers designed for energy efficient operation of buildings and to enable buildings to provide grid services via. participation in demand response programs. State-of-the-art building energy modeling techniques either rely on Physics based models, or extensive instrumentation of the building envelope to gather “big” data to train machine learning based models such as deep neural networks. While Physics based models are often limited by their accuracy, it is not always feasible to gather a significant amount of field data required to train machine learning based models with sufficient accuracy. In this paper, we explore the use of transfer learning-based strategies to address unsatisfactory accuracy of models for estimating building energy consumption when available field data for training is sparse or of unacceptable quality. In particular, we transfer knowledge in the form of data and parameters, from Physics based simulation frameworks to the field to improve the model accuracy, thus resulting in a Physics-informed Machine Learning framework. We evaluated the efficacy of our approach on field data collected from six commercial buildings and our results indicate that the proposed transfer learning based models provide comparative (and in some cases better) accuracy than state-of-the-art machine learning and deep learning solutions, with just one month of field data.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Empirical validation of building energy simulation model input parameter for multizone commercial building during the cooling season

This paper presents a critical advancement in Building Energy Modeling (BEM) through an empirical validation approach using a high-quality dataset from a multizone commercial office building in Oak Ridge, TN, USA. BEM is widely utilized in diverse construction applications, but its effectiveness relies on the accuracy of its predictions. The study focuses on empirical validation of input parameters in BEM, including building envelope data, infiltration modeling, and rooftop unit system performance curves. The validation of simulation input parameters leads to substantial improvements in the accuracy of simulation results. Notable both NMBE and cv (RMSE) values are reduced by 0.5 % for indoor air temperature and 17 % for indoor air relative humidity compared to the previous model. At the system level, both NMBE and cv (RMSE) values are reduced by 2 % for fan energy consumption and 4 % for cooling energy consumption, compared to the previous model. A literature review highlights a significant gap in empirical validation studies, which predominantly concentrate on either component-level or whole building validation. Furthermore, many studies employ simplified setups that may not faithfully represent the complexities of multizone commercial buildings. This paper distinguishes itself by emphasizing the critical importance of component-level input parameter validation. It underlines the need to validate data related to building envelope components and HVAC system performance curves, resulting in more accurate simulation outcomes. In conclusion, the utilization of actual multizone commercial building data enhances the study's practical relevance. In summary, this research underscores the pivotal role of input parameter validation in enhancing the accuracy and reliability of BEM.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Quantum Software Engineering (Dagstuhl Seminar 24512)

The Dagstuhl Seminar 24512 on "Quantum Software Engineering" was held from December 15 to 20, 2024. It brought together 26 participants from industry and academia from 13 different countries, including senior and junior researchers as well as practitioners in the field of Quantum Software Engineering. The aim of the seminar was to advance software engineering methods and tools for the engineering of hybrid quantum systems by promoting personal interaction and open discussion among researchers who are already working in this emerging area of knowledge. The first day of the seminar was devoted to the topic "When software engineering meets quantum mechanics", while the second day focused on "Quantum software engineering and its challenges." During both days, 16 invited presentations were given. The rest of the seminar was organized into three working groups to address the topics "Quantum Software Design, Modelling and Architecturing", "Adaptive Hybrid Quantum Systems", and "Quantum Software Quality Assurance". The seminar was a very fruitful experience for all participants both in terms of scientific outcomes and in terms of the personal relationships that were generated to jointly address future experiences.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Development and scaling of MeV x-ray radiography at NIF-ARC

We investigate the generation of MeV x-rays using the Advanced Radiography Capability laser system at the National Ignition Facility using 1, 10, and 38 ps pulse durations, with laser energies reaching up to 4 kJ and using compound parabolic concentrators. Hydrodynamic simulations using up-to-date measurements of the contrast of the ARC laser are conducted, allowing us to employ an electron scaling model that incorporates scale length and pulse duration, which aligns closely with the observed temperature distributions. Comparable x-ray sources, in terms of dose, are generated when using a 10 ps pulse duration with 2.4 kJ at ∼1.9 ± 0.4 × 10 18 W/cm 2 and when using a 38 ps pulse duration with 4 kJ at 9.9 ± 0.4 × 10 17 W/cm 2 , both achieving ∼16 rad in air at 1 m for x-ray energies > 0.5 MeV. Radiographs performed on the laser “line-of-sight” show significant improvements in image quality than radiographs performed at 65 degrees to the laser axis. We verify the radiography performance using Monte Carlo Simulations.

Physics - Plasma physics↗

DOE OSTI2024

Dynamic Simulation Modeling and Control of a Desiccant Assisted Direct-expansion Air Handling Unit

Desirable built environments demand simultaneous regulation of thermal comfort and indoor air quality (IAQ) with energy-efficient operation of heating, ventilation and air conditioning (HV AC) systems, which involves controls of temperature, humidity and airborne contaminants simultaneously. This paper presents the efforts of dynamic modeling and initial development control strategy for a desiccant-assisted multi-functional air handling unit (AHU) coupled with a direct-expansion rooftop unit (RTU) system, which aims to achieve multiple functions for indoor environment conditioning with energy efficient control. The RTU-AHU system includes a desiccant wheel for dehumidification and a conceptual direct air capture (DAC) filtering device for CO2 regulation. A Modelica-based dynamic model is developed for this conceptual system, and a simple decentralized control strategy is designed, which combines a differential-enthalpy based AHU return-air ratio control, a demand-controlled ventilation, and supply-air temperature humidity control via the RTU and DW controls. The proposed control method is evaluated with the Modelica simulation model for a selected set of scenarios

Pan, Chao↗

DOE OSTI2026

Machine learning-based bias-corrected future projections of ozone concentrations from a chemistry-climate model

Reliable projection of future near-surface ozone is crucial for air quality management and health risk assessment. However, potential biases in spatial distribution, magnitude and trends in ozone concentrations simulated by global chemistry-climate models limit their applicability in regional-scale evaluations. In this study, LightGBM, a machine learning (ML) algorithm is applied to correct biases in CESM2-simulated ozone concentrations over China, the United States and Europe and calibrate future ozone projections under two diverse Shared Socioeconomic Pathways (SSP1-2.6 and SSP5-8.5) scenarios from 2020 to 2060. The ML-based correction significantly improves the spatial distribution and reduces the model bias by 40%–60%. It also reverses the potentially incorrect trend of ozone change under SSP1-2.6 in eastern China. When applying ML-based bias correction to CESM2 future projections, warm season mean ozone concentrations decrease across China, the United States, and Europe by –13.5, –17.9, and –13.7 µg/m³, respectively, between 2020 and 2060 in SSP1-2.6, while they increase by 9.4, 2.0, and 5.2 µg/m³ in SSP5-8.5. Decomposition analysis show that changes in anthropogenic emissions dominate future ozone changes in both scenarios, while strong climate penalty from ozone changes occurs in polluted eastern China and climate benefit is found in western China, the United States and Europe under SSP5-8.5. These findings demonstrate the value of combining ML with chemistry-climate models to produce more accurate air quality projections, thereby informing more effective and region-specific environmental protection strategies.

Chemistry Model↗

DOE OSTI2022

On the control of electron heating for optimal laser radiation pressure ion acceleration

We study the onset of electron heating in intense laser–solid interactions and its impact on the spectral quality of radiation pressure accelerated ions in both hole boring and light sail regimes. Two- and three-dimensional particle-in-cell (PIC) simulations are performed over a wide range of laser and target parameters and reveal how the pulse duration, profile, polarization and target surface stability control the electron heating, the dominant ion acceleration mechanisms and the ion spectra. We find that the onset of strong electron heating is associated with the growth of the Rayleigh–Taylor-like instability at the front surface and must be controlled to produce high-quality ion beams, even when circularly polarized lasers are employed. We define a threshold condition for the maximum duration of the laser pulse that allows mitigation of electron heating and radiation pressure acceleration of narrow energy spread ion beams. The model is validated by three-dimensional PIC simulations, and the few experimental studies that reported low energy spread radiation pressure accelerated ion beams appear to meet the derived criteria. The understanding provided by our work will be important in guiding future experimental developments, for example for the ultrashort laser pulses becoming available at state-of-the-art laser facilities, for which we predict that proton beams with $\sim$ 150–250 MeV, $\sim$ 30% energy spread, and a total laser-to-proton conversion efficiency of $\sim$ 20% can be produced.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗