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DOE OSTI2025

Analysis of the HAE activity in the TJ-II stellarator using a Landau closure model

The aim of this study is to analyze the stability of helical Alfvén eigenmodes (HAEs) in TJ-II discharges and the stabilizing effect of the energetic particles generated by the neutral beam injector (NBI) on pressure gradient-driven modes (PGDMs). HAE and PGDM stability is studied using the linear version of the gyro-fluid code FAR3d and the continuous structure by the STELLGAP code. First, Alfvén eigenmode (AE) and PGDM activity observed in the experiments is reproduced by the simulations, identifying unstable m/n = 4/7 − 2/3 and 7/12 − 5/8 HAEs triggered around ρ = 0.66 showing a frequency of 209 and 204 kHz, respectively, as well as 5/3 PGDM. Next, a parametric study is performed with respect to the thermal ion density and iota profile in the middle-outer plasma region to verify the robustness of the simulation results with respect to the uncertainty of experimental profiles. The analysis confirms that experimental uncertainty does not cause large deviations in the simulation results, showing the destabilization of the same HAEs for all the configurations tested. The simulations also indicate the decay of the 5/3 PGDM growth rate as the energetic particle (EP) population in the plasma increases, consistent with the experiment. Stability analysis of the n = 3, 7, 11, n = 5, 9, 13, n = 6, 10, 14, and n = 8, 12 helical families is performed with respect to the NBI operational regime for different EP energies, β as well as deposition profiles. The most unstable configuration is the radially localized on-axis NBI operation (stiff EP density profile gradients nearby the magnetic axis). Using the simulation model that reproduces the observed Alfvén activity, we extend the study to analyze NBI performance within a theoretical framework. It shows that increasing NBI voltage (which raises EP energy) leads to a degradation in NBI performance for a given power (related to EP β and their density). To achieve better NBI operation, higher voltage must be balanced with lower injection power, ensuring stable AEs while keeping the same EP β.

Plasma confinement↗

DOE OSTI2024

Thermal and Well Flow Performance of Closed-Loop Geothermal in the Wattenberg Area: Preprint

Closed-loop geothermal systems provide an alternative to resource-constrained hydrothermal systems and stimulation-intensive enhanced geothermal systems. In this work, we apply the slender-body theory (SBT) model, to simulate the well flow and heat transfer performance of U-loop well designs drilled in the Wattenberg area of the Denver-Julesburg Basin. Three U-loop well patterns are investigated including a single, double, and multi-lateral design. The subsurface within area is characterized by deep, hot (> 200degreesC) igneous/metamorphic basement rock underlying multiple sedimentary formations. The lateral section(s) of the U-loop lies within a target depth of 6 km where temperatures are estimated to approach 300degreesC. As a base case, conduction-only heat transfer is investigated through simulations with the SBT model within U-loops with open-hole laterals that exchange heat directly with the hot dry rock using water as a working fluid. The utilization of supercritical CO2 as a heat transfer fluid is also considered. For each scenario, the system performance in terms of annual heat production and temperature profile over a 20-year project lifetime are assessed. Also, the levelized costs of heat and electricity (LCOH and LCOE) are determined using a top-down technoeconomic analysis model. The results show that the performance and cost optimized U-loop design is one having an injection-production well spacing of 1,000 meters with ten 50-meter-spaced laterals that traverse a subsurface system with a temperature gradient of 60degreesC/km. By injecting 20 degreesC-water at a rate of 60 kg/s through this loop, an average heat production of 19 MWth can be achieved, resulting in an LCOE and LCOH of $136/MWh and $1.53/GJ, respectively, over a 20-year project life.

closed-loop geothermal↗

DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗

DOE OSTI2025

Thermal and Well Flow Performance of Closed-Loop Geothermal in the Wattenberg Area

Closed-loop geothermal systems provide an alternative to resource-constrained hydrothermal systems and stimulation-intensive enhanced geothermal systems. In this work, we apply the slender-body theory (SBT) model, to simulate the well flow and heat transfer performance of U-loop well designs in the Wattenberg area of the Denver-Julesburg Basin. Three U-loop well patterns are investigated, including a single-, double-, and multi-lateral design. The subsurface within the area of interest is characterized by deep, hot (> 200 degrees C) igneous/metamorphic basement rock underlying multiple sedimentary formations. The lateral section(s) of the U-loop lie(s) within a target depth of 6 km, where temperatures are estimated to approach 300 degrees C. As a base case, conduction-only heat transfer is investigated through simulations with the SBT model within U-loops with open-hole laterals that exchange heat directly with the hot, dry rock using water as a working fluid. The utilization of supercritical CO2 as a heat transfer fluid is also considered. For each scenario, the system performance in terms of annual heat production and temperature profile over a 20-year project lifetime are assessed. Also, the levelized costs of heat and electricity (LCOH and LCOE) are determined using a top-down techno-economic analysis model. The results show that the performance- and cost-optimized U-loop design is one having an injection-production well spacing of 1,000 meters with ten 50-meter-spaced laterals that traverse a subsurface system with a temperature gradient of 60 degrees C/km. By injecting 20 degrees C-water at a rate of 60 kg/s through this loop, an average heat production of 19 MWth (i.e., 2.2 MWe net plant output) can be achieved, resulting in an LCOE and LCOH of $136/MWhe and $1.53/GJ, respectively, over a 20-year project life.

closed-loop geothermal↗

DOE OSTI2025

Large-scale tearing-mode hazard function analysis with standard matched equilibrium reconstructions

The association between features from standard tokamak equilibrium reconstructions and the onset of n = 1 tearing modes (TMs) is analyzed at scale. The TM onset rate is directly modeled with a ‘hazard’ function which gives the expected number of onsets (per unit time spent) in a given equilibrium parameter region. In particular the different statistical modeling performance achieved for magnetics-only reconstructions and motional Stark effect (MSE) enhanced reconstructions is studied. It is observed that a better hazard model for the TM onset rate can be built with the MSE-enhanced equilibria compared to the matched magnetics-only situation. This advantage disappears if internal profile details are withheld from the matched analysis. Plausibility of the hazard function is further demonstrated with visualizations of global trends in the operational space, and time-traces from specific tokamak discharges. As a result, TMs typically degrade tokamak plasma performance and may lead to plasma termination, motivating this statistical study.

equilibrium↗

DOE OSTI2025

Role of perturbed parallel magnetic field effects in predicting turbulent transport in NSTX

This study presents analysis of gyrokinetic simulations on the National Spherical Torus Experiment (NSTX) to investigate the effects of electromagnetic fields on plasma turbulence and transport. The simulations, performed with varying levels of fidelity using the gyrokinetic CGYRO code, include electrostatic (ES), single-field electromagnetic (EM1), and two-field electromagnetic (EM2) models. A detailed comparison across the simulation database reveals that electromagnetic effects increase both predicted growth rates and quasilinear fluxes, with EM2 simulations producing stronger turbulence than ES and EM1 cases. Quasilinear modeling using QLGYRO demonstrates that while the perturbed parallel magnetic field (δB ∥ ) does not drastically affect the total flux at experimental gradients, it leads to a shift in the dominant instability, altering mode structures from microtearing to kinetic ballooning modes (KBMs). The proximity of the plasma profiles to the KBM threshold is explored, with the experimental conditions being near the onset of KBM-driven transport. The KBM, with its large growth rates, is identified as a potential driver of electron temperature flattening, as it can rapidly transport heat across flux surfaces. Performing stability analysis shows core-localized unstable a low- mode that could contribute to the flattening at the early times of the discharge. TGYRO predictive modeling, incorporating both TGLF and QLGYRO, indicates that the inclusion of δB ∥ significantly improves the accuracy of temperature profile predictions in NSTX high-beta plasmas, although challenges remain in modeling the sharp flux discontinuities caused by KBM-driven instabilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Reconstruction of current profiles from external magnetic and MSE measurements on DIII-D

This work introduces a new current model into the EFIT code for plasma current profile reconstruction. Using this model, edge-localized current density profiles are reconstructed solely from external magnetic measurements. Quantitative comparisons show that edge current profiles obtained with the new current model align closely with those from kinetic equilibrium reconstruction. The new model enables current density reconstruction with fewer diagnostics than kinetic equilibrium reconstruction (Lao et al 1990 Nucl. Fusion 30 1035–49), demonstrating that edge-localized current density information can be obtained from external magnetic measurements only, without the help of kinetic profiles and internal diagnostics, and without using the bootstrap current model. Furthermore, with the constraints of external magnetic and MSE measurements, current profiles in full radius obtained from the new model are in good agreement with the results of kinetic equilibrium reconstruction, which not only improves the efficiency of current reconstruction but also helps avoid possible errors caused by different kinds of diagnoses. Possible applications are also discussed, and a brief analysis of the evolution of the full-radius current density is performed. Noticeable decreases in both the magnitude and gradient of the edge current around the time of ELM bursts are observed. Moreover, analysis of the full radius current density profiles ( ρ N = 0 − 1.0, ρN denotes to square root of the normalized toroidal flux) reveals that as the edge current changes, the inner current also changes following a sinusoidal-like pattern at almost all time slices during four type-I ELMs in discharge 161493. The current evolution in the inner region ( ρ N = 0.2 − 0.6) is synchronized with the boundary region ( ρ N = 0.89 − 1.0), while the intermediate region ( ρ N = 0.6 − 0.89) shows opposite behavior. This sinusoidal-like variations in full-radius current density profile indicates strong core-pedestal coupling, suggesting ELMs significantly affect core plasmas, though current changes manifest differently across radial regions.

EFIT↗

DOE OSTI2024

Geant4-based Analysis of Faraday Cup Performance for PIP-II Laser Wire Scanner System

The Proton Improvement Plan-II (PIP-II) accelerator upgrade at Fermilab marks a significant advancement in high-energy physics research. This initiative aims to enhance Fermilab's accelerator complex by replacing the existing linear accelerator (linac) with a warm front end (WFE) capable of accelerating H- beams up to 2.1 MeV. Subsequently, a superconducting linac (SCL), that further accelerates these beams up to 800 MeV. To accurately measure the transverse beam profile, traditional wire scanners will be utilized in the WFE section, while Laser wire scanners will be implemented along the SCL. The Faraday cup for the Laser wire scanners has been designed using the GEANT4 simulation toolkit. This poster presents a detailed analysis of its performance along the SCL, focusing on electron absorption, secondary electron emission, backscattering, etc.

Wijethunga, S. A.K.↗

DOE OSTI2025

Throughput Measurements and Profile Analysis of Cloud Networks

Cloud networks utilize virtual connections to connect virtual machines distributed across cloud sites. They are increasingly deployed due to flexible provisioning using software and cost-effectiveness in not requiring to build physical network infrastructure. However, their extensive virtualization makes it unclear how well the established practices of conventional networks translate to them. Here, we study throughput measurements over a Google Cloud network using a matching hardware emulated conventional network, which provide production and exploratory conditions, respectively. The measurements span connections representing local, cross-continental and around the Earth distances. We study the effects of parallel flows, congestion control algorithms and retransmissions on the network throughput profile expressed as a function of RTT. We compare the throughput profile of Google Cloud network with those of emulated network under various loss conditions, including those too disruptive or expensive in the former. Our analysis based on the concave-convex shape and utilization-concavity coefficients of throughput profiles indicates an overall agreement of performance between the two networks, thereby justifying the use of conventional network emulations to analyze cloud networks. In terms of practical use, our study establishes that BBR and BBRv2 alpha TCP achieve higher throughput compared to loss-based congestion control algorithms under most network configurations, especially, under losses at large RTT.

Phanekham, Derek [Southern Methodist Univ., Dallas↗

DOE OSTI2024

Characterizing the effect of hypersonic boundary layer turbulence on antenna performance: A computational approach

The degradation of antenna performance during hypersonic re-entry is a well known phenomenon that can lead to complete radio blackout. Recent additions to the Empire code establish it as a tool for the study and analysis of the problem. Coupling to the Sandia Parallel Aerodynamics and Reentry Code (SPARC) enables the electromagnetic analysis of realistic re-entry plasma profiles. The geometric flexibility afforded by both Empire and SPARC allow the consideration of arbitrary vehicle and antenna configurations. We have used this tool to study antenna performance during re-entry when the boundary layer becomes turbulent. A concise description of line-of-sight transmissions, which employs advanced statistical methods, was developed. New insights into the low altitude reflectometer readings of RAM-C2 are offered. Techniques for the reconstruction of the re-entry plasma profile from reflectometer data were explored.

42 ENGINEERING↗

DOE OSTI2025

Doppler Backscattering Data Analysis and Integrated Modeling with OMFIT

One Modeling Framework for Integrated Tasks (OMFIT) is a widely used software tool in the magnetic fusion research community. OMFIT provides magnetic fusion energy researchers with a framework for the development of special-purpose physics modules. This paper describes an OMFIT physics module pertaining to the Doppler Backscattering (DBS) fusion plasma diagnostic. DBS measures density fluctuations and flow velocity through plasma scattering of electromagnetic waves. The OMFIT DBS module was developed to analyze experimental DBS data and facilitate modeling of DBS systems installed on multiple tokamak devices. The OMFIT DBS module is designed to support several analysis workflows: detailed analysis of experimental data, experimental planning, and theory-based synthetic diagnostic modeling. The DBS module uses integrated modeling by leveraging other OMFIT physics modules to perform tasks related to DBS, e.g. ray/beam–tracing simulations, edge-localized mode–synchronized data analysis, magnetic equilibrium reconstruction, and fitting kinetic profile data. Furthermore, this paper describes several supported workflows and serves a reference for the OMFIT DBS module.

Doppler backscattering↗

DOE OSTI2026

Valorization of consolidated bioprocessing residues for bioplastics

This study demonstrates an organic solvent-free processing strategy to valorize consolidated bioprocessing (CBP) residues, from switchgrass and poplar biomass, into functional poly(butylene succinate) (PBS)-based biocomposites using high-shear homogenization (HSH). HSH transformed the switchgrass and poplar CBP residues (CBP-R) into fine, uniformly distributed particles and microfibers. The composites of PBS with homogenized switchgrass residues (H-CBP-R-SG) or homogenized poplar residues (H-CBP-R-P) at a 70/30 weight ratio exhibited improved processability and mechanical integrity, with the Young's modulus for the PBS/H-CBP-R-SG and PBS/H-CBP-R-P nearly doubling to 0.66 ± 0.07 GPa and 0.65 ± 0.04 GPa, respectively, compared to neat PBS (0.36 ± 0.02 GPa). Dynamic Mechanical Analysis (DMA) reveals a significant suppression of the tan δ peak magnitude, indicating that HSH-mediated physical activation facilitates stress transfer in composites typical of covalent chemical grafting systems. While the transition to a stiffness-dominated profile reduces ductility, the resulting composites exhibit the dimensional stability and resistance to thermal warping required for high-fidelity FDM 3D printing and injection molding. Beyond material performance, comprehensive techno-economic analysis (TEA) and life cycle assessment (LCA) confirmed that diverting CBP residues into composite products can improve the economic viability of the biorefinery without substantially increasing biorefinery global warming potential (GWP). At a 30 wt% blend ratio, incorporating residuals into PBS yielded a minimum selling price for the composite of $\$4.07$ per kg compared to the conventional bioplastic price of $\$5.00$ per kg. This approach aligns with circular bioeconomy principles by converting waste streams into value-added products. Furthermore, this innovative strategy addresses key challenges in bioplastic development, including cost, compatibility, and performance, while simultaneously advancing waste minimization strategies for sustainable manufacturing systems.

09 BIOMASS FUELS↗

DOE OSTI2026

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗

DOE OSTI2024

Growth of Native Oxides of Niobium Thin Films for Superconducting Qubits with Etching Chemistry

Niobium thin films have been broadly applied in building superconducting qubits for quantum computing hardware. While improvements have been made by device engineering efforts, scaling the energy-sensitive quantum system requires materials study for further improvements. In this study, we performed XPS and ToF-SIMS analysis for Nb thin films across samples with different manufacturing techniques. By varying the air exposure time of the samples, this research comparatively investigates the chemical and depth profile of native oxides before and after the etching process. We observe a rapid logarithmic growth of oxide thickness across all samples and the dominant presence and growth of Niobium pentoxide in atomic percentage concentration on the surface. This comparative study provides insight into oxides mitigation strategies and correlation with qubits performance.

Lei, Zhicheng↗

DOE OSTI2025

OptiBench: An Optimization Benchmark Tool for Renewable Energy Problems

We propose a benchmark framework and visualization tool, OptiBench, for analyzing the performance of state-of-the-art optimization solvers across a variety of optimization problems in renewable energy research. Our framework is designed from the ground up in the Julia programming language and enables analysis at scale on high performance computing (HPC) systems. Our visualization tool allows effortless evaluation of optimization solver performance, robustness, and accuracy through intuitive plots, e.g., performance profiles, heat maps, and distribution plots. We have tested three benchmark suites relevant to the modeling of renewable energy systems, viz., CUTEst, PGLib-OPF, and WaterTAP water treatment optimization problems. We illustrate benchmarking of CUTEst using OptiBench on the National Renewable Energy Laboratory's (NREL) HPC Kestrel. Our findings indicate that MA57 HSL linear solver demonstrated the best overall performance for an experimental IPOPT implementation. Our work is ongoing and we intend to add support for more optimization solvers and benchmark test suites in the future.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2026

OptiBench: An Optimization Benchmark Tool for Renewable Energy Problems

We propose a benchmark framework and visualization tool, OptiBench, for analyzing the performance of state-of-the-art optimization solvers across a variety of optimization problems in renewable energy research. Our framework is designed from the ground up in the Julia programming language and enables analysis at scale on high performance computing (HPC) systems. Our visualization tool allows effortless evaluation of optimization solver performance, robustness, and accuracy through intuitive plots, e.g., performance profiles, heat maps, and distribution plots. We have tested three benchmark suites relevant to the modeling of renewable energy systems, viz., CUTEst, PGLib-OPF, and WaterTAP water treatment optimization problems. We illustrate benchmarking of CUTEst using OptiBench on the National Laboratory of the Rockies's (NLR) HPC Kestrel. Our findings indicate that MA57 HSL linear solver demonstrated the best overall performance for an experimental IPOPT implementation. Our work is ongoing and we intend to add support for more optimization solvers and benchmark test suites in the future.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Microscopic Understanding of the Effects of Impurities in Low RRR SRF Cavities

The SRF community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurities of niobium coupons with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing, temperature mapping, frequency vs temperature analysis, and materials studies reveals a microscopic picture of why low RRR cavities experience low BCS resistance behavior more prominently than their high RRR counterparts. We evaluate how differences in the mean free path, grain structure, and impurity profile affect RF performance. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

Howard, K.↗

DOE OSTI2024

Microscopic understanding of the effects of impurities in low RRR SRF cavities

Howard, K.↗