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Results for “Computed Structure Models”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Feedback density and causal complexity of simulation model structure

Measures of simulation model complexity generally focus on outputs; we propose measuring the complexity of a model’s causal structure to gain insight into its fundamental character. This article introduces tools for measuring causal complexity. First, we introduce a method for developing a model’s causal structure diagram, which characterises the causal interactions present in the code. Causal structure diagrams facilitate comparison of simulation models, including those from different paradigms. Next, we develop metrics for evaluating a model’s causal complexity using its causal structure diagram. We discuss cyclomatic complexity as a measure of the intricacy of causal structure and introduce two new metrics that incorporate the concept of feedback, a fundamental component of causal structure. The first new metric introduced here is feedback density, a measure of the cycle-based interconnectedness of causal structure. The second metric combines cyclomatic complexity and feedback density into a comprehensive causal complexity measure. Finally, we demonstrate these complexity metrics on simulation models from multiple paradigms and discuss potential uses and interpretations. These tools enable direct comparison of models across paradigms and provide a mechanism for measuring and discussing complexity based on a model’s fundamental assumptions and design.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Uncertainty Quantification of Metal Additive Manufacturing Processing Conditions Through the use of Exascale Computing

Metal additive manufacturing (AM) is a disruptive manufacturing technology that opens the design space for parts outside those possible from traditional manufacturing methods. In order to accelerate industry and R&D needs to certify AM parts, the Exascale Additive Manufacturing project (ExaAM) has developed a suite of exascale-ready computational tools to model the process-to-structure-to-properties (PSP) relationship for additively manufactured metal components. One such tool is an uncertainty quantification (UQ) pipeline to quantify the effect that uncertainty in processing conditions has on local mechanical responses. We present an overview of this pipeline and its required simulation and workflow codes. Using the Oak Ridge National Laboratory’s (ORNL) exascale computer, Frontier, we utilize this pipeline to cross multiple length and time scales to predict the local mechanical response of a location within a complex AM bridge part, AMB2018-01 produced by the National Institute of Standards and Technology (NIST) as part of their 2018 AM-Bench test series. Our results are then compared to experimental mechanical tests of parts from the NIST build to quantify the error in the ExaAM UQ workflow.

Carson, Robert↗
DOE OSTI2022

Mechanical properties of zeolite-templated carbons from approximate density functional theory calculations

Zeolite-templated carbon (ZTC) is a unique porous carbonaceous material whose structure is ordered at the nanometre scale, enabling a representative periodic description at the atomistic level. Utilizing an existing, well-defined reference model for ZTCs, a structural library of varying compositions was developed by refinement using density-functional tight-binding (DFTB) potentials parameterized for materials science applications. We first determined the quantum chemical-refined structures of models with CH, CHO, CHON, CHOB, and CHOBN compositions with various degrees of heteroatom substitution. These structural models comprise the characteristic morphological features of highly porous carbon materials, such as open-blade surfaces, edges, saddles, and closed-strut formations, spanning a range of curvatures and characteristic sizes. Second, we carried out alternating compression and expansion of the CHO model unit cell to determine the lowest energy structure as well as to obtain its bulk modulus in order to demonstrate a close connection between macroscopic observations and atomic-scale structures. Further, the agreement between experimental measurements and the computational model is remarkable and demonstrates the power of approximate density functional theory as a cost-effective computational tool with chemical accuracy for the investigation of structure/property relationships in real-world carbon-based solids.

03 NATURAL GAS↗
DOE OSTI2025

Orthorhombic Structures as Inorganic Halide Perovskite Models for High-Throughput DFT Investigations

Although high-symmetry Pm-3m space group cubic models are computationally efficient for high-throughput density functional theory (DFT) calculations of inorganic ternary (ABX 3 ) halide perovskites (HPs), they frequently predict band gaps (E g ) that disagree with experiment. Conversely, while low-symmetry cubic polymorphous networks (PN) comprised of 160 to 320 atoms incur significantly greater computational cost, they predict E g ’s that are more closely aligned with experiment. Here, in this study, we compare the DFT total energies and E g ’s predicted by four high-symmetry structure models (Pnma orthorhombic, R3m trigonal, P4/mbm tetragonal, and Pm-3m cubic) to cubic PNs for 5 experimentally characterized ternary HPs and find that the orthorhombic model computes Eg’s with the smallest MAD of 0.23 eV relative to the PNs. Pair distribution functions and DFT-computed total energies show that octahedral tilting, which is present in the 20-atom orthorhombic and 160-atom cubic PN models but not in the 5-atom cubic models, stabilizes all 5 compositions in our benchmarking set. We also find that imposing PN constraints when generating and optimizing these orthorhombic structures by fixing the unit cell lattice vectors and displacing the atoms prior to ionic relaxation with DFT, which we call the orthorhombic surrogate model (OSM), lowers the MAD of E g predictions to 0.09 eV. Our OSM predicts the PN band gaps of an additional 95 theoretical inorganic ternary HPs with MAD of 0.08 eV, supporting its usage in high-throughput DFT investigations to closely estimate PN band gaps with much less computational expense.

14 SOLAR ENERGY↗
DOE OSTI2024

A Finite Difference informed Random Walk solver for simulating radiation defect evolution in polycrystalline structures with strongly inhomogeneous diffusivity

Diffusivity of species and defects on grain boundaries is usually several orders of magnitude larger than that inside grains. Such strongly inhomogeneous diffusivity requires prohibitively high computational demands for modeling microstructural evolution. Here, this paper presents a highly-efficient numerical solver, combining the Finite Difference method and Random Walk model, designed for accurately modeling strongly inhomogeneous diffusion within polycrystalline structures. The proposed solver, termed Finite Difference informed Random Walk (FDiRW), integrates a customized Finite Difference (cFD) scheme tailored for fast diffusion along thin grain boundaries represented by a single-layer of nodes. Numerical experiments demonstrate that the FDiRW solver achieves an impressive efficiency gain of 1560x compared to traditional Finite Difference methods while maintaining accuracy, making it feasible for personal computer machines to handle diffusional systems with strongly inhomogeneous diffusivity across static polycrystalline microstructures. The model has been successfully applied to simulate radiation defect evolution, showcasing its scalability to engineering scales in both length and time dimensions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Sparse thermal data for cellular automata modeling of grain structure in additive manufacturing

Grain growth in the wake of the melt pool formed during alloy-based additive manufacturing (AM) is complex and multifaceted, depending on parameters governing heat transport, fluid flow, and solidification itself. Cellular automata (CA) models have proven effective in providing computationally efficient and physically sound predictions of grain structure for several AM problems, but their efficiency is tied to the performance of heat transport models. CA models use only a small portion of the problem's temperature data (near the moving melt pool boundary), and much of the CA calculations do not affect the final result due to re-melting of material. Coupling of and communication between heat transport and solidification models, and eliminating operations irrelevant towards final grain structure prediction, will be necessary for using these methods for efficient simulation of large parts. In this work, we introduce a procedure of decoupling the CA from temperature field simulation, using files of relevant temperature data written by the heat transport model. This approach is validated against the standard coupling approach using data obtained through the computational fluid dynamics software OpenFOAM. Negligible differences are seen in grain size, volume, and texture distributions for multilayer simulation of test problems, while the quantity of temperature data for these test problems was reduced by four orders of magnitude (from 100s of GB to 10s of MB) and the code performance sped up by a factor of around 50. Furthermore, variability in microstructure as a function of cell size, substrate, time step, and nucleation parameters is studied, and it is found that cell sizes less than or equal to 1.67 μm and sufficiently small time steps yield Αstatistically equivalent microstructures. Finally, a potential use case for this CA approach—the layer-wise convergence in grain structure starting from extremes in initial grain size—is examined. This approach's ability to simulate expected trends in nucleation and epitaxial grain growth for large regions of microstructure, simulated independently of heat transport models themselves, should prove useful for investigation of various microstructure uncertainties and prediction of part-scale experimental results.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Computing real time correlation functions on a hybrid classical/quantum computer

Quantum devices may overcome limitations of classical computers in studies of nuclear structure functions and parton Wigner distributions of protons and nuclei. In this talk, we discuss a worldline approach to compute nuclear structure functions in the high energy Regge limit of QCD using a hybrid quantum computer, by expressing the fermion determinant in the QCD path integral as a quantum mechanical path integral over 0 + 1-dimensional fermionic and bosonic world-lines in background gauge fields. Our simplest example of computing the well-known dipole model result for the structure function F 2 in the high energy Regge limit is feasible with NISQ era technology using few qubits and shallow circuits. We note this example can be scaled up in complexity and extended in scope to compute structure functions, scattering amplitudes and other real-time correlation functions in QCD, relevant for example to describe non-equilibrium transport of quarks and gluons in a Quark-Gluon-Plasma.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Characterization of the atomic-level structure of γ-alumina and (111) Pt/γ-alumina interfaces

The atomic-level structure of platinum/γ-alumina interfaces is characterized in a model system of dense γ-alumina embedded with faceted Pt NPs produced by implantation of platinum ions into sapphire followed by thermal annealing in air at 800 °C. Aberration-corrected scanning transmission electron microscopy (STEM) was used to collect atomic-resolution images, which are compared to STEM image simulations of two experimentally-based bulk models of γ-alumina by Smrčok et al. and Zhou and Snyder. A density functional theory (DFT) based model of (111) interfaces with different chemical terminations (O, Al 1 , Al 2 ) of the γ-alumina developed by Oware Sarfo et al. is also compared to experimental STEM data from Pt/γ-alumina interfaces. Further, the Smrčok γ-alumina model provides a better fit than the Zhou structure to the bulk of the γ-alumina. The oxygen-terminated Oware Sarfo model best fits the experimental data and is a very good model close to the interface. However, the fit of the interface model to the experimental data is poorer beyond the third atomic layer in the γ-alumina. This is attributed to compromises required in the design of the model to limit the cell size and computational time for DFT calculations. Understanding the accuracy and limits of the structural models of γ-alumina and Pt/γ-alumina interfaces is important to further the understanding of the structure/property relationships in this system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Review of the Effects of Polymer Binder Properties on Microstructure and Irreversible Volume Growth of Plastic Bonded Explosives Formulations

The rational design of effective polymeric binders for the formulation of plastic-bonded explosives (PBX) is challenging due to their inherent compositional complexity. The composites comprise irregularly shaped energetic material (EM) powders coated with low weight fractions of polymer via non-equilibrium processes such as slurry coating. Defects can deleteriously affect PBX stability and performance: nano- to micrometer-scale voids can act as loci for hot spots, lowering deflagration and detonation temperatures in unpredictable ways. Furthermore, some nominally desirable polymer properties are at odds with each other: e. g. good flow characteristics are desirable for coating and adhesion, but mechanical stiffness is needed to prevent deformation and cracking of PBX under mechanical stress. Good binder adhesion is critical, but the best means to predict and measure adhesion in PBX is not obvious. Experimental methods of determining binder adhesion on model surfaces may not capture polymer structural configurations relevant to deposition during coating. Molecular dynamics-based computational models have predicted key observables in PBX formulation, suggesting that they may be powerful tools for binder selection. In this review, primarily recent (~2006 and later) literature on polymeric binders for insensitive HE (IHE) is surveyed. We focus on how binder properties influence observable PBX properties as resistance to irreversible volume growth and void formation in PBX formulations mainly (but not exclusively) featuring 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as the EM (e. g. PBX 9502, LX-17 and others). Conclusions from these studies yield useful guidelines for choosing HE binder candidates, as well as for the general design of highly-filled polymer composite materials. Finally, studies describing challenges in PBX formulation with the newer and more energetically dense high explosive, LLM-105, will be discussed.

adhesion↗
DOE OSTI2023

Scalable computations for nonstationary Gaussian processes

Nonstationary Gaussian process models can capture complex spatially varying dependence structures in spatial datasets. However, the large number of observations in modern datasets makes fitting such models computationally intractable with conventional dense linear algebra. In addition, derivative-free or even first-order optimization methods can be very slow to converge when estimating many spatially varying parameters. In this paper, we present a computational framework which couples an algebraic block diagonal plus low-rank covariance matrix approximation with stochastic trace estimation to facilitate the efficient use of second-order solvers for maximum likelihood estimation of Gaussian process models with many parameters. We demonstrate the effectiveness of these methods by simultaneously fitting 192 parameters in the popular nonstationary model of Paciorek and Schervish using 107,600 sea surface temperature anomaly measurements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Variational study of the Kitaev-Heisenberg-Gamma model

Here we compute the low-energy excitation spectrum and the dynamical spin structure factor of the Kitaev-Heisenberg-Gamma model through a variational approach based on the exact fractionalized excitations of the pure Kitaev honeycomb model. This novel approach reveals the physical reason for the asymmetric stability of the Kitaev spin liquid phases around the ferromagnetic and antiferromagnetic Kitaev limits. Moreover, we demonstrate that the fractionalized excitations form bound states in specific regions of each Kitaev spin liquid phase and that certain phase transitions induced by Heisenberg and Gamma interactions are driven by the condensation of such a bound state. Remarkably, this bound state appears as a sharp mode in the dynamical spin structure factor, while its condensation patterns at the appropriate phase transitions provide a simple explanation for the magnetically ordered phases surrounding each Kitaev spin liquid phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Machine learning assisted derivation of minimal low-energy models for metallic magnets

Abstract We consider the problem of extracting a low-energy spin Hamiltonian from a triangular Kondo Lattice Model (KLM). The non-analytic dependence of the effective spin-spin interactions on the Kondo exchange excludes the use of perturbation theory beyond the second order. We then introduce a Machine Learning (ML) assisted protocol to extract effective two- and four-spin interactions. The resulting spin model reproduces the phase diagram of the original KLM as a function of magnetic field and single-ion anisotropy and reveals the effective four-spin interactions that stabilize the field-induced skyrmion crystal phase. Moreover, this model enables the computation of static and dynamical properties with a much lower numerical cost relative to the original KLM. A comparison of the dynamical spin structure factor in the fully polarized phase computed with both models reveals a good agreement for the magnon dispersion even though this information was not included in the training data set.

Sharma, Vikram (ORCID:0000000189105519)↗
DOE OSTI2025

Machine learning of 27Al NMR electric field gradient tensors for crystalline structures from DFT

NMR crystallography has emerged as a promising technique for the determination and refinement of atomic coordinates in crystal structures. The crystal structure of compounds containing quadrupolar nuclei, such as 27Al, can be improved by directly comparing solid-state NMR measurements to DFT computations of the electric field gradient (EFG) tensor. The non-negligible computational cost of these first-principles calculations limits the applicability of this method to all but the most well-defined structures. We developed a fast, low-cost machine learning model to predict EFG parameters based on local structural motifs and elemental parameters. We computed 8081 EFG tensors from 1681 27Al crystalline solids using DFT and benchmarked them against 105 experimentally measured 27Al sites. Surprisingly, simple local geometric features dominate the predictive performance of the resulting random-forest model, yielding an R2 value of 0.98 and an RMSE of 0.61 MHz for CQ, the quadrupolar coupling constant. This model accuracy should enable pre-refining future structural assignments before finally validating with first-principles calculations. Such a catalogue of 27Al NMR tensors can serve as a tool for researchers assigning complex NMR spectra influenced by the nuclear electric quadrupole interaction.

Sun, He↗
DOE OSTI2022

Atomically Dispersed Platinum in Surface and Subsurface Sites on MgO Have Contrasting Catalytic Properties for CO Oxidation

Atomically dispersed metals on metal oxide supports are a rapidly growing class of catalysts. Developing an understanding of where and how the metals are bonded to the supports is challenging because support surfaces are heterogeneous, and most reports lack a detailed consideration of these points. In this work, we report two atomically dispersed CO oxidation catalysts having markedly different metal–support interactions: platinum in the first layer of crystalline MgO powder and platinum in the second layer of this support. Structural models have been determined on the basis of data and computations, including those determined by extended X-ray absorption fine structure and X-ray absorption near edge structure spectroscopies, infrared spectroscopy of adsorbed CO, and scanning transmission electron microscopy. The data demonstrate the transformation of surface to subsurface platinum as the temperature of sample calcination increased. Catalyst performance data demonstrate the lower activity but greater stability of the subsurface platinum than of the surface platinum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The confluence of machine learning and multiscale simulations

Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. In conclusion, this confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

MISPR : an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗