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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.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

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

Optimization on Manifolds via Graph Gaussian Processes

This paper integrates manifold learning techniques within a Gaussian process upper confidence bound algorithm to optimize an objective function on a manifold. Our approach is motivated by applications where a full representation of the manifold is not available and querying the objective is expensive. We rely on a point cloud of manifold samples to define a graph Gaussian process surrogate model for the objective. Query points are sequentially chosen using the posterior distribution of the surrogate model given all previous queries. We establish regret bounds in terms of the number of queries and the size of the point cloud. Several numerical examples complement the theory and illustrate the performance of our method.

Bayesian optimization↗
DOE OSTI2025

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Compiling Quantum Circuits for Dynamically Field-Programmable Neutral Atoms Array Processors

Dynamically field-programmable qubit arrays (DPQA) have recently emerged as a promising platform for quantum information processing. In DPQA, atomic qubits are selectively loaded into arrays of optical traps that can be reconfigured during the computation itself. Leveraging qubit transport and parallel, entangling quantum operations, different pairs of qubits, even those initially far away, can be entangled at different stages of the quantum program execution. Such reconfigurability and non-local connectivity present new challenges for compilation, especially in the layout synthesis step which places and routes the qubits and schedules the gates. In this paper, we consider a DPQA architecture that contains multiple arrays and supports 2D array movements, representing cutting-edge experimental platforms. Within this architecture, we discretize the state space and formulate layout synthesis as a satisfiability modulo theories problem, which can be solved by existing solvers optimally in terms of circuit depth. For a set of benchmark circuits generated by random graphs with complex connectivities, our compiler OLSQ-DPQA reduces the number of two-qubit entangling gates on small problem instances by 1.7x compared to optimal compilation results on a fixed planar architecture. To further improve scalability and practicality of the method, we introduce a greedy heuristic inspired by the iterative peeling approach in classical integrated circuit routing. Using a hybrid approach that combined the greedy and optimal methods, we demonstrate that our DPQA-based compiled circuits feature reduced scaling overhead compared to a grid fixed architecture, resulting in 5.1X less two-qubit gates for 90 qubit quantum circuits. These methods enable programmable, complex quantum circuits with neutral atom quantum computers, as well as informing both future compilers and future hardware choices.

Physics↗
DOE OSTI2021

A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure

In this work, cascading transmission line failures are studied through a dynamical model of the power system operating under fixed conditions. The power grid is modeled as a stochastic dynamical system where first-principles electromechanical dynamics are excited by small Gaussian disturbances in demand and generation around a specified operating point. In this context, a single line failure is interpreted in a large deviation context as a first escape event across a surface in phase space defined by line security constraints. The resulting system of stochastic differential equations admits a transverse decomposition of the drift, which leads to considerable simplification in evaluating the quasipotential (rate function) and, consequently, computation of exit rates. Tractable expressions for the rate of transmission line failure in a restricted network are derived from large deviation theory arguments and validated against numerical simulations. Extensions to realistic settings are considered, and individual line failure models are aggregated into a Markov model of cascading failure inspired by chemical kinetics. Cascades are generated by traversing a graph composed of weighted edges representing transitions to degraded network topologies. Numerical results indicate that the Markov model can produce cascades with qualitative power-law properties similar to those observed in empirical cascades.

Kinetic Monte Carlo, rare events, Cascading Failur↗
DOE OSTI2022

Entropic lens on stabilizer states

The n-qubit stabilizer states are those left invariant by a 2 n -element subset of the Pauli group. The Clifford group is the group of unitaries which take stabilizer states to stabilizer states; a physically motivated generating set, the Hadamard, phase, and controlled-not (cnot) gates which comprise the Clifford gates, impose a graph structure on the set of stabilizers. We explicitly construct these structures, the “reachability graphs,” at n ≤ 5. When we consider only a subset of the Clifford gates, the reachability graphs separate into multiple, often complicated, connected components. Seeking an understanding of the entropic structure of the stabilizer states, which is ultimately built up by cnot gate applications on two qubits, we are motivated to consider the restricted subgraphs built from the Hadamard and cnot gates acting on only two of the n qubits. We show how the two subgraphs already present at two qubits are embedded into more complicated subgraphs at three and four qubits. We argue that no additional types of subgraph appear beyond four qubits, but that the entropic structures within the subgraphs can grow progressively more complicated as the qubit number increases. Starting at four qubits, some of the stabilizer states have entropy vectors which are not allowed by holographic entropy inequalities. Here, we comment on the nature of the transition between holographic and nonholographic states within the stabilizer reachability graphs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning

Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. As a result, the test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Crystal structure of ponazuril, C 18 H 14 F 3 N 3 O 6 S

The crystal structure of ponazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Ponazuril crystallizes in space group P2 1 /c (#14) with a = 8.49511(6), b = 12.38696(6), c = 18.84239(17) Å, β = 96.7166(4)°, V = 1969.152(12) Å 3 , and Z = 4. N–H∙∙∙O hydrogen bonds link the molecules into chains along the a-axis, with a graph set C1,1(6). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Entanglement perspective on the quantum approximate optimization algorithm

Many quantum algorithms seek to output a specific bitstring solving the problem of interest—or a few if the solution is degenerate. It is the case for the quantum approximate optimization algorithm (QAOA) in the limit of large circuit depth, which aims to solve quadratic unconstrained binary optimization problems. Hence, the expected final state for these algorithms is either a product state or a low-entangled superposition involving a few bitstrings. What happens in between the initial N -qubit product state | 0 〉 ⊗ N and the final one regarding entanglement? Here, we consider the QAOA algorithm for solving the paradigmatic MaxCut problem on different types of graphs. We study the entanglement growth and spread resulting from randomized and optimized QAOA circuits and find that there is a volume-law entanglement barrier between the initial and final states. We also investigate the entanglement spectrum in connection with random matrix theory. In addition, we compare the entanglement production with a quantum annealing protocol aiming to solve the same MaxCut problems. Finally, we discuss the implications of our results for the simulation of QAOA circuits with tensor network-based methods relying on low-entanglement for efficiency, such as matrix product states.

Dupont, Maxime↗
DOE OSTI2022

Multi-task graph neural networks for simultaneous prediction of global and atomic properties in ferromagnetic systems *

Abstract We introduce a multi-tasking graph convolutional neural network, HydraGNN, to simultaneously predict both global and atomic physical properties and demonstrate with ferromagnetic materials. We train HydraGNN on an open-source ab initio density functional theory (DFT) dataset for iron-platinum with a fixed body centered tetragonal lattice structure and fixed volume to simultaneously predict the mixing enthalpy (a global feature of the system), the atomic charge transfer, and the atomic magnetic moment across configurations that span the entire compositional range. By taking advantage of underlying physical correlations between material properties, multi-task learning (MTL) with HydraGNN provides effective training even with modest amounts of data. Moreover, this is achieved with just one architecture instead of three, as required by single-task learning (STL). The first convolutional layers of the HydraGNN architecture are shared by all learning tasks and extract features common to all material properties. The following layers discriminate the features of the different properties, the results of which are fed to the separate heads of the final layer to produce predictions. Numerical results show that HydraGNN effectively captures the relation between the configurational entropy and the material properties over the entire compositional range. Overall, the accuracy of simultaneous MTL predictions is comparable to the accuracy of the STL predictions. In addition, the computational cost of training HydraGNN for MTL is much lower than the original DFT calculations and also lower than training separate STL models for each property.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Physically Informed Machine Learning Prediction of Electronic Density of States

The electronic structure of a material, such as its density of states (DOS), provides key insights into its physical and functional properties and serves as a valuable source of high-quality features for many materials screening and discovery workflows. Still, the computational cost of calculating the DOS, most commonly with density functional theory (DFT), becomes prohibitive for meeting high-fidelity or high-throughput requirements, necessitating a cheaper but sufficiently accurate surrogate. To fulfill this demand, we develop a general machine learning method based on graph neural networks for predicting the DOS purely from atomic positions, six orders of magnitude faster than DFT. This approach can effectively use large materials databases and be applied generally across the entire periodic table to materials classes of arbitrary compositional and structural diversity. We furthermore devise a highly adaptable scheme for physically informed learning which encourages the DOS prediction to favor physically reasonable solutions defined by any set of desired constraints. This functionality provides a means for ensuring that the predicted DOS is reliable enough to be used as an input to downstream materials screening workflows to predict more complex functional properties, which rely on accurate physical features.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Topological Link Models of Multipartite Entanglement

We introduce a novel model of multipartite entanglement based on topological links, generalizing the graph/hypergraph entropy cone program. We demonstrate that there exist link representations of entropy vectors which provably cannot be represented by graphs or hypergraphs. Furthermore, we show that the contraction map proof method generalizes to the topological setting, though now requiring oracular solutions to well-known but difficult problems in knot theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Crystal structure of diclazuril, C 17 H 9 Cl 3 N 4 O 2

The crystal structure of diclazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Diclazuril crystallizes in space group P2 1 /a (#14) with a = 27.02080(18), b = 11.42308(8), c = 5.36978(5) Å, β = 91.7912(7)°, V = 1656.629(15) Å 3 , and Z = 4. The crystal structure consists of layers of molecules parallel to the ac-plane. A strong N–H∙∙∙O hydrogen bond links the molecules into dimers along the a-axis with a graph set R2,2(8). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

A Unification Framework for Euclidean and Hyperbolic Graph Neural Networks

Hyperbolic neural networks have recently gained significant attention due to their promising results on several graph problems including node classification and link prediction. The primary reason for this success is the effectiveness of hyperbolic space in capturing the inherent hierarchy of graph datasets. However, they are limited in terms of generalization, scalability, and have inferior performance when applied to non-hierarchical datasets. In this paper, we take a completely different perspective for modeling hyperbolic networks and answer the following question: is an Euclidean model able to approximate a function or behavior in the hyperbolic space? Extending the universal approximation theory developed for Euclidean models, We draw an analogy from the hyperbolic components to the Euclidean counterparts and conclude that, in order to capture hierarchical features, it is possible to generalize hyperbolic models to be a special case of Euclidean models with the proposed Pseudo-Poincaré technique. We applied our non-linear hyperbolic normalization to the current state-of-the-art homogeneous and multi-relational graph networks and demonstrate significant improvements in performance compared to both Euclidean and hyperbolic counterparts. The primary impact of this work lies in its ability to capture hierarchical features in the Euclidean space, and thus, can replace hyperbolic networks without any loss in performance metrics while simultaneously leveraging the power of Euclidean networks such as interpretability and efficient execution of various model components.

Khatir, Mehrdad↗
DOE OSTI2022

Learning Distributed Geometric Koopman Operator for Sparse Networked Dynamical Systems

Koopman operator theory provides an alternative to study nonlinear networked dynamical systems by mapping the state space to an abstract higher dimensional space where the system evolution is linear. Recent works show the application of graph neural networks (GNNs) to learn state to object-centric embeddings and achieve centralized block-wise computation of Koopman operator (KO) under additional assumptions on the underlying agents properties and constraints on the KO structure. However, the computational complexity of learning the Koopman increases exponentially for networked systems where the number of possible system states grows in a combinatorial fashion with the number of nodes. The learning challenge is further amplified for sparse networks by two factors: 1) sample sparsity for learning the Koopman operator in the non-linear space, and 2) the divergence in the dynamics of individual nodes or from one subgraph to another. Our work aims to address these challenge by formulating the representation learning of networked dynamical systems into a multi-agent paradigm and learning the Koopman operator in a distributive manner. The computational as well as performance advantages of distributed Koopman is predominant for sparse networks whereas for fully connected networks, it is shown to coincide with the centralized one. The empirical study on rope system, network of oscillators and a synthetic power system show comparable and superior performance along with computational benefits with the state-of-the-art methods.

Mukherjee, Sayak↗
DOE OSTI2023

Crystal structure of deracoxib, C 17 H 14 F 3 N 3 O 3 S

The crystal structure of deracoxib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Deracoxib crystallizes in space group Pbca (#61) with a = 9.68338(11), b = 9.50690(5), c = 38.2934(4) Å, V = 3525.25(3) Å 3 , and Z = 8. The molecules stack in layers parallel to the ab-plane. N–H∙∙∙O hydrogen bonds link the molecules along the b-axis, in chains with the graph set C1,1(4), as well as more-complex patterns. N–H∙∙∙N hydrogen bonds link the layers. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Machine Learning Vacancy Formation Energy in Nickel-Based Superalloys

Creep performance plays a key role in nickel-based superalloys for high temeprature applications. Creep behavior depends on many parameters such as strength, dislocations, diffusivity, and microstructural stability in addition to temeprature, applied stress, and oxidation. This work focuses on predicting vacancy formation energy in nickel-based superalloys using machine learning approach. High-throughput density functional theory (DFT) calculations are performed on Ni-based alloys with the addition of various alloying elements to predict the vacancy formation energy and vacancy concentration. Machine learning is performed using various models including graph neural networks.

creep performance↗
DOE OSTI2023

Crystal structure of oxibendazole, C 12 H 15 N 3 O 3

The crystal structure of oxibendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxibendazole crystallizes in space group C2/c (#15) with a = 23.18673(22), b = 5.35136(5), c = 19.88932(13) Å, β = 97.0876(9)°, V = 2449.018(17) Å 3 , and Z = 8. The structure consists of hydrogen-bonded layers of planar molecules parallel to the bc-plane. Strong N–H∙∙∙N hydrogen bonds link the molecules into dimers, with a graph set R2,2(8). N–H∙∙∙O hydrogen bonds further link these dimers into layers parallel to the bc-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗