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Physics-informed machine learning to predict solvatochromic parameters of designer solvents with case studies in CO 2 and lignin dissolution

The polarity of solvents plays a critical role in various research applications, particularly in their solubilities. Polarity is conveniently characterized by the Kamlet-Taft parameters that is, the hydrogen bonding acidity (α), the basicity (β), and the polarizability (π*). Obtaining Kamlet-Taft parameters is very important for designer solvents, namely ionic liquids (ILs) and deep eutectic solvents (DESs). However, given the unlimited theoretical number of combinations of ionic pairs in ILs and hydrogen-bond donor/acceptor pairs in DESs, experimental determination of their Kamlet-Taft parameters is impractical. To address this, the present study developed two different machine learning (ML) algorithms to predict Kamlet-Taft parameters for designer solvents using quantum chemically derived input features. The ML models developed in the present study showed accurate predictions with high R 2 and low RMSE values. Further, in the context of present interest in the circular bioeconomy, the relationship between the basicities and acidities of designer solvents and their ability to dissolve lignin and carbon dioxide (CO 2 ) is discussed. Our method thus guides the design of effective solvents with optimal Kamlet-Taft parameter values dissolving and converting biomass and CO 2 into valuable chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning Approaches to Increasing Value of Spaceflight Omics Databases

The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may soon enable unique insight into which measured phenomena correlate to biological mechanisms that are truly affected by spaceflight conditions; which are most likely to be confounded by other variables; and which are insufficiently characterized, significantly increasing existing and future science return from ISS and spaceflight missions.

Gentry, Diana↗

Applications and Techniques for Fast Machine Learning in Science

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science—the concept of integrating powerful ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Uncertainty based Online Ensemble on Non-Stationary Data for Fusion Science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior due to drifts in the data. The drifts can arise from both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with non-stationary data streams.Online learning can be used to continuously adapt the models with new data as it is acquired. However, traditional online learning can suffer from short-term performance degradation, as ground truth are not available before making the prediction. To address this challenge, we propose uncertainty aware ensemble approach for online learning. We use Deep Gaussian Process Approximation (DGPA) technique for calibrated uncertainty estimation and use the uncertainty values to guide a meta-algorithm that produces predictions based on ensemble of learners. Moreover, DGPA also provides uncertainty estimation along with the predictions for decision makers. This paper demonstrates that the proposed method outperforms traditional online learning approach, and a naive ensemble without uncertainty guidance by about 7% and 6%, respectively, on B-coil deflection prediction at DIII-D Fusion Facility.

Rajput, Kishansingh [Thomas Jefferson National Acc↗

Uncertainty based Online Ensemble on Non-Stationary Data for Fusion Science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior due to drifts in the data. The drifts can arise from both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with non-stationary data streams.Online learning can be used to continuously adapt the models with new data as it is acquired. However, traditional online learning can suffer from short-term performance degradation, as ground truth are not available before making the prediction. To address this challenge, we propose uncertainty aware ensemble approach for online learning. We use Deep Gaussian Process Approximation (DGPA) technique for calibrated uncertainty estimation and use the uncertainty values to guide a meta-algorithm that produces predictions based on ensemble of learners. Moreover, DGPA also provides uncertainty estimation along with the predictions for decision makers. This paper demonstrates that the proposed method outperforms traditional online learning approach, and a naive ensemble without uncertainty guidance by about 7% and 6%, respectively, on B-coil deflection prediction at DIII-D Fusion Facility.

Rajput, Kishansingh [Thomas Jefferson National Acc↗

Hydrogen-induced degradation dynamics in silicon heterojunction solar cells via machine learning

Abstract Among silicon-based solar cells, heterojunction cells hold the world efficiency record. However, their market acceptance is hindered by an initial 0.5% per year degradation of their open circuit voltage which doubles the overall cell degradation rate. Here, we study the performance degradation of crystalline-Si/amorphous-Si:H heterojunction stacks. First, we experimentally measure the interface defect density over a year, the primary driver of the degradation. Second, we develop SolDeg, a multiscale, hierarchical simulator to analyze this degradation by combining Machine Learning, Molecular Dynamics, Density Functional Theory, and Nudged Elastic Band methods with analytical modeling. We discover that the chemical potential for mobile hydrogen develops a gradient, forcing the hydrogen to drift from the interface, leaving behind recombination-active defects. We find quantitative correspondence between the calculated and experimentally determined defect generation dynamics. Finally, we propose a reversed Si-density gradient architecture for the amorphous-Si:H layer that promises to reduce the initial open circuit voltage degradation from 0.5% per year to 0.1% per year.

14 SOLAR ENERGY↗

Energy storage emerging: A perspective from the Joint Center for Energy Storage Research

Energy storage is an integral part of modern society. A contemporary example is the lithium (Li)-ion battery, which enabled the launch of the personal electronics revolution in 1991 and the first commercial electric vehicles in 2010. Most recently, Li-ion batteries have expanded into the electricity grid to firm variable renewable generation, increasing the efficiency and effectiveness of transmission and distribution. Important applications continue to emerge including decarbonization of heavy-duty vehicles, rail, maritime shipping, and aviation and the growth of renewable electricity and storage on the grid. This perspective compares energy storage needs and priorities in 2010 with those now and those emerging over the next few decades. The diversity of demands for energy storage requires a diversity of purpose-built batteries designed to meet disparate applications. Advances in the frontier of battery research to achieve transformative performance spanning energy and power density, capacity, charge/discharge times, cost, lifetime, and safety are highlighted, along with strategic research refinements made by the Joint Center for Energy Storage Research (JCESR) and the broader community to accommodate the changing storage needs and priorities. Innovative experimental tools with higher spatial and temporal resolution, in situ and operando characterization, first-principles simulation, high throughput computation, machine learning, and artificial intelligence work collectively to reveal the origins of the electrochemical phenomena that enable new means of energy storage. This knowledge allows a constructionist approach to materials, chemistries, and architectures, where each atom or molecule plays a prescribed role in realizing batteries with unique performance profiles suitable for emergent demands.

Trahey, Lynn↗

deeprob/ThioesteraseEnzymeSpecificity: EnZymClass-first-release

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

Banerjee, Deepro↗

Synthetic data-driven deep learning for label-free autonomous atomic force microscopy

Atomic force microscopy (AFM) is a widely used tool for nanoscale characterization across materials science, energy research, and biology. However, its adoption in high-throughput materials discovery and statistically driven studies remains limited by a strong dependence on expert operator input and by the scarcity of annotated experimental AFM datasets needed to enable data-driven automation. Here, we introduce SimuScan, a synthetic-data–driven framework that enables reliable AFM feature identification, segmentation, and targeted imaging without requiring large manually labeled experimental datasets. SimuScan generates tunable, high-fidelity synthetic AFM images of defined morphologies while incorporating realistic experimental artifacts, including tip–sample convolution, noise, flattening distortions, and surface debris. These datasets are shown to support scalable, label-free training of modern deep learning models for AFM analysis. When integrated into data-driven AFM workflows, SimuScan-trained models can locate and analyze nanoscale structures across large datasets and guide targeted follow-up imaging. We validate this approach on nanostructured surfaces, DNA assemblies, and bacterial cells, demonstrating robust generalization across diverse sample types with minimal operator intervention. More broadly, this work establishes a general strategy for generating explicitly conditioned, task-relevant synthetic data to improve the reliability of downstream models in autonomous microscopy.

Millan-Solsona, Ruben [Oak Ridge National Laborato↗

Enhancing stability, magnetic anisotropy, and coercivity of manganese aluminum: Machine learning, ab initio , and micromagnetic modeling

The binary manganese aluminum (MnAl) alloy with L⁢1 0 crystal structure is a promising rare earth (RE) element-free permanent magnetic material because of its exceptional magnetic properties. However, experimentally synthesizing it in a stable bulk form is extremely challenging. Here, in this study, an alternative method of stabilizing the material, a pathway for experimental synthesis and validation, is proposed and theoretically verified. This is done by partially substituting Mn and Al sites with Fe and Ni and identifying its enhanced phase stability, saturation magnetization density, magnetic anisotropy, and coercivity from density functional theory (DFT), machine learning (ML) crystal graph convolution neural network (CGCNN), and micro-magnetic modeling. When considering a fixed 50% Ni, the magnetic anisotropy increases with the increasing Fe content but decreases the formation energy. The calculated formation energies, elastic constants, and phonon frequencies demonstrate that the binary and quaternary compositions are stable. Most importantly, in 50% Fe and Ni-substituted-equiatomic phase, magnetic anisotropy constants and saturation magnetization density increase by 56% and 23% as compared to the MnAl. Further, the coercivity of the equiatomic phase predicted with micro-magnetic modeling is higher by 17% than the parent compound.

Bhandari, Churna [Ames National Laboratory, and Io↗

SQMS Quantum R&D in Machine Learning, Optimization and Sensing beyond Fundamental Physics Applications

This newly formed team at SQMS under the Ecosystem Thrust is looking to develop capabilities impacting societal advances outside the core domain of HEP and condensed matter physics. We explicitly leverage the experimental and algorithmic innovations developed across all groups as well as connect to broad-scope external projects of the diverse team of PIs. As the inaugural set of projects, we are studying numerically quantum machine learning models inspired by efficiently trainable echo-state and orthogonal neural networks and developing designs for related experiments to be performed on quantum processors based on SQMS SRF cQED technology and Rigetti s transmon arrays. Investigated models exploit ideas and lessons learned from multiple prior work by SQMS team members in a variety of internal and external activities [R1]. Target initial applications include noisy signal processing, potentially captured by quantum sensors or noisy QPUs, as well as simulation and classification of healthcare data. For instance, image reconstruction of the brain s electrical properties by solving the inverse Maxwell equation problem with uncertainty [R2] through a hybrid quantum-classical physics-informed architecture for time-dependent processes [R3]. The group is also investigating the application and development of novel quantum sensors based on magnetic levitation of a superconducting sphere coupled to a superconducting qubit. This coupling enables high-precision measurements of the position of the sphere, which can be used for sensitive detection of forces, enabling practical applications such as gravimetry for geophysics analysis, or accelerometry for GPS-denied navigation [R4] [R1] Rieffel, Eleanor G., Ata Akbari Asanjan, M. Sohaib Alam, Namit Anand, David E. Bernal Neira, Sophie Block, Lucas T. Brady et al. "Assessing and advancing the potential of quantum computing: A NASA case study." Future Generation Computer Systems (2024). [R2] Yu, X., Serrall s, J.E., Giannakopoulos, I.I., Liu, Z., Daniel, L., Lattanzi, R. and Zhang, Z., 2023. Pifon-ept: Mr-based electrical property tomography using physics-informed fourier networks. IEEE Journal on Multiscale and Multiphysics Computational Techniques. [R3] Wudarski, Filip, Daniel OConnor, Shaun Geaney, Ata Akbari Asanjan, Max Wilson, Elena Strbac, P. Aaron Lott, and Davide Venturelli. "Hybrid quantum-classical reservoir computing for simulating chaotic systems." arXiv preprint arXiv:2311.14105 (2023). [R4] Higgins, Gerard, Saarik Kalia, and Zhen Liu. "Maglev for dark matter: Dark-photon and axion dark matter sensing with levitated superconductors." Physical Review D 109.5 (2024): 055024.

Venturelli, Davide↗

hls4ml: An Open-Source Codesign Workflow to Empower Scientific Low-Power Machine Learning Devices

Accessible machine learning algorithms, software, and diagnostic tools for energy-efficient devices and systems are extremely valuable across a broad range of application domains. In scientific domains, real-time near-sensor processing can drastically improve experimental design and accelerate scientific discoveries. To support domain scientists, we have developed hls4ml, an open-source software-hardware codesign workflow to interpret and translate machine learning algorithms for implementation with both FPGA and ASIC technologies. We expand on previous hls4ml work by extending capabilities and techniques towards low-power implementations and increased usability: new Python APIs, quantization-aware pruning, end-to-end FPGA workflows, long pipeline kernels for low power, and new device backends include an ASIC workflow. Taken together, these and continued efforts in hls4ml will arm a new generation of domain scientists with accessible, efficient, and powerful tools for machine-learning-accelerated discovery.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021)View full citation, Nat. Methods, 18, 186–193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, sub­tomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L1/L2 losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.

contrast enhancement↗

Robust Molecular Predictive Methods for Novel Polymer Discovery and Applications

Polymeric materials are ubiquitous in modern society and they play an instrumental role in almost all industries, undoubtedly including the energy and environment sectors. Increased demand of energy and awareness to sustainability both necessitates the development of novel polymers with enhanced properties. Unfortunately, their structural and behavioral complexity render such discovery challenging and impeded. To address this problem, scientists are developing various computational modeling techniques and leveraging their power to depict the relationship between structural characteristics of polymers and their properties (such as rheological behaviors), and use such prediction to guide the design and syntheses of novel polymeric materials with enhanced performances. Unfortunately, predicting the relationships between polymer structure and composition with rheological properties via atomistic modeling is still a major challenge because of the extended time and length scales involved. Studying dynamic shear viscosity and linear viscoelasticity using molecular models requires capabilities that have been elusive, including representation of large molecular weight chains with an effective internal scale capable of describing entanglement, shear-rates that are in the s-1 scale with accurate quantitative stresses, and chemically-realistic combinations of both homogeneous and heterogeneous systems. Motivated by these unmet challenges, the overall technical objective of this DOE-STTR Phase II project is to develop robust molecular predictive methods for advanced polymer discovery and applications and especially for designing and demonstrating the “smart” polymer-based waterflooding enhanced oil recovery (EOR) process. In particular, we apply state-of-the-art molecular modeling methods developed by our academic partner, Materials Stimulation Center (MSC) at California Institute of Technology (Caltech), to facilitate and accelerate the experimental discovery processes. During the Phase I of this project, we had focused on development and demonstration of the molecular modeling methods to describe rheological properties of non-Newtonian polymer fluids, and to improve our fundamental understandings of shear-thickening mechanism and kinetics. In Phase II, we further apply the theoretical models to guide our experimental programs to improve our design of smart rheology modifier (SRM) polymers and their optimization for EOR. Specifically, we have three objectives in the Phase II study: (1) to further improve out computational modeling methods, coupling with the advanced machine learning algorithms; (2) to develop cost-effective and efficient SRM-flooding process suitable for EOR applications under typical reservoir conditions; and (3) to further explore the application of our molecular predictive models for innovative material discovery in other industrial applications. The recent development of our multiscale predictive framework allows the successful prediction of rheological properties from the chemical structure for polymers of experimentally relevant molecular weights, and provides an in-silico machine learning engine for screening novel compositions and structures with optimized non-Newtonian response, required for both shear-thinning and shear-thickening applications. Our framework provides: (1) procedures and tools for systematic coarsening from atomistic models and reverse mapping of coarse-grain models to atomistic, (2) unique ab initio methods to characterize the atomistic origin of colloidal and interfacial interactions and phenomena, (3) systematic structure and composition builders based on practical descriptors that drive rheological changes in polymer melts and diluted polymer mixtures, (4) a rheological properties engine capable of predicting viscosity in the zero-shear limit and under realistic dynamic conditions (for shear-rates commensurate with experiments) for large heterogeneous systems, (5) coarse-grain force fields with improved non-bond descriptions based on accurate quantum mechanics, (6) an in-silico screening machine learning engine that feeds from the systematic model builders to cover the descriptors search space, computes the rheological properties from converged trajectories spanning sub-milliseconds and ranks them for each structure/composition using an automated viscosity-vs-shear rate fitness function that can be tuned for shear-thickening, shear-thinning and other rheological responses.

02 PETROLEUM↗

A physics-informed deep learning description of Knudsen layer reactivity reduction

A physics-informed neural network (PINN) is used to evaluate the fast ion distribution in the hot spot of an inertial confinement fusion target. The use of tailored input and output layers to the neural network is shown to enable a PINN to learn the parametric solution to the Vlasov–Fokker–Planck equation in the absence of any synthetic or experimental data. As an explicit demonstration of the approach, the specific problem of Knudsen layer fusion yield reduction is treated. Here, the predictions from the Vlasov–Fokker–Planck PINN are used to provide a non-perturbative solution of the fast ion tail in the vicinity of the hot spot, thus allowing the spatial profile of the fusion reactivity to be evaluated for a range of collisionalities and hot spot conditions. Excellent agreement is found between the predictions of the Vlasov–Fokker–Planck PINN and the results from traditional numerical solvers with respect to both the energy and spatial distribution of fast ions and the fusion reactivity profile, demonstrating that the Vlasov–Fokker–Planck PINN provides an accurate and efficient means of determining the impact of Knudsen layer yield reduction across a broad range of plasma conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Physics-Informed Deep Learning Description of Knudsen Layer Reactivity Reduction

A physics-informed neural network (PINN) is used to evaluate the fast ion distribution in the hot spot of an inertial confinement fusion target. The use of tailored input and output layers to the neural network is shown to enable a PINN to learn the parametric solution to the Vlasov–Fokker–Planck equation in the absence of any synthetic or experimental data. As an explicit demonstration of the approach, the specific problem of Knudsen layer fusion yield reduction is treated. Here, the predictions from the Vlasov–Fokker–Planck PINN are used to provide a non-perturbative solution of the fast ion tail in the vicinity of the hot spot, thus allowing the spatial profile of the fusion reactivity to be evaluated for a range of collisionalities and hot spot conditions. Excellent agreement is found between the predictions of the Vlasov–Fokker–Planck PINN and the results from traditional numerical solvers with respect to both the energy and spatial distribution of fast ions and the fusion reactivity profile, demonstrating that the Vlasov–Fokker–Planck PINN provides an accurate and efficient means of determining the impact of Knudsen layer yield reduction across a broad range of plasma conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Distributed heterogeneous compute infrastructure for the study of additive manufacturing systems

We present the current status of a large-scale computing framework to address the need of the multidisciplinary effort to study chemical dynamics. Specifically, we are enabling scientists to process and store experimental data, run large-scale computationally expensive high-fidelity physical simulation, and analyze these results using the state-of-the-art data analytics tools, machine learning, and uncertainty quantification methods using heterogeneous computing resources, such as CPU and GPU cluster. The framework can integrate or abstract out multiple domains based on roles. In order to develop this framework, we have leveraged an existing framework coupled with in-house heterogeneous computing resources. We present the results of using this framework on a single metadata triggered workflow to accelerate an additive manufacturing use case.

heterogeneous computing, hpc, workflows, reproduci↗

Protein sequence design with a learned potential

The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

59 BASIC BIOLOGICAL SCIENCES↗