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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Reweighting configurations generated by transferable, machine learned models for protein sidechain backmapping

Multiscale modeling requires the linking of models at different levels of detail, with the goal of gaining accelerations from lower fidelity models while recovering fine details from higher resolution models. Communication across resolutions is particularly important in modeling soft matter, where tight couplings exist between molecular-level details and mesoscale structures. While multiscale modeling of biomolecules has become a critical component in exploring their structure and self-assembly, backmapping from coarse-grained to fine-grained, or atomistic, representations presents a challenge, despite recent advances through machine learning. A major hurdle, especially for strategies utilizing machine learning, is that backmappings can only approximately recover the atomistic ensemble of interest. We demonstrate conditions for which backmapped configurations may be reweighted to exactly recover the desired atomistic ensemble. By training separate decoding models for each sidechain type, we develop an algorithm based on normalizing flows and geometric algebra attention to autoregressively propose backmapped configurations for any protein sequence. Critical for reweighting with modern protein force fields, our trained models include all hydrogen atoms in the backmapping and make probabilities associated with atomistic configurations directly accessible. We also demonstrate, however, that reweighting is extremely challenging despite state-of-the-art performance on recently developed metrics and generation of configurations with low energies in atomistic protein force fields. Through detailed analysis of configurational weights, we show that machine-learned backmappings must not only generate configurations with reasonable energies, but also correctly assign relative probabilities under the generative model. These are broadly important considerations in generative modeling of atomistic molecular configurations.

Monroe, Jacob I. [Univ. of Arkansas, Fayetteville,↗
DOE OSTI2026

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Chemistry↗
DOE OSTI2021

Critical phenomena of the layered ferrimagnet Mn 3 Si 2 Te 6 following proton irradiation

The critical phenomena and magnetic entropy of the quasi-2D ferrimagnetic crystal, Mn 3 Si 2 Te 6 (MST), is analyzed along the easy axis (H || ab) as a function of proton irradiance. The critical exponents β and γ do not fall into any particular universality class upon proton irradiation. However, for pristine and irradiated samples, the critical exponents lie closer to mean field-like interactions; therefore, long-range interactions are presumed to be sustained in MST. The effective spatial dimensionality reveals that MST remains at d =3 under proton irradiation, whereas spin dimensionality transitions from an initial n =1 to n =2 and n =3 for 1 × 10 15 and 5 × 10 15 H + /cm 2 , indicating XY and Heisenberg interactions, respectively. The spin correlation function reveals an increase in magnetic correlations at 5 × 10 15 H + /cm 2 . Maximum change in magnetic entropy at 3 T is the largest for 5 × 10 15 H + /cm 2 at 2.45 J/kg K, in comparison to 1.60 J/kg K for pristine MST. These results intriguingly align with previous findings on MST where magnetization increased by ~50% at 5 × 10 15 H + /cm 2 , in comparison to its pristine counterpart [Martinez et al., Appl. Phys. Lett. 116, 172404 (2020)]. Magnetic entropy derived from heat capacity analysis shows no large deviations across the proton irradiated samples suggesting that the antiferromagnetic (AFM) coupling between the Mn sites is stable even after proton irradiation. This implies that magnetization is enhanced through a strengthening of the super-exchange interaction between Mn atoms mediated through Te rather than a weakening of the AFM component.

2D materials↗
DOE OSTI2022

High-electric-field behavior of the metal-insulator transition in TiS3 nanowire transistors

We investigate the behavior of the metal-insulator transition (MIT) in TiS 3 nanowire field-effect transistors, in the strongly nonequilibrium limit that has, thus far, largely been neglected. Under high electric fields within the TiS 3 channel (≤115 kV/cm), we observe the emergence of a critical fixed point, separating insulating and metallic regions in the transfer curves of the device. The critical gate voltage that defines this fixed point evolves systematically with the drain bias (field), allowing us to map out a phase diagram that identifies the conditions for metallicity or for insulating behavior. Dependent upon the choice of the gate voltage used to tune the carrier concentration in the nanowire, the existence of the field-induced MIT allows the TiS 3 to be either insulating or metallic over an extensive range of temperature. The possible connection of this strongly nonequilibrium state to some form of charge density wave is discussed.

2D materials↗
DOE OSTI2022

Bifurcation-driven vertical plasma displacement

This paper considers vertical plasma motion resulting from plasma current decay during the disruption event. The presented filament-based model describes the motion in the ideal wall limit as an adiabatically slow evolution of the plasma equilibrium. Here, the equilibrium exhibits a pitchfork bifurcation when the decaying plasma current passes a critical value determined by the external magnetic field. This bifurcation affects the disruption-induced mechanical loads on the first wall.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Building Inclusive Educational and Career Pathways in Fusion Energy

This paper was written in preparation for the Workforce Accelerator for Fusion Energy Development conference, which was funded by the National Science Foundation. Prior to the conference, participants from academia, government, industry, national laboratories, and nonprofit organizations worked together to write White papers. Held in Hampton, Virginia, in May 2024, the conference convened participants to discuss various topics in support of workforce development in fusion energy. As the fusion industry expands, efforts to recruit and retain a diverse workforce, ensure equitable access to fusion education, and gain public support will be critical to meeting workforce needs in this field. We outline strategic recommendations across three vital areas: improving diversity data collection; supporting career advancement and retention with a diversity, equity, inclusion, accessibility, and belonging focus; and strengthening community engagement and education in fusion energy.

Cote, Laleh [Lawrence Berkeley National Laboratory↗
DOE OSTI2026

Statistical inference of anomalous thermal transport with uncertainty quantification for interpretive 2D SOL models

The critical task of inferring anomalous cross-field transport coefficients is addressed in simulations of boundary plasmas with fluid models. A workflow for parameter inference in the UEDGE fluid code is developed using Bayesian optimization with parallelized sampling and integrated uncertainty quantification. In this workflow, transport coefficients are inferred by maximizing their posterior probability distribution, which is generally multidimensional and non-Gaussian. Uncertainty quantification is integrated throughout the optimization within the Bayesian framework that combines diagnostic uncertainties and model limitations. As a concrete example, we infer the anomalous electron thermal diffusivity $\chi_\perp$ from an interpretive 2D model describing electron heat transport in the conduction-limited region with radiative power loss. The workflow is first benchmarked against synthetic data and then tested on H-, L-, and I-mode discharges to match their midplane temperature and divertor heat flux profiles. We demonstrate that the workflow efficiently infers diffusivity and its associated uncertainty, generating 2D profiles that match 1D measurements. Future efforts will focus on incorporating more complicated fluid models and analyzing transport coefficients inferred from a large database of experimental results.

Bayesian optimization↗
DOE OSTI2023

APC Nb 3 Sn superconductors based on internal oxidation of Nb–Ta–Hf alloys

In the last few years, a new type of Nb 3 Sn superconducting composite, containing a high density of artificial pinning centers (APC) generated via an internal oxidation approach, has demonstrated a significantly superior performance relative to present, state-of-the-art commercial Nb3Sn conductors. This was achieved via the internal oxidation of Nb-4at.%Ta-1at.%Zr alloy. On the other hand, our recent studies have shown that internal oxidation of Nb–Ta–Hf alloys can also lead to dramatic improvements in Nb 3 Sn performance. Here in this work we follow up on this latter approach, fabricating a 61-stack APC wire based on the internal oxidation of Nb-4at.%Ta-1at.%Hf alloy, and compare its critical current density (J c ) and irreversibility field with APC wires made using Nb-4at.%Ta-1at.%Zr. A second goal of this work was to improve the filamentary design of APC wires in order to improve their wire quality and electromagnetic stability. Our new modifications have led to significantly improved residual resistivity ratio and stability in the conductors, while still keeping non-Cu J c at or above the conductor J c specification required by the proposed Future Circular Collider. Further improvement via optimization of the wire recipe and design is ongoing. Finally, additional work needed to make APC conductors ready for applications in magnets is discussed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Spherical tokamak physics research in preparation for the operation of NSTX-U

The National Spherical Torus Experiment Upgrade (NSTX-U) is preparing to resume operation, representing a crucial step toward realizing compact, cost-effective fusion pilot plants. In advance of this, extensive modeling and data analysis have been conducted to advance the physics basis for low-aspect-ratio, high-performance plasma regimes, focusing on three core objectives: confinement and stability, power and particle handling, and steady-state operation. Significant progress has been made in understanding the electron temperature flattening in high-β plasmas, which is shown to be driven by a complex interplay of magnetohydrodynamic instabilities (e.g. non-resonant infernal modes), fast-ion-driven Alfvén eigenmodes, and electron and ion-scale micro-instabilities, particularly Kinetic Ballooning Modes (KBMs), whose destabilization is strongly dependent on parallel magnetic field fluctuations (δB ∥ ). Furthermore, a new gyrokinetic critical pedestal model was developed, accurately predicting pedestal structure by identifying KBMs as the primary stability limit, offering a critical constraint for future high-confinement scenarios. To address the challenge of high heat flux, novel liquid lithium plasma-facing components were modeled. The analysis confirmed that lithium vapor shielding is a self-regulating mechanism for heat mitigation, while also emphasizing that strong main ion parallel flow is essential to minimize core lithium contamination. Finally, progress toward steady-state operation was anchored by developing the required physics basis and control tools. This includes predictive modeling for reversed magnetic shear sustainment, demonstrating that magnetic island-induced bootstrap current reduction is negligible in STs, and advancing real-time control and disruption avoidance capabilities. The development of high-speed surrogate models (e.g. MMMNet) provides computationally efficient tools vital for non-inductive scenario optimization and integrated, low-disruptivity operations planned for NSTX-U.

NSTX-U↗
DOE OSTI2022

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Abstract Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.

Morgado, Leonor (ORCID:0000000237605180)↗
DOE OSTI2020

Loschmidt-amplitude wave function spectroscopy and the physics of dynamically driven phase transitions

In this work, we introduce the Loschmidt amplitude as a powerful tool to perform spectroscopy of generic many-body wave functions and use it to interrogate the wave function obtained after ramping the transverse field quantum Ising model through its quantum critical point. Previous results are confirmed and a more complete understanding of the population of defects and of the effects of magnon-magnon interaction or finite-size corrections is obtained. The influence of quantum coherence is clarified.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Sketched Nanoscale KTaO 3 -Based Superconducting Quantum Interference Device

The discovery of two-dimensional superconductivity in LaAlO 3 /KTaO 3 (111) and (110) interfaces has raised significant interest in this system. In this paper, we report the first successful fabrication of a direct current superconducting quantum interference device (dc-SQUID) in the KTO system. The key device elements, superconducting weak links, are created by conductive atomic force microscope lithography, which can reversibly control the conductivity at the LAO/KTO (110) interface with nanoscale resolution. The periodic modulation of the SQUID critical current 𝐼 c ⁡(𝐵) with magnetic field corresponds well with our theoretical modeling, which reveals a large kinetic inductance of the superconducting two-dimensional electron gas in KTO. The kinetic inductance of the SQUID is tunable by electrical gating from the back, due to the large dielectric constant of KTO. The demonstration of weak links and SQUIDs in KTO broadens the scope for exploring the underlying physics of KTO superconductivity, including the role of spin-orbit coupling, pairing symmetry, and inhomogeneity. It also promotes KTO as a versatile platform for a growing family of quantum devices, which could be applicable in the realm of quantum computing and information.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Nonideal stability analysis of differentially rotating plasmas with global curvature effects

The linear stability of global nonaxisymmetric modes in differentially rotating, magnetized, nonideal plasma is critical to classifying turbulence and transport phenomena. We investigate the competition between the local magneto-rotational instability (MRI) and the magneto-curvature instability (MCI)—a distinct nonaxisymmetric low-frequency curvature-driven global branch that appears alongside MRI. Here, to accomplish this, we developed a nonideal global spectral method, which is validated against NIMROD code simulations. This spectral approach allows for the direct derivation of an extended effective potential formalism and a resistive Alfvénic resonance condition, providing a framework for direct analysis of energy contributions and confinement mechanisms. Our study reveals that the global, low-frequency MCI persists at low magnetic Reynolds numbers (Rm), whereas the localized, high-frequency MRI is stabilized by diffusive broadening of its structure around its Alfvénic resonances. Consequently, we identify the global MCI branch as the primary onset mechanism for nonaxisymmetric magnetohydrodynamic instability in systems with finite curvature, e.g., astrophysical rotators. We establish distinct parameter regimes for mode dominance: MCI prevails in geometrically moderate-thickness disks with intermediate curvature and radial gaps, while MRI dominates in thin, low-curvature disks with large radial gaps. Mode competition is also highly sensitive to the flow profile, particularly vorticity and its gradient, with nonuniform shear profiles exhibiting more robust instability due to flow curvature (i.e., the second derivative of the flow profile) and shear contributions. A key outcome is the development of spectral diagrams derived from the global spectral method. These diagrams comprehensively map dominant instabilities and their characteristics, offering a predictive tool for critical onset parameters (i.e., flow curvature, magnetic field, and Rm) and facilitating the interpretation of experimental and simulation results. Notably, these diagrams demonstrate that the global MCI is generally the sole unstable mode at the initial onset of nonaxisymmetric instability.

Haywood, Alexander [Princeton Univ., NJ (United St↗
DOE OSTI2025

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Arasteh, Kourosh [Lawrence Livermore National Labo↗
DOE OSTI2025

A review of laser materials processing paradigms

Laser-based processing of materials has progressed from traditional applications such as macroscale cutting and welding, to sophisticated techniques, including ultrafast micromachining, additive manufacturing, and surface engineering at micro- and nano-metric scales. Innovations in laser source technology, particularly the advent of high-power and ultrashort-pulse lasers, have expanded the range of processable materials, enabled a plethora of manufacturing applications, and propelled groundbreaking research in optics, photonics, electronics, and biomedical domains. In this article, we provide a concise, yet broad review of the congruent evolution of lasers and materials processing, and highlight seminal developments in the field over the years, combined with a critical assessment of the state of the art. Finally, we also provide an outlook on emerging needs, as well as a roadmap of anticipated developments in laser technologies and materials platforms over the next 50 years.

Lasers↗
DOE OSTI2023

Physics-based Induced Earthquake Forecasting: Process Understanding, and Hazards Mitigation

Disposal of saltwater co-produced with oil and gas is linked to elevated seismicity in the Central and Midwest US. There is a concern that these events may lead to widespread damage and an overall increase in seismicity. Thus an improved understanding of the spatially and temporally variable deformation and stress field associated with fluid injection operation is critically necessary for evaluating time-varying seismic hazards. Despite the improvements in seismic monitoring capacity and the resulting decrease in the magnitude detection threshold, estimates of induced earthquake probability remain elusive due to insufficient models incapable of accounting for the complex physics governing the process of induced seismicity. The proposed research effort will comprehensively analyze, integrate, and interpret geodetic, injection, and seismic data in the vicinity of the injection sites in Oklahoma to resolve the 4-dimensional distribution of pore pressure and stress in the shallow crust. This project, in particular, is focused on exploring the statistical relation between injection operation and increased earthquake hazard. The amplitude of and the extent to which pore pressure changes are determined by some factors, in particular, the hydrogeological properties of the rocks, such as diffusivity. Thus the available deformation data will be used to constrain hydrogeological properties of the medium, to accurately resolve the evolution of crustal stresses due to fluid injection. Having the time-varying models of stress changes, a statistical framework will be implemented to estimate the time-dependent probability of large earthquakes on the nearby fault systems. These data and models help to improve seismic hazard estimates and aid in constructing operational-induced earthquake forecast models. This information can also be integrated into the updated U.S. National Seismic Hazard Map, which local communities and authorities use in their earthquake risk estimates and mitigation efforts.

58 GEOSCIENCES↗
DOE OSTI2024

Efficient Dimension Reduction of Complex Three-dimensional CO2 Saturation using Deep Learning Models

In the domain of deep learning (DL), dimension reduction is crucial for enhancing training efficiency and mitigating overfitting, particularly when managing complex data such as three-dimensional (3D) saturation data. The 3D saturation data in the context of geological carbon storage (GCS) presents unique challenges due to its inherent sparsity and the abrupt transitions at plume boundaries, known as shock fronts. To address the challenges, we proposed a novel DL framework that integrates dimension reduction with advanced 3D reconstruction techniques. Our model leveraged latent variables derived from 2D average saturation data, offering a robust and efficient solution tailored to the intricate dynamics of 3D saturation fields. The proposed framework can extract the critical features of the high-dimensional data while reducing the variable numbers, which is more tractable for DL models and enhances the model robustness and accuracy. Therefore, it provides a novel approach for modeling and analyses in complex geological scenarios, which finds great potential applications in environmental monitoring and energy storage.

Wang, Hongsheng↗