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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Improved Treatment of 1–4 Interactions in Force Fields for Molecular Dynamics Simulations

Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled nonbonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield accurate torsional energy barriers, it often leads to inaccurate forces and erroneous geometries and creates an interdependence between dihedral terms and nonbonded interactions, complicating parametrization and reducing transferability. Here, in this paper, we demonstrate that 1-4 interactions can be accurately modeled using only bonded coupling terms, eliminating the need for arbitrarily scaled nonbonded interactions altogether. Furthermore, by leveraging the automated parametrization capabilities of the Q-Force toolkit, we efficiently determine the necessary coupling terms without the need for manual adjustment. Our approach is first validated on a range of small molecule systems, encompassing both flexible and rigid structures, and shows a significant improvement in force field accuracy, obtaining subkcal/mol mean absolute error for every molecule tested. We further extend the bonded-only model for 1-4 interactions to Amber ff14sb, CHARMM36, and OPLS-AA force fields to reproduce ab initio gas and implicit solvent ϕ,ψ surfaces of alanine dipeptide.

Abdullah, Aalim S. [University of California, Berk↗
DOE OSTI2024

Machine Learning-Based Identification of the Interface Regions for Coupling Local and Nonlocal Models

Local-nonlocal coupling approaches provide a means to combine the computational efficiency of local models and the accuracy of nonlocal models. However, the coupling process can be challenging, requiring expertise to identify the interface between local and nonlocal regions. Here, this study introduces a machine learning-based approach to automatically detect the regions in which the local and nonlocal models should be used. The method uses loading functions evaluated at grid points to decide the model selection at those points. Training of the networks is based on datasets provided by classes of loading functions for which reference coupling configurations are computed using accurate coupled solutions, where accuracy is measured in terms of the relative error between the solution to the coupling approach and the solution to the nonlocal model. We study two approaches that vary in data structure. The first, the full-domain input data approach, uses the entire load vector and outputs a complete label vector, performing a global classification. The second, a window-based approach, processes loads into windows and addresses the problem as a node-wise classification where each window's central point is classified individually. The classification problems are solved via deep learning algorithms based on convolutional neural networks. The performance of these approaches is studied on one-dimensional numerical examples using F1-scores and accuracy metrics. Notably, the windowing approach achieves an accuracy of 0.96 and an F1-score of 0.97, highlighting its potential to automate coupling processes effectively and enhance computational efficiency in material science applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control

Abstract Algal cultivations are strongly influenced by light and dark cycles. In this study, genome-scale metabolic models were applied to optimize nutrient supply during alternating light and dark cycles of Chlorella vulgaris . This approach lowered the glucose requirement by 75% and nitrate requirement by 23%, respectively, while maintaining high final biomass densities that were more than 80% of glucose-fed heterotrophic culture. Furthermore, by strictly controlling glucose feeding during the alternating cycles based on model-input, yields of biomass, lutein, and fatty acids per gram of glucose were more than threefold higher with cycling compared to heterotrophic cultivation. Next, the model was incorporated into open-loop and closed-loop control systems and compared with traditional fed-batch systems. Closed-loop systems which incorporated a feed-optimizing algorithm increased biomass yield on glucose more than twofold compared to standard fed-batch cultures for cycling cultures. Finally, the performance was compared to conventional proportional-integral-derivative (PID) controllers. Both simulation and experimental results exhibited superior performance for genome-scale model process control (GMPC) compared to traditional PID systems, reducing the overall measured value and setpoint error by 80% over 8 h. Overall, this approach provides researchers with the capability to enhance nutrient utilization and productivity of cell factories systematically by combining genome-scale models and controllers into an integrated platform with superior performance to conventional fed-batch and PID methodologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy of solute in solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of conformational entropy of solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal/mol for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

25 ENERGY STORAGE↗
DOE OSTI2020

Suggested Modifications for Bifacial Capacity Testing

Capacity tests such as those described in ASTM 2848 and IEC 61724-2 are widely used during the contracting and acceptance testing of photovoltaic systems. With the increasing deployment of bifacial photovoltaic modules, there is a need to develop a standardized approach to capacity test these systems. Although variability and bias error were inherently higher for the measured capacity of bifacial systems, they could be reduced to a level consistent with the monofacial reference system by appropriate incorporation of rear irradiance—either measured or modeled. Three field installations provided bifacial system capacity that was measured with a mean bias error and standard deviation within 1% over the 2–10-month observation period. Capacity test accuracy could be improved further by using the measured back-of-module temperature and the IEC 61724-2 test method for well curated systems.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2022

Stability Analysis of Substituted Cobaltocenium [Bis(cyclopentadienyl)cobalt(III)] Employing Chemistry-Informed Neural Networks

Cobaltocenium derivatives are promising components of the anion exchange membranes due to their excellent thermal and alkaline stability under the operating conditions of a fuel cell. Here we present an efficient modeling approach of assessing the chemical stability of substituted cobaltocenium CoCp 2 + based on the computed electronic structure enhanced by machine learning techniques. Within the aqueous environment, the positive charge of the metal cation is balanced by the hydroxide anion through formation of the CoCp 2 + OH¯ complexes, whose dissociation is studied within the implicit solvent employing density functional theory. The data set of about 118 species based on 42 substituent groups characterized by a range of electron- donating (ED) and electron-withdrawing (EW) properties is constructed and analyzed. Given 12 carefully chosen chemistry-informed descriptors of the complexes and relevant fragments, the stability of the complexes is found to strongly correlate with the energies of the highest occupied and lowest unoccupied molecular orbitals, modulated by a switching function of the Hirshfeld charge. The latter is used as a measure of the electron withdrawing-donating character of the substituents. Based on this observation from the conventional regression analysis, two fully connected, feed-forward neural network (FNN) models with different unit structures, called the chemistry-informed (CINN) and the quadratic (QNN) neural networks, are developed. Both models predict the bond dissociation energies of the cobaltocenium complexes with mean relative errors less than 5.40% and average absolute errors less than 0.94 kcal/mol. The results show the potential of QNN to efficiently capture more complex relationships. Here, the concept of incorporating the domain (chemical) knowledge/insight into the neural network structure paves the way to applications of machine learning techniques with small data sets, ultimately leading to better predictive models compared to the conventional regression analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Data assimilation empowered neural network parametrizations for subgrid processes in geophysical flows

In the past couple of years, there has been a proliferation in the use of machine learning approaches to represent subgrid-scale processes in geophysical flows with an aim to improve the forecasting capability and to accelerate numerical simulations of these flows. Despite its success for different types of flow, the online deployment of a data-driven closure model can cause instabilities and biases in modeling the overall effect of subgrid-scale processes, which in turn leads to inaccurate prediction. To tackle this issue, we exploit the data assimilation technique to correct the physics-based model coupled with the neural network as a surrogate for unresolved flow dynamics in multiscale systems. In particular, we use a set of neural network architectures to learn the correlation between resolved flow variables and the parametrizations of unresolved flow dynamics and formulate a data assimilation approach to correct the hybrid model during their online deployment. We illustrate our framework in a set of applications of the multiscale Lorenz 96 system for which the parametrization model for unresolved scales is exactly known, and the two-dimensional Kraichnan turbulence system for which the parametrization model for unresolved scales is not known a priori. Our analysis, therefore, comprises a predictive dynamical core empowered by (i) a data-driven closure model for subgrid-scale processes, (ii) a data assimilation approach for forecast error correction, and (iii) both data-driven closure and data assimilation procedures. We show significant improvement in the long-term prediction of the underlying chaotic dynamics with our framework compared to using only neural network parametrizations for future prediction. Moreover, we demonstrate that these data-driven parametrization models can handle the non-Gaussian statistics of subgrid-scale processes, and effectively improve the accuracy of outer data assimilation workflow loops in a modular nonintrusive way.

42 ENGINEERING↗
DOE OSTI2026

Ensemble Effects on Hydroxide Bond Dissociation Free Energies in Polyoxovanadate Clusters

Understanding structure-property relationships is foundational to numerous modern chemistries, such as proton-coupled electron transfer (PCET). However, an experimentally measured property is the result of the behavior from an ensemble of molecules. Neglecting ensemble effects, especially under complex chemical environments, may obfuscate these relationships and lead to discrepancies between theory and experiment. In this work, we demonstrate the impact of configurational entropy and local chemical environments on hydroxide bond dissociation free energies [BDFE- (O−H)] for a set of polyoxovanadate nanoclusters, at ambient conditions. The O−H bond strengths are investigated via density functional theory (DFT) coupled with statistical thermodynamic analysis and bilinear modeling, and compared with previous experimental results on the same systems, namely electrochemical solutions of: [V 6 O 13−x (OH) x (TRIOL R ) 2 ] −2 (x = 2, 4, 6; R = NO 2 , Me) and [V 6 O 11−x (OMe) 2 (OH) x (TRIOL NO 2 ) 2 ] −2 (x = 2, 4). Interestingly, we find that ensemble effects, even at room temperature, can account for a significant portion of the BDFE(O−H) trend with the degree of reduction via H atom binding, which cannot be fully captured by single-structure, static DFT calculations. Moreover, we find that the ensemble effects may be replicated statistically, requiring only enumeration of energetically accessible H-binding sites. With the ensemble effects resolved, we present a simple bilinear model to reconcile remaining biases between experiment and ensemble-informed theory, which corelate with clusterspecific electronic environment differences. The bilinear model achieves outstanding accuracy vs experiments with a root-mean squared error of 0.4 kcal/mol. Finally, based on the physicochemical characteristics of hydrogen interaction with polyoxometalates, we present a simple methodology that captures the BDFE(O−H) trend while dramatically reducing required DFT calculations by 98% and achieving accuracy within 1 kcal/mol. Overall, this work elucidates the roles and structural origins of configurational entropy and chemical effects on polyoxometalate hydroxide bond energies, with potential applicability to various atomically precise metal oxide systems. Importantly, it introduces models for rapid and highly accurate property calculations in connection with experiments.

Cluster chemistry↗
DOE OSTI2023

Variational quantum simulation of the critical Ising model with symmetry averaging

Here we investigate the use of deep multiscale entanglement renormalization ansatz (DMERA) circuits as a variational ansatz. We use the exactly solvable one-dimensional critical transverse-field Ising model as a test bed. Numerically exact simulation of the quantum circuit ansatz can in this case be carried out to hundreds of qubits by exploiting efficient classical algorithms for simulating matchgate circuits. We find that, for this system, the DMERA strongly outperforms a standard quantum approximate optimization algorithm (QAOA)–style ansatz, and that a major source of systematic error in correlation functions approximated using the DMERA is the breaking of the translational and Kramers-Wannier symmetries of the transverse-field Ising model. We are able to reduce this error by up to four orders of magnitude by symmetry averaging, without incurring additional cost in qubits or circuit depth. Here, we propose that this technique for mitigating systematic error could be applied to noisy intermediate-scale quantum (NISQ) simulations of physical systems with other symmetries.

1-dimensional spin chains↗
DOE OSTI2022

Verification of MOOSE/Bison's Heat Conduction Solver Using Combined Spatiotemporal Convergence Analysis

Bison is a computational physics code that uses the finite element method to model the thermo-mechanical response of nuclear fuel. Since Bison is used to inform high-consequence decisions, it is important that its computational results are reliable and predictive. One important step in assessing the reliability and predictive capabilities of a simulation tool is the verification process, which quantifies numerical errors in a discrete solution relative to the exact solution of the mathematical model. One step in the verification process—called code verification—ensures that the implemented numerical algorithm is a faithful representation of the underlying mathematical model, including partial differential or integral equations, initial and boundary conditions, and auxiliary relationships. In this paper, the code verification process is applied to spatiotemporal heat conduction problems in Bison. Simultaneous refinement of the discretization in space and time is employed to reveal any potential mistakes in the numerical algorithms for the interactions between the spatial and temporal components of the solution. For each verification problem, the correct spatial and temporal order of accuracy is demonstrated for both first- and second-order accurate finite elements and a variety of time-integration schemes. Furthermore, these results provide strong evidence that the Bison numerical algorithm for solving spatiotemporal problems reliably represents the underlying mathematical model in MOOSE. The selected test problems can also be used in other simulation tools that numerically solve for conduction or diffusion.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Deep learning surrogate model for kinetic Landau-fluid closure with collision

In this work, the kinetic Landau-fluid (LF) closure with collision and periodic boundary condition is used in the development of the deep learning (DL) surrogate model. A classical neural network, namely, feedforward neural network or sometimes termed multilayer perceptron, is constructed and trained to learn the kinetic LF closure in the static limit and arbitrary mean free path in configuration space. The preliminary relation between best hyperparameters and critical parameters for data generation is found. Compared with the numerical approach (non-Fourier method) of the LF closure, the deep learning surrogate model shows an order of magnitude of improvement in terms of accuracy. Perhaps most importantly, the surrogate model closure has been integrated for the first time with fluid simulations. Our DL-enabled fluid simulations, for the first time, give the correct Landau damping rate for a wide range of wave vectors, while the Hammett–Perkins closure cannot produce the correct damping rate. We correctly connect the collisionless Hammett–Perkins closure and collisional Braginskii closure to reproduce the intrinsic nonlocal feature of the heat flux with DL techniques. We address the most concerning error accumulation problem and find that simulations with the deep learning surrogate model are as good as, if not better than, simulations with the analytic closure in terms of long-term numerical stability in the linear Landau damping test.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Verification of a quasi-linear model for gyrokinetic turbulent transport

The verification and calibration of a new quasi-linear transport model with a large database of gyrokinetic turbulence simulations is presented in this paper. In a previous paper (Staebler et al 2020 Plasma Phys. Control. Fusion 63 015013), a model for the saturated spectrum of electric potential fluctuations was developed based on the properties of the non-linear 3D spectrum. In this paper, a modification to the overall multiplicative factor in this model is found to be necessary to improve the fit to scans of the temperature and density gradients. The error in the fit of the quasi-linear fluxes of electron and ion energy fluxes is significantly better than for previous saturation models. The spectral shift model for the impact of equilibrium E × B velocity shear (Staebler et al 2013 Phys. Rev. Lett. 110 055003) and the zonal flow mixing model for electron-scale turbulence (Staebler et al 2016 Phys. Plasmas 23 062518) are both revised to be compatible with this new model. Furthermore, the models for the loss of bounce averaging and electron collisions in the TGLF reduced linear equations (Staebler et al 2005 Phys. Plasmas 12 102508) are also changed to improve the linear eigenmodes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Vertical-Axis Wind Turbine Steady and Unsteady Aerodynamics for Curved Deforming Blades

Vertical-axis wind turbines’ simpler design and low center of gravity make them ideal for floating wind applications. However, efficient design optimization of floating systems requires fast and accurate models. Low-fidelity vertical-axis turbine aerodynamic models, including double multiple streamtube and actuator cylinder theory, were created during the 1980s. Commercial development of vertical-axis turbines all but ceased in the 1990s until around 2010 when interest resurged for floating applications. Despite the age of these models, the original assumptions (2-D, rigid, steady, straight bladed) have not been revisited in full. When the current low-fidelity formulations are applied to modern turbines in the unsteady domain, aerodynamic load errors nearing 50% are found, consistent with prior literature. However, a set of steady and unsteady modifications that remove the majority of error is identified, limiting it near 5%. This paper shows how to reformulate the steady models to allow for unsteady inputs including turbulence, deforming blades, and variable rotational speed. A new unsteady approximation that increases numerical speed by 5–10× is also presented. Combined, these modifications enable full-turbine unsteady simulations with accuracy comparable to higher-fidelity vortex methods, but over 5000× faster.

17 WIND ENERGY↗
DOE OSTI2026

Active learning emulators for nuclear two-body scattering in momentum space

In this work we extend the active learning emulators for two-body scattering in coordinate space with error estimation, recently developed by Maldonado et al. [Phys. Rev. C 112, 024002], to coupled-channel scattering in momentum space. Our full-order model (FOM) solver is based on the Lippmann-Schwinger integral equation for the scattering t-matrix as opposed to the radial Schrödinger equation. We use (Petrov-)Galerkin projections and high-fidelity calculations at a few snapshots across the parameter space of the interaction to construct efficient reduced-order models (ROMs), trained by a greedy algorithm for locally optimal snapshot selection. Both the FOM solver and the corresponding ROMs are implemented efficiently in Python using Google's JAX library. We present results for emulating scattering phase shifts in coupled and uncoupled channels and cross sections, and assess the accuracy of the developed ROMs and their computational speedup factors. We also develop emulator error estimation for both the t-matrix and the total cross section. The software framework for reproducing and extending our results is publicly available. Together with our recent advances in developing active-learning emulators for three-body scattering, these emulator frameworks set the stage for full Bayesian calibrations of chiral nuclear interactions and optical models against scattering data with quantified emulator errors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Rapid wavefield forecasting for earthquake early warning via deep sequence to sequence learning

We propose a deep learning model, WaveCastNet, to forecast high-dimensional wavefields. WaveCastNet integrates a convolutional long expressive memory architecture into a sequence-to-sequence forecasting framework, enabling it to model long-term dependencies and multiscale patterns in both space and time. By sharing weights across spatial and temporal dimensions, WaveCastNet requires significantly fewer parameters than more resource-intensive models such as transformers, resulting in faster inference times. Crucially, WaveCastNet also generalizes better than transformers to rare and critical seismic scenarios, such as high-magnitude earthquakes. Here, we show the ability of the model to predict the intensity and timing of destructive ground motions in real time, using simulated data from the San Francisco Bay Area. Furthermore, we demonstrate its zero-shot capabilities by evaluating WaveCastNet on real earthquake data. Our approach does not require estimating earthquake magnitudes and epicenters, steps that are prone to error in conventional methods, nor does it rely on empirical ground-motion models, which often fail to capture strongly heterogeneous wave propagation effects.

Geophysics↗
DOE OSTI2021

Surrogate Model of Flexible Research Platform EnergyPlus Models to Enable Sensitivity Analysis

This letter report describes the surrogate models developed from the EnergyPlus model of Oak Ridge National Laboratory’s Flexible Research Platform. Two data-driven black-box models were developed, and the outputs of the surrogate models were compared with the EnergyPlus model. The two models developed are a multilayer perceptron deep learning model, and a long short-term memory (LSTM) neural network model. The three factors for selecting the black-box models are scalability, computation time, and accuracy. A total of 107 input variables were the dominant variables in determining the outputs of building energy consumptions and thermal comfort. A total of 54 output variables were identified as the prediction targets, including the system- and zone-level outputs. The large set of the simulation cases were generated by integrating sensor errors into an emulator based on EnergyPlus and Python EMS, which includes advanced control sequences from ASHRAE Guideline 36-2018: High-Performance Sequences of Operation. The surrogate models were developed based on a set of large-scale simulation runs (i.e., 4,000 runs) on a cloud platform. The comparison analysis shows that the two black-box models had good accuracy for predicting new outputs for sensitivity analysis using the root mean square error metric. As a next step, the developed surrogate models will be used to perform sensitivity analysis for different sensor impacts (e.g., sensor types, sensor locations).

42 ENGINEERING↗
DOE OSTI2023

Liouvillian dynamics of the open Schwinger model: String breaking and kinetic dissipation in a thermal medium

Understanding the dynamics of bound state formation is one of the fundamental questions in confining quantum field theories such as Quantum Chromodynamics (QCD). One hadronization mechanism that has garnered significant attention is the breaking of a string initially connecting a fermion and an antifermion. Deepening our understanding of real-time string-breaking dynamics with simpler, lower dimensional models like the Schwinger model can improve our understanding of the hadronization process in QCD and other confining systems found in condensed matter and statistical systems. Here in this paper, we consider the string-breaking dynamics within the Schwinger model and investigate its modification inside a thermal medium, treating the Schwinger model as an open quantum system coupled to a thermal environment. Within the regime of weak coupling between the system and environment, the real-time evolution of the system can be described by a Lindblad evolution equation. We analyze the Liouvillian gaps of this Lindblad equation and the time dependence of the system’s von Neumann entropy. We observe that the late-time relaxation rate decreases as the environment correlation length increases. Moreover, when the environment correlation length is infinite, the system exhibits two steady states, one in each of the sectors with definite charge-conjugation-parity (CP) quantum numbers. For parameter regimes where an initial string breaks in vacuum, we observe a delay of the string breaking in the medium, due to kinetic dissipation effects. Conversely, in regimes where an initial string remains intact in vacuum time evolution, we observe string breaking (melting) in the thermal medium. We further discuss how the Liouvillian dynamics of the open Schwinger model can be simulated on quantum computers and provide an estimate of the associated Trotter errors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Code Verification of Multiple Physics-Fidelity Models in Hypersonic Aerodynamics

Hypersonic aerodynamics models exist across a range of physics fidelities with associated computational expenses. These models may be run independently or in a multifidelity framework that leverages their complementary strengths of speed for lower-fidelity and accuracy for higher-fidelity models. This work presents applied code verification of two lower-fidelity models contained within the Sandia hypersonic aerodynamics code. Each model has a different form that requires individualized verification approaches, including comparison to analytical solutions as well as manufactured solutions with order-of-accuracy testing. In conclusion, results of this effort include the identification and resolution of code errors and shortcomings, as well as the demonstration of code correctness and consistency for both models.

Aerodynamics↗