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At least 109 records · Page 6

Representations of Materials for Machine Learning

High-throughput data generation methods and machine learning (ML) algorithms have given rise to a new era of computational materials science by learning the relations between composition, structure, and properties and by exploiting such relations for design. However, to build these connections, materials data must be translated into a numerical form, called a representation, that can be processed by an ML model. Data sets in materials science vary in format (ranging from images to spectra), size, and fidelity. Predictive models vary in scope and properties of interest. Here, we review context-dependent strategies for constructing representations that enable the use of materials as inputs or outputs for ML models. Furthermore, we discuss how modern ML techniques can learn representations from data and transfer chemical and physical information between tasks. Finally, we outline high-impact questions that have not been fully resolved and thus require further investigation.

36 MATERIALS SCIENCE↗

Direct Chemical Vapor Deposition Synthesis of Porous Single-Layer Graphene Membranes with High Gas Permeances and Selectivities

Single-layer graphene containing molecular-sized in-plane pores is regarded as a promising membrane material for high-performance gas separations due to its atomic thickness and low gas transport resistance. However, typical etching-based pore generation methods cannot decouple pore nucleation and pore growth, resulting in a trade-off between high areal pore density and high selectivity. In contrast, intrinsic pores in graphene formed during chemical vapor deposition are not created by etching. Therefore, intrinsically porous graphene can exhibit high pore density while maintaining its gas selectivity. Here in this work, the density of intrinsic graphene pores is systematically controlled for the first time, while appropriate pore sizes for gas sieving are precisely maintained. As a result, single-layer graphene membranes with the highest H 2 /CH 4 separation performances recorded to date (H 2 permeance > 4000 GPU and H 2 /CH 4 selectivity > 2000) are fabricated by manipulating growth temperature, precursor concentration, and non-covalent decoration of the graphene surface. Moreover, it is identified that nanoscale molecular fouling of the graphene surface during gas separation where graphene pores are partially blocked by hydrocarbon contaminants under experimental conditions, controls both selectivity and temperature dependent permeance. Overall, the direct synthesis of porous single-layer graphene exploits its tremendous potential as high-performance gas-sieving membranes.

chemical vapor deposition↗

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗

Griffin: A MOOSE-based reactor physics application for multiphysics simulation of advanced nuclear reactors

Griffin is a Multiphysics Object-Oriented Simulation Environment (MOOSE) based reactor physics application for multiphysics simulations of advanced reactor designs jointly developed by Idaho National Laboratory and Argonne National Laboratory. This paper summarizes the motivation, significance, architecture, design, and features of Griffin. Griffin offers flexible and extensible features to address the challenges associated with advanced reactor designs. These features range from fundamental particle transport to specific reactor physics tasks. The features cover a wide range including on-the-fly and traditional two-step cross-section generation methods, steady-state and transient transport solvers suitable for both heterogeneous and homogeneous models, high-fidelity depletion where thousands of isotopes can be tracked and low-fidelity depletion characterized by burnup, etc. The most fundamental aspect that sets Griffin apart from other reactor analysis codes is that it is developed based on the MOOSE framework. A modular development approach is strongly enforced, with multiphysics being an essential element considered since the beginning of Griffin’s development. Griffin links various MOOSE physics modules and couples to other MOOSE-based applications and non-MOOSE-based applications for multiphyiscs simulations. Griffin includes three modules: ISOXML for preparing and managing multigroup cross sections, radiation transport for solving the neutron transport equation, and reactor analysis for user-oriented reactor physics analysis functionalities. Griffin uses various finite element methods for spatial discretization, multigroup approximation for energy discretization and discrete ordinates method, spherical harmonics expansion method, and diffusion approximation for streaming direction discretization to solve the neutron transport equation. Griffin’s flexibility is evidenced through Griffin’s various applications to fast reactor, high-temperature reactor, pebble bed reactor, molten salt reactor, and microreactor designs. Griffin development follows the software quality assurance procedure for MOOSE-based applications and with software requirements consistent with the ASME NQA-1 standard. Griffin has been adopted into the reactor analysis system for the U.S. NRC and is in use at U.S. companies, universities and national laboratories.

97 MATHEMATICS AND COMPUTING↗

Creation of hollow silica-fiberglass soft ceramics for thermal insulation

Hollow-structured materials show promise in thermal insulation because the shells encapsulating gaseous voids can interrupt heat transport pathways. Here, in this study, we present two low-cost routes to fabricate hollow silica nanoshells, via gas-phase and liquid-phase methods. The gas-phase synthesis method generates hollow shells by a droplet surface precipitation mechanism in a flame aerosol reactor. The liquid-phase synthesis route forms hollow shells by removal of a carbon template, which is produced by hydrothermal reaction of glucose. Both approaches (gas- and liquid-phase) provide hollow silica with amorphous structure, low thermal conductivity (0.023 and 0.026 W m –1 K –1 ), small particle size (442 and 383 nm), thin shell (35 and 36 nm), and low density (0.015 and 0.033 g cm –3 ). We employed high shear mechanical mixing to fabricate hollow silica-fiberglass composite ceramics. The resulting three-dimensional network provides the ceramics with robust mechanical elasticity and fire-retardancy while maintaining low thermal conductivity, dramatically outperforming an analogous material using commercial silica gel in place of the hollow nanoshells. Our findings provide two practical routes to synthesize hollow silica, either of which can be used to manufacture a class of hollow shell-fiber nanocomposite soft ceramics for energy-saving applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine learning assisted phase and size-controlled synthesis of iron oxide particles

Synthesis of iron oxides with specific phases and particle sizes is a crucial challenge in various fields, including materials science, energy storage, biomedical applications, environmental science, and earth science. However, despite significant advances in this area, much of the current palette of particle outcomes has been based on time-consuming trial-and-error exploration of synthesis conditions. The present study was designed to explore a very different approach to 1) predict the outcome of synthesis from specified reaction parameters based on using machine learning (ML) techniques, and 2) correlate sets of parameters to obtain products with desired outcomes by a newly designed recommendation algorithm. To achieve this, four ML algorithms were tested, namely random forest, logistic regression, support vector machine, and k-nearest neighbor. Among the models, random forest outperformed the others, attaining 96% and 81% accuracy when predicting the phase and size of iron oxide particles in the test dataset. Surprisingly, the permutation feature importance analysis revealed that volume, which may strongly relate to pressure, was one of the important features, along with precursor concentration, pH, temperature, and time, influencing the phase and size of iron oxide particles during synthesis. To verify the robustness of the random forest models, prediction and experimental results were compared based on 24 randomly generated methods in additive and non-additive systems not included in the datasets. The predictions of product phase and particle size from the models agreed well with the experimental results. Furthermore, a searching and ranking algorithm was developed to recommend potential synthesis parameters for obtaining iron oxide products with the desired phase and particle size from previous studies in the dataset. Furthermore, this study lays the foundation for a closed-loop approach in materials synthesis and preparation, beginning with suggesting potential reaction parameters from the dataset and predicting potential outcomes, followed by conducting experiments and analyses, and ultimately enriching the dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subject-specific modeling framework for particle deposition using computational fluid dynamics

Quantifying particle deposition and dose in the respiratory tract requires a physiologically realistic representation and reproducible computational workflows. However, existing modeling frameworks, such as the International Commission on Radiological Protection (ICRP) compartmental models and the Multiple Path Particle Dosimetry (MPPD) tool, lack detailed deposition profiles and subject-specific capabilities. The combination of advances in computer vision algorithms applied to the respiratory tract and Computational Fluid and Particle Dynamics (CFPD) allows high-fidelity simulations of particle behavior in anatomically accurate geometries derived from individual CT scans. The segmentation, preprocessing, and file preparation task for a CFPD simulation was often time-consuming, and no prior studies to-date have yet presented a fully automated framework. This work presents a fully automated workflow to obtain individualized particle deposition profiles in the human respiratory tract. The pipeline starts with segmenting upper and lower airway geometries using morphological and deep learning-based methods, generating three-dimensional (3D) models from CT imaging data. Next, a series of algorithms are presented to quality check and prepare the 3D geometry for a CFD or CFPD simulation. The preprocessing step includes correcting geometric artifacts, enforcing a physically consistent mesh, and automatically identifying and capping multiple outlets, which is required for CFD/CFPD simulations. These processed models are then input into open-source (OpenFOAM) or commercial (StarCCM+) CFD solvers, where flow and transient particle transport equations — including turbulence and particle–wall interactions are solved under realistic breathing conditions. Finally, the resulting particle deposition profiles can be integrated with Monte Carlo radiation transport codes and state-of-the-art computational phantoms to assess organ-specific absorbed doses in scenarios of radioactive aerosol inhalation. The presented work streamlines respiratory tract segmentation, preprocessing for CFD/CFPD simulations, and integration with dose assessment workflows, reducing manual intervention and improving access to high-fidelity, subject-specific modeling. The high precision in predicted particle deposition and dose distributions can improve personalized treatment strategies in respiratory medicine and refine dose estimates for radiation protection.

AI↗

UQpy: A general purpose Python package and development environment for uncertainty quantification

In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ) in mathematical and physical systems. The software serves as both a user-ready toolbox that includes many of the latest methods for UQ in computational modeling and a convenient development environment for Python programmers advancing the field of UQ. The paper presents an introduction to the software's architecture and existing capabilities, divided in the code in a set of modules centered around different UQ tasks such as sampling methods, generation of random processes and random fields, probabilistic inverse modeling, reliability analysis, surrogate modeling, and active learning. The paper also highlights the importance of the RunModel module, which is used to drive simulations in the uncertainty analyses performed in UQpy. This module conveniently allows the user to define computational models directly in Python, or to run simulations from a third-party software in serial or in parallel. To illustrate the various capabilities, two examples are tracked throughout the paper and analyzed repeatedly for various UQ tasks. The first is a Python model solving a nonlinear structural dynamics problem, used to illustrate UQpy's capabilities in sampling and forward propagation of high dimensional random vectors (stochastic processes), and probabilistic inference. The second model is a third-party Abaqus finite element model solving the thermomechanical response of a beam structure. This example is used to illustrate UQpy's capabilities in variance reduction sampling techniques, reliability analysis, surrogate modeling and active learning techniques.

97 MATHEMATICS AND COMPUTING↗

The Intermetallic Reactivity Database: Compiling Chemical Pressure and Electronic Metrics toward Materials Design and Discovery

Here, the advent of high-throughput Density Functional Theory (DFT) calculations has supported the creation of large databases containing the quantitative output necessary for constructing theoretical phase diagrams and predicting physical properties. In this Article, we present a complementary resource, the Intermetallic Reactivity Database (IRD), focused on the chemical bonding features of solid-state structures and indicators of potential structural transformations. Each IRD entry augments common features, such as band structures and density of states (DOS) distributions, with chemically motivated information including DFT-Chemical Pressure (CP) schemes and visualizable representations of the atomic charges. Together, these data types enable the rationalization and prediction of potential structural phenomena encountered in intermetallic chemistry, as we illustrate with four examples: the origins of the Y 2 Ni 2 Mg structure in terms of CP features of its parent structures, the anticipation of intergrowth phases from the net atomic CPs collected in Al-containing binary phases, the correlation between trends in the CP schemes of CaCu 5 -type phases and experimentally observed structural variations, and finally, the development of theoretical methodology with the testing of a streamlined method generating DFT-CP schemes. Altogether, these examples highlight how the IRD supports the creation of models of structural chemistry that extend beyond the bounds of its entries.

36 MATERIALS SCIENCE↗

Identification of Known and Novel Monomers for Poly(hydroxyurethanes) from Biobased Materials

Sourcing polymers from biobased materials is desirable for a transition to a more sustainable world. However, finding new monomers sourced from biobased molecules requires extensive experimental effort, due to the fact that most biomolecules lack the functional groups or properties needed to serve as a monomer in a particular polymeric system without chemical modification. In this work, we demonstrate a computational screening method to obtain monomers of a non-isocyanate polyurethane (NIPU), polyhydroxyurethane (PHU), from biomolecules. Our method generates candidate monomers from a list of 15 selected biobased starting molecules by performing chemical transformations that are standard to chemical catalysis and organic synthesis on these starting molecules and then screening the results for molecules with moieties that can be used as monomers for a PHU. Product molecules from two generations of reaction, a total number of 20,057, were analyzed automatically to identify molecules that have two or more epoxy or cyclic carbonate functional groups as candidates for further derivatization. These 21 candidate molecules were then subjected to another two generations of reaction, producing a set of 17,913 additional molecules. Further scrutiny of this set for desired functional groups characterizing PHUs and querying against the PubChem database was carried out, and 15 known molecules that are commercially available were identified, with the desirable features that they are predicted to be derived from biobased starting molecules in four or fewer steps. Moreover, molecule space generated from this process was primarily comprised of molecules that were not known to PubChem, indicating the framework also has the ability to generate novel candidate monomers that originate from biobased starting points.

36 MATERIALS SCIENCE↗

Pynta-An Automated Workflow for Calculation of Surface and Gas-Surface Kinetics

Many important industrial processes rely on heterogeneous catalytic systems. However, given all possible catalysts and conditions of interest, it is impractical to optimize most systems experimentally. Automatically generated microkinetic models can be used to efficiently consider many catalysts and conditions. However, these microkinetic models require accurate estimation of many thermochemical and kinetic parameters. Manually calculating these parameters is tedious and error prone, involving many interconnected computations. Here, we present Pynta, a workflow software for automating the calculation of surface and gas–surface reactions. Pynta takes the reactants, products, and atom maps for the reactions of interest, generates sets of initial guesses for all species and saddle points, runs all optimizations, frequency, and IRC calculations, and computes the associated thermochemistry and rate coefficients. It is able to consider all unique adsorption configurations for both adsorbates and saddle points, allowing it to handle high index surfaces and bidentate species. Pynta implements a new saddle point guess generation method called harmonically forced saddle point searching (HFSP). HFSP defines harmonic potentials based on the optimized adsorbate geometries and which bonds are breaking and forming that allow initial placements to be optimized using the GFN1-xTB semiempirical method to create reliable saddle point guesses. This method is reaction class agnostic and fast, allowing Pynta to consider all possible adsorbate site placements efficiently. We demonstrate Pynta on 11 diverse reactions involving monodenate, bidentate, and gas-phase species, many distinct reaction classes, and both a low and a high index facet of Cu. Our results suggest that it is very important to consider reactions between adsorbates adsorbed in all unique configurations for interadsorbate group transfers and reactions on high index surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Technoeconomic Model and Pathway to <$2/kg Green Hydrogen Using Integrated Halide Perovskite Photoelectrochemical Cells

The cost of gray hydrogen produced via fossil fuel-based steam-methane reforming has led the U.S. Department of Energy to specify <$\$$2/kg H 2 as a target for commercially competitive green hydrogen generation methods. Integrated photoelectrochemical cells have been proposed as a solar-to-hydrogen conversion technology. In this paper we describe a technoeconomically feasible pathway to reaching <$\$$2/kg green H 2 using integrated photoelectrochemical cells with halide perovskite photoabsorbers, low-cost conductive barriers, and low precious metal-content catalysts in an aqueous, membrane-separated cell. A base-case solar-to-hydrogen conversion efficiency of 20%, stable lifetime of 10 years, and a combined electrocatalyst-plus-panel cost of $\$$50/m 2 enabled a levelized cost of hydrogen of $\$$2.43/kg, which dropped below $\$$2/kg with improved performance metrics including material cost, improvements in process design, or subsidies. We relate these metrics to lab-scale reports to recommend best research practices for scientists and funding agencies working at this intersection of photovoltaics, electrocatalysis, and surface science.

$1/kg↗

Information-entropy-driven generation of material-agnostic datasets for machine-learning interatomic potentials

In contrast to their empirical counterparts, machine-learning interatomic potentials (MLIAPs) promise to deliver near-quantum accuracy over broad regions of configuration space. However, due to their generic functional forms and extreme flexibility, they can catastrophically fail to capture the properties of novel, out-of-sample configurations, making the quality of the training set a determining factor, especially when investigating materials under extreme conditions. We propose a novel automated dataset generation method based on the maximization of the information entropy of the feature distribution, aiming at an extremely broad coverage of the configuration space in a way that is agnostic to the properties of specific target materials. The ability of the dataset to capture unique material properties is demonstrated on a range of unary materials, including elements with the FCC (Al), BCC (W), HCP (Be, Re and Os), graphite (C), and trigonal (Sb, Te) ground states. MLIAPs trained to this dataset are shown to be accurate over a range of application-relevant metrics, as well as extremely robust over very broad swaths of configurations space, even without dataset fine-tuning or hyper-parameter optimization, making the approach extremely attractive to rapidly and autonomously develop general-purpose MLIAPs suitable for simulations in extreme conditions.

36 MATERIALS SCIENCE↗

Increasing the hardness of posiform planting using random QUBOs for programmable quantum annealer benchmarking

Posiform planting is a method for constructing QUBO instances with a unique planted solution that can be tailored to arbitrary connectivity graphs. In this study we investigate making posiform planted QUBOs computationally harder by fusing many smaller random Ising models, whose global minimum is computed classically, with posiform planted QUBOs. The unique ground state of the resulting QUBO is the concatenation of (exactly one of) the ground states of each smaller problem. Our method generates QUBO instances that have a unique solution, are native to the hardware graph, and have tunable computational hardness. We use our QUBOs to benchmark three D-Wave quantum annealing processors (with 563–5627 qubits), and compare them against simulated annealing and Gurobi. Surprisingly, we find that the D-Wave ground state sampling success rate is not dependent on the glued random QUBO size, and that some QUBO classes are solved at high success rates at short annealing times on the Zephyr processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Full-stack Quantification of Variability in Predicting Ion Transport Properties using Machine-learned Interatomic Potentials

Machine-learned interatomic potentials (MLIPs) have become the state-of-the-art for performing accurate, scalable molecular dynamics (MD) simulations. It is therefore crucial to understand and quantify the reliability of MLIPs for downstream property predictions. Uncertainty in predicted properties can arise from limitations in first-principles training data, intrinsic MLIP model errors in representing the data, and the statistical noise introduced during subsequent MD simulations. Using ion transport in Li7P3S11 as a case study, we systematically assess the impact of training set size and selection, neural network stochasticity, and MD sampling statistics on predicted diffusivity and activation energy. We find that when using equivariant MLIP architectures with standard MD protocols, uncertainty arising from MD sampling dominates over model-induced errors. In contrast, MLIP errors relative to the underlying first-principles data are consistently minor. Given this, there are two main routes to improving the accuracy of predictions based on MLIP potentials: adopting higher accuracy reference data generation methods, and improving the MD sampling statistics.

36 MATERIALS SCIENCE↗

Direct pulse-level compilation of arbitrary quantum logic gates on superconducting qutrits

Advanced simulations and calculations on quantum computers require high-fidelity implementations of quantum operations. The universal gateset approach builds complex unitaries from a small set of primitive gates, often resulting in a long gate sequence, which is typically a leading factor in the total accumulated error. Compiling a complex unitary for processors with higher-dimensional logical elements, such as qutrits, exacerbates the accumulated error per unitary, since an even longer gate sequence is required. Optimal control methods promise time- and resource-efficient compact gate sequences and, therefore, higher fidelity. These methods generate pulses that can directly implement any complex unitary on a quantum device. In this work, we demonstrate that any arbitrary qubit and qutrit gate can be realized with high fidelity, which can significantly reduce the length of a gate sequence. We generate and test pulses for a large set of randomly selected arbitrary unitaries on several quantum processing units (QPUs): the Lawrence Livermore National Laboratory Quantum Device and Integration Testbed’s (QuDIT’s) standard QPU and three of Rigetti’s QPUs: Ankaa-2, Ankaa-9Q-1, and Aspen-M-3. On the QuDIT platform’s standard QPU, the average fidelity of random qutrit gates is 97.9 ± 0.5% measured with conventional QPT and 98.8 ± 0.6% from QPT with gate folding. Rigetti’s Ankaa-2 achieves random qubit gates with an average fidelity of 98.4 ± 0.5% (conventional QPT) and 99.7 ± 0.1% (QPT with gate folding). On Ankaa-9Q-1 and Aspen-M-3, the average fidelities with conventional qubit QPT measurements were higher than 99% (see Appendix). Here we show that optimal control gates are robust to drift for at least 3 h and that the same calibration parameters can be used for all implemented gates. Our work promises that the calibration overheads for optimal control gates can be made small enough to enable efficient quantum circuits based on this technique.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Probing the Effects of NO x and SO x Impurities on Oxy-Fuel Combustion in Supercritical CO 2 : Shock Tube Experiments and Chemical Kinetic Modeling

The direct-fired supercritical carbon dioxide cycles are one of the most promising power generation methods in terms of their efficiency and environmental friendliness. Two important challenges in implementing these cycles are the high pressure (300 bar) and high CO 2 dilution (>80%) in the combustor. The design and development of supercritical oxy-combustors for natural gas require accurate reaction kinetic models to predict the combustion outcomes. The presence of a small amount of impurities in natural gas and other feed streams to oxy-combustors makes these predictions even more complex. During oxy-combustion, trace amounts of nitrogen present in the oxidizer is converted to NO x and gets into the combustion chamber along with the recirculated CO 2 . Similarly, natural gas can contain a trace amount of ammonia and sulfurous impurities that get converted to NO x and SO x and get back into the combustion chamber with recirculated CO 2 . In this work, a reaction model is developed for predicting the effect of impurities such as NO x and SO x on supercritical methane combustion. The base mechanism used in this work is GRI Mech 3.0. H 2 S combustion chemistry is obtained from Bongartz et al. while NOx chemistry is from Konnov. The reaction model is then optimized for a pressure range of 30–300 bar using high-pressure shock tube data from the literature. It is then validated with data obtained from the literature for methane combustion, H 2 S oxidation, and NO x effects on ignition delay. The effect of impurities on CH 4 combustion up to 16 atm is validated using NO x -doped methane studies obtained from the literature. In order to validate the model for high-pressure conditions, experiments are conducted at the UCF shock tube facility using natural gas identical mixtures with N 2 O as an impurity at ~100 bar. Current results show that there is a significant change in ignition delay with the presence of impurities. A comparison is made with experimental data using the developed model and predictions are found to be in good agreement. The model developed was used to study the effect of impurities on CO formation from sCO 2 combustors. It was found that NO x helps in reducing CO formation while the presence of H 2 S results in the formation of more CO. The reaction mechanism developed herein can also be used as a base mechanism to develop reduced mechanisms for use in CFD simulations.

Energy & Fuels↗