Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “tensor learning”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

180 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Variational Neural-Network Ansatz for Continuum Quantum Field Theory

Physicists dating back to Feynman have lamented the difficulties of applying the variational principle to quantum field theories. In nonrelativistic quantum field theories, the challenge is to parametrize and optimize over the infinitely many n-particle wave functions comprising the state’s Fock-space representation. Here we approach this problem by introducing neural-network quantum field states, a deep learning ansatz that enables application of the variational principle to nonrelativistic quantum field theories in the continuum. Our ansatz uses the Deep Sets neural network architecture to simultaneously parametrize all of the n-particle wave functions comprising a quantum field state. We employ our ansatz to approximate ground states of various field theories, including an inhomogeneous system and a system with long-range interactions, thus demonstrating a powerful new tool for probing quantum field theories.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Performance evaluations of signed and unsigned noisy approximate quantum Fourier arithmetic

The Quantum Fourier Transform (QFT) grants competitive advantages, especially in resource usage and circuit approximation, for performing arithmetic operations on quantum computers, and offers a potential route toward a numerical quantum-computational paradigm. In this paper, we utilize efficient techniques to implement QFT-based integer addition and multiplications. These operations are fundamental to various quantum applications including Shor’s algorithm, weighted-sum optimization problems in data processing and machine learning, and quantum algorithms requiring inner products. We carry out performance evaluations of these implementations based on IBM’s superconducting-qubit architecture using different compatible noise models. We isolate the sensitivity of the component quantum circuits on both one-/two-qubit gate error rates, and the number of the arithmetic operands’ superposed integer states. We analyze performance and identify the most effective approximation depths for unsigned quantum addition and quantum multiplication within the given context. We then perform a similar analysis of signed addition and compare to the unsigned results. We observe significant dependency of the optimal approximation depth on the degree of machine noise and the number of superposed states in certain performance regimes. Finally, we elaborate on the algorithmic challenges—relevant to signed, unsigned, modular and non-modular versions—that could also be applied to current implementations of QFT-based subtraction, division, exponentiation, and their potential tensor extensions. Here, we analyze the performance trends in our results and speculate on possible future developments within this computational paradigm.

Computational models↗
DOE OSTI2023

Harnessing Neural Networks for Elucidating X-ray Absorption Structure–Spectrum Relationships in Amorphous Carbon

Improved understanding of structural and chemical properties through local experimental probes, such as X-ray absorption near-edge structure (XANES) spectroscopy, is crucial for the understanding and design of functional materials. In recent years, significant advancements have been made in the development of data science approaches for the automated interpretation of XANES structure–spectrum relationships. However, existing studies have primarily focused on crystalline solids and small molecules, while fewer efforts have been devoted to disordered systems. Thus, in this work, we demonstrate the development of neural network models for predicting and interpreting XANES spectra of amorphous carbon (a-C) from local structural descriptors. Comparison between different structural descriptors expectedly shows that the inclusion of both bond length and bond angle information is necessary for an accurate prediction of the spectra. Among the descriptors considered in this work, we find that the local many-body tensor representation yields the highest accuracy and greatest interpretability so that it can be leveraged to understand the importance of structural motifs in determining XANES spectra. Furthermore, we also discuss performance of neural network models for predicting both local structure features, such as bond lengths and bond angles, and global chemical composition, such as the sp:sp 2 :sp 3 ratio.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Robust training of machine learning interatomic potentials with dimensionality reduction and stratified sampling

Abstract Machine learning interatomic potentials (MLIPs) enable accurate simulations of materials at scales beyond that accessible by ab initio methods and play an increasingly important role in the study and design of materials. However, MLIPs are only as accurate and robust as the data on which they are trained. Here, we present DImensionality-Reduced Encoded Clusters with sTratified (DIRECT) sampling as an approach to select a robust training set of structures from a large and complex configuration space. By applying DIRECT sampling on the Materials Project relaxation trajectories dataset with over one million structures and 89 elements, we develop an improved materials 3-body graph network (M3GNet) universal potential that extrapolates more reliably to unseen structures. We further show that molecular dynamics (MD) simulations with the M3GNet universal potential can be used instead of expensive ab initio MD to rapidly create a large configuration space for target systems. We combined this scheme with DIRECT sampling to develop a reliable moment tensor potential for titanium hydrides without the need for iterative augmentation of training structures. This work paves the way for robust high-throughput development of MLIPs across any compositional complexity.

Qi, Ji (ORCID:0000000158089931)↗
DOE OSTI2024

Neural network emulation of spontaneous fission

Large-scale computations of fission properties are an important ingredient for nuclear reaction network calculations simulating rapid neutron-capture process (the 𝑟 process) nucleosynthesis. Due to the large number of fissioning nuclei potentially contributing to the 𝑟 process, a microscopic description of fission based on nuclear density functional theory (DFT) is computationally challenging. Here, we explore the use of neural networks (NNs) to construct DFT emulators capable of predicting potential energy surfaces and collective inertia tensors across the whole nuclear chart, starting from a minimal set of DFT calculations. We use constrained Hartree-Fock-Bogoliubov (HFB) calculations to predict the potential energy and collective inertia tensor in the axial quadrupole and octupole collective coordinates, for a set of nuclei in the 𝑟-process region. We then employ NNs to emulate the HFB energy and collective inertia tensor across the considered region of the nuclear chart. Least-action pathways characterizing spontaneous fission half-lives and fragment yields are then obtained by means of the nudged elastic band method. The potential energy predicted by NNs agrees with the DFT value to within a root-mean-square error of 500 keV, and the collective inertia components agree to within an order of magnitude. These results are largely independent of the NN architecture. The exit points on the outer turning line are found to be well emulated. For the spontaneous fission half-lives the NN emulation provides values that are found to agree with the DFT predictions within a factor of 10 3 across more than 70 orders of magnitude. Neural networks are able to emulate the potential energy and collective inertia well enough to reasonably predict physical observables. Future directions of study, such as the inclusion of additional collective degrees of freedom and active learning, will improve the predictive power of microscopic theory and further enable large-scale fission studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Magnetohydrodynamics with physics informed neural operators

Abstract The modeling of multi-scale and multi-physics complex systems typically involves the use of scientific software that can optimally leverage extreme scale computing. Despite major developments in recent years, these simulations continue to be computationally intensive and time consuming. Here we explore the use of AI to accelerate the modeling of complex systems at a fraction of the computational cost of classical methods, and present the first application of physics informed neural operators (NOs) (PINOs) to model 2D incompressible magnetohydrodynamics (MHD) simulations. Our AI models incorporate tensor Fourier NOs as their backbone, which we implemented with the TensorLY package. Our results indicate that PINOs can accurately capture the physics of MHD simulations that describe laminar flows with Reynolds numbers Re ⩽ 250 . We also explore the applicability of our AI surrogates for turbulent flows, and discuss a variety of methodologies that may be incorporated in future work to create AI models that provide a computationally efficient and high fidelity description of MHD simulations for a broad range of Reynolds numbers. The scientific software developed in this project is released with this manuscript.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

xSDK: Building an ecosystem of highly efficient math libraries for exascale

Current efforts to build increasingly powerful computer architectures are opening up new avenues for more complex and higher fidelity simulations coupled with data analytics and learning, leading to new scientific insights and deeper understanding. At one extreme, exascale computers will be much faster than previous computer generations (performing 10 18 operations per second—that is, 1,000 times faster than petascale). To achieve these performance improvements, computer architectures are becoming increasingly complex, with deep memory hierarchies, very high node and core counts, and heterogeneous features such as graphics processing units (GPUs). Such architectural changes impact the full breadth of computing scales, as heterogeneity pervades even current-generation laptops, workstations, and moderate-sized clusters. While emerging advanced architectures provide unprecedented opportunities, they also present significant challenges for developers of scientific applications, such as multiphysics and multiscale codes, who must adapt their software to handle disruptive changes in architectures and new programming models that have not yet stabilized. Developers must consider increasing concurrency while reducing communication and synchronization, and other complexities such as the potential for using mixed precision to leverage the compute power available in low-precision tensor cores. On one hand, developers must implement new scientific capabilities, which in turn increase code complexity. On the other hand, the codes must be ported to new architectures, requiring the inclusion of new programming models and the restructuring of code to achieve good performance. Addressing these issues is beyond the capability of any single person or team—leading to the need for collaboration among many teams, who encapsulate their expertise in reusable software and work together to create sustainable software ecosystems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗
DOE OSTI2024

HydraGNN_Predictive_GFM_2024 - Ensemble of predictive graph foundation models for ground state atomistic materials modeling

We provide the ensemble of fifteen pre-trained graph foundation models (GFMs) for atomistic materials modeling applications. Each one of the fifteen GFMs has been trained on five open-source datasets that (once aggregated) amount to over 154 million atomistic structures, which cover over two-thirds of the natural elements of the periodic table and that comprises a broad set of organic and inorganic compounds. This vast set of atomistic structures comprises ground state configurations that are dynamically stable (i.e., equilibrated structures with atomic forces approximately close to zero values) as well as dynamically unstable structures (i.e., non-equilibrium structures with non-negligible non-zero values of atomic forces). The ensemble of datasets aggregated does NOT include excited states. The datasets have been curated to remove atomistic structures with spectral norm of the force tensor above 100 eV/angstrom. Moreover, a linear term of the energy was computed for each dataset using a linear regression model that uses the chemical concentration of each natural element as regressor. The linear term predicted by the linear regression model has been subtracted from each original energy value to perform a re-alignment of the energy values across different electronic structures approximation theories performed to generate the diverse multi-source, multi-fidelity datasets. The folder "ADIOS_files" contains the set of pre-processed datasets in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used for the development and training of GFMs in this work. The "ADIOS_files" directory contains 6 sub-directories named as follows: - ANI1x-v3.bp - MPTrj-v3.bp - OC2020-20M-v3.bp - OC2020-v3.bp - OC2022-v3.bp - qm7x-v3.bp Each sub-directory contains the pre-processed datasets converted in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used to the development, training, and performance testing of the ensemble go predictive graph foundation models. Each GFM was developed using HydraGNN (https://github.com/ORNL/HydraGNN) as underlying graph neural network (GNN) architecture. The multi-task learning (MTL) capability of HydraGNN was used to simultaneously train the GFMs on labeled values for direct predictions of energy (a total system property of an atomistic structure that measures the chemical stability) and atomic forces (an atomic level property of an atomistic structure that measures the dynamical stability). The hyper parameters of the GFM have been tuned using scalable hyperparameter optimization (HPO) algorithms implemented in the software DeepHyper (https://github.com/deephyper/deephyper). The pre-training of each HPO trial was performed using distributed data parallelism (DDP) to scale the training across 128 compute nodes of the exascale OLCF supercomputer Frontier. Each HPO trial was trained only for 10 epochs and an early stopping was performed to avoid wasting significant computational resources on GNN architectures that were clearly underperforming. For each HPO trial, the 'omnistat' tool developed by (AMD Research - Advanced Micro Device) was used to measure the total energy consumption in kWh. The ensemble of GFMs was obtained by selecting the fifteen best performing HPO trials. Four models have been selected for their clear advantage in accuracy, and these are the GFMs with IDs 229, 156, 147, 260. Additional eleven models have been selected based on judicious balance between accuracy and energy consumption needed for training, and these are the GFMs with IDs 165, 78, 137, 1, 175, 171, 181, 67, 179, 167, 351. Each selected GFM of the ensemble was continued to cumulate a total of at most 30 epochs. In some cases, the total number of epochs actually performed was les than 30 due to two combined factors: (1) the size of the GFM (i.e., the number of model parameters to train) and (2) the total wall-clock time for which the computational resources could be allocated on OLCF-Frontier. The "Ensemble_of_models" directory contains 15 sub-directories named as follows: - gfm_0.229 - gfm_0.156 - gfm_0.147 - gfm_0.260 - gfm_0.165 - gfm_0.78 - gfm_0.137 - gfm_0.1 - gfm_0.175 - gfm_0.171 - gfm_0.181 - gfm_0.67 - gfm_0.179 - gfm_0.167 - gfm_0.351 Each one of these sub-directories refers to one of the fifteen HPO trials that have been selected to continue the pre-training with at most 30 epochs. With each sub-directory associated with a specific HPO trial, the following files can be found: - config.json: file for argument parsing to develop and train an HydraGNN architecture - gfm_0.ID_epoch_N.pk: file with model parameters for HPO ID trial after N epochs of training The ensemble of fifteen GFM architectures was used for (1) ensemble averaging to stabilize the predictions of energy and atomic forces after pre-training for post-processing analysis and (2) ensemble uncertainty quantification (UQ). The code used to develop, pre-train, and load the pre-trained models for post-processing analysis is available on the ORNL-GitHub at the following link: https://github.com/ORNL/HydraGNN/tree/Predictive_GFM_2024

36 MATERIALS SCIENCE↗
DOE OSTI2024

Effective many-body interactions in reduced-dimensionality spaces through neural network models

Accurately describing properties of challenging problems in physical sciences often requires complex mathematical models that are unmanageable to tackle head on. Therefore, developing reduced-dimensionality representations that encapsulate complex correlation effects in many-body systems is crucial to advance the understanding of these complicated problems. However, a numerical evaluation of these predictive models can still be associated with a significant computational overhead. To address this challenge, in this paper we discuss a combined framework that integrates recent advances in the development of active-space representations of coupled cluster (CC) downfolded Hamiltonians with neural network approaches. The primary objective of this effort is to train neural networks to eliminate the computationally expensive steps required for evaluating hundreds or thousands of Hugenholtz diagrams, which correspond to multidimensional tensor contractions necessary for evaluating a many-body form of downfolded effective Hamiltonians. Using small molecular systems (the H 2 O and HF molecules) as examples, we demonstrate that training neural networks employing effective Hamiltonians for a few nuclear geometries of molecules can accurately interpolate or extrapolate their forms to other geometrical configurations characterized by different intensities of correlation effects. We also discuss differences between effective interactions that define CC downfolded Hamiltonians with those of bare Hamiltonians defined by Coulomb interactions in the active spaces. Published by the American Physical Society 2024

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Bridging the Gap Between LLMs and LNS with Dynamic Data Format and Architecture Codesign

Deep neural networks (DNNs) have achieved tremendous success in the past few years. However, their training and inference demand exceptional computational and memory resources. Quantization has been shown as an effective approach to mitigate the cost, with the mainstream data types reduced from FP32 to FP16/BF16 and recently FP8 in the latest NVIDIA H100 GPUs. With increasingly aggressive quantization, however, the conventional floating-point formats suffer from limited precision in representing numbers around zero. Recently, NVIDIA demonstrated the potential of using a Logarithmic Number System (LNS) for the next generation of tensor cores. While LNS mitigates the hurdles in representing small numbers, in this work we observed a mismatch between LNS and the emerging Large Language Models (LLM), where LLM exhibits significant outliers when directly adopting the LNS format. In this paper, we present a data-format/architecture codesign to bright this gap. On the format side, we propose a dynamic LNS format to flexibly represent outliers at a higher precision, by exploiting asymmetry in the LNS representation and identifying outliers through a per-vector basis. On the architecture side, for demonstration, we realize the dynamic LNS format in a systolic array, which can handle the irregularity of the outliers at runtime. We implement our approach on an Alveo U280 FPGA as a prototype. Experimental results show that our design can effectively handle the outliers and resolve the mismatch between LNS and LLM, contributing to an accuracy improvement of 15.4% and 16% over the floating-point and the original LNS baselines, using four state-of-the-art LLM models. Our observation and design lay a solid foundation for the large-scale adoption of the LNS format in the next-generation deep learning hardware.

Haghi, Pouya↗
DOE OSTI2023

Fundamental aspects of Spacetime and Quantum Fields

The proposal contained two goals: firstly, placing fundamental bound on thermalization in Quantum Field Theories (QFTs) and, secondly, developing our understanding of emergent spacetime from matrices through concrete models. Since the previous reporting period, in collaboration with Sean Hartnoll we have continued our study of entanglement edge modes in matrix quantum mechanics (MQM). This has resulted in two papers. The first applies our construction for the Matrix Quantum Hall system first to fuzzy sphere states known to correspond to stringy M2-branes in MQM. Entanglement in these states using machine learning methods have also been studied by Sean Hartnoll and Xizhi Han in previous work done under this grant. Our construction builds on this work, and further demonstrates how area laws on fuzzy geometries emerge from strongly coupled systems. The second paper generalizes this construction to all noncommutative geometries with curvature much larger than the noncommutativity parameter. We demonstrate that despite UV/IR mixing effects, the structure of entanglement edge mode irreducible representations is determined by the boundary area of subsystems. On manifolds without global symmetries, we have demonstrated that nonlocal effects inherent to noncommutative geometries resum into a change of frame of the metric structure, similar to the change from string frame to Einstein frame for entanglement entropies calculated in string theory. These advancements lay the groundwork for future progress in the understanding of emergent geometry from large-N theories. Using these techniques, we are currently working on applying our methods to noncom mutative geometries whose construction is not so well understood, such as the fuzzy 5-sphere. Despite their opacity these objects are quite important, as string physics in the bulk of holographic systems bears many features of noncommutative geometry. We have also laid the groundwork of applying our methods to tensor networks, one of the most powerful models for understanding how geometry emerges from entanglement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Coarse-grain cluster analysis of tensors with application to climate biome identification

A tensor provides a concise way to codify the interdependence of complex data. Treating a tensor as a d-way array, each entry records the interaction between the different indices. Clustering provides a way to parse the complexity of the data into more readily understandable information. Clustering methods are heavily dependent on the algorithm of choice, as well as the chosen hyperparameters of the algorithm. However, their sensitivity to data scales is largely unknown. In this work, we apply the discrete wavelet transform to analyze the effects of coarse-graining on clustering tensor data. We are particularly interested in understanding how scale affects clustering of the Earth's climate system. The discrete wavelet transform allows classification of the Earth's climate across a multitude of spatial-temporal scales. The discrete wavelet transform is used to produce an ensemble of classification estimates, as opposed to a single classification. Each element of the ensemble is a clustering at a different spatial-temporal scale. Information theoretic approaches are used to identify important scale lengths in clustering the L15 Climate Datset. We also discover a sub-collection of the ensemble that spans the majority of the variance observed, allowing for efficient consensus clustering techniques that can be used to identify climate biomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Bridging the gap between simulated and experimental ionic conductivities in lithium superionic conductors

Lithium superionic conductors (LSCs) are of major importance as solid electrolytes for next-generation all-solid-state lithium-ion batteries. While ab initio molecular dynamics have been extensively applied to study these materials, there are often large discrepancies between predicted and experimentally measured ionic conductivities and activation energies due to the high temperatures and short time scales of such simulations. Here, we present a strategy to bridge this gap using moment tensor potentials (MTPs). We show that MTPs trained on energies and forces computed using the van der Waals optB88 functional yield much more accurate lattice parameters, which in turn leads to accurate prediction of ionic conductivities and activation energies for the Li 0·33 La 0·56 TiO 3 , Li 3 YCl 6 and Li 7 P 3 S 11 LSCs. NPT MD simulations using the optB88 MTPs also reveal that all three LSCs undergo a transition between two quasi-linear Arrhenius regimes at relatively low temperatures. This transition can be traced to an increase in the number and diversity of diffusion pathways, in some cases with a change in the dimensionality of diffusion. Furthermore, this work presents not only an approach to develop high accuracy MTPs, but also outlines the diffusion characteristics for LSCs which is otherwise inaccessible through ab initio computation.

25 ENERGY STORAGE↗
DOE OSTI2021

Extended Lagrangian Born–Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models

We report extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Data-Efficient Dimensionality Reduction and Surrogate Modeling of High-Dimensional Stress Fields

Tensor datatypes representing field variables like stress, displacement, velocity, etc., have increasingly become a common occurrence in data-driven modeling and analysis of simulations. Numerous methods [such as convolutional neural networks (CNNs)] exist to address the meta-modeling of field data from simulations. As the complexity of the simulation increases, so does the cost of acquisition, leading to limited data scenarios. Modeling of tensor datatypes under limited data scenarios remains a hindrance for engineering applications. Here, in this article, we introduce a direct image-to-image modeling framework of convolutional autoencoders enhanced by information bottleneck loss function to tackle the tensor data types with limited data. The information bottleneck method penalizes the nuisance information in the latent space while maximizing relevant information making it robust for limited data scenarios. The entire neural network framework is further combined with robust hyperparameter optimization. We perform numerical studies to compare the predictive performance of the proposed method with a dimensionality reduction-based surrogate modeling framework on a representative linear elastic ellipsoidal void problem with uniaxial loading. The data structure focuses on the low-data regime (fewer than 100 data points) and includes the parameterized geometry of the ellipsoidal void as the input and the predicted stress field as the output. The results of the numerical studies show that the information bottleneck approach yields improved overall accuracy and more precise prediction of the extremes of the stress field. Additionally, an in-depth analysis is carried out to elucidate the information compression behavior of the proposed framework.

artificial intelligence↗
DOE OSTI2026

Correlating Protein Dynamics and Catalytic Activity of a Model Hydrogenase Using Paramagnetic and Biological Nuclear Magnetic Resonance Spectroscopy

Rational catalyst design remains a significant challenge, with electronic structure, steric, and electrostatic effects known to contribute to activity. Recently, dynamics has been recognized as another factor that impacts catalysis, though identifying and predicting these effects has remained out of reach. Nickel-substituted rubredoxin (NiRd), a protein-based mimic of a hydrogenase enzyme, serves as a model catalytic system in which dynamics can be systematically investigated with respect to activity. While over 30 secondary-sphere mutants of NiRd have been shown to be catalytically active, no significant correlation was observed between the rates and catalytic overpotential or electronic structure, prompting questions about the protein-derived factors that modulate activity. Here, in this work, NMR spectroscopy was used to investigate the roles of substrate accessibility, protein dynamics, and protein stability in controlling catalysis. Significant paramagnetic effects from the nickel center (S = 1) isolate the methylene proton resonances of the metal-coordinating cysteine residues. The sensitivity of resonance positions and linewidths to local environment offers an opportunity to study dynamical molecular changes around the metal center with high resolution. Machine learning algorithms were employed to identify correlations between the catalytic activity and the paramagnetic NMR spectra. These analyses revealed spectroscopic features of specific cysteine protons that report on catalytic overpotential and increased turnover rates, which are further supported by the results obtained using high-field NMR techniques. Collectively, these studies indicate the potential for multifrequency NMR techniques to resolve key contributors to catalytic activity and highlight the importance of local and outer-sphere dynamics.

Protein Engineering↗
DOE OSTI2026

Local reduced-order modeling for electrostatic plasmas by physics-informed solution manifold decomposition

Despite advancements in high-performance computing and modern numerical algorithms, computational cost remains prohibitive for multi-query kinetic plasma simulations. Here, in this work, we develop data-driven reduced-order models (ROMs) for collisionless electrostatic plasma dynamics, based on the kinetic Vlasov-Poisson equation. Our ROM approach projects the equation onto a linear subspace defined by the proper orthogonal decomposition (POD) modes. We introduce an efficient tensorial method to update the nonlinear term using a precomputed third-order tensor. We capture multiscale behavior with a minimal number of POD modes by decomposing the solution manifold into multiple time windows and creating temporally local ROMs. We consider two strategies for decomposition: one based on the physical time and the other based on the electric field energy. Applied to the 1D1V Vlasov–Poisson simulations, that is, prescribed E-field, Landau damping, and two-stream instability, we demonstrate that our ROMs accurately capture the total energy of the system both for parametric and time extrapolation cases. The temporally local ROMs are more efficient and accurate than the single ROM. In addition, in the two-stream instability case, we show that the energy-windowing reduced-order model (EW-ROM) is more efficient and accurate than the time-windowing reduced-order model (TW-ROM). With the tensorial approach, EW-ROM solves the equation approximately 90 times faster than Eulerian simulations while maintaining a maximum relative error of 7.5% for the training data and 11% for the testing data.

Electrostatic plasmas↗