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At least 451 records · Page 25

Protein-based models offer mechanistic insight into complex nickel metalloenzymes

There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox–neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. Finally, this opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mesh-based super-resolution of fluid flows with multiscale graph neural networks

A graph neural network (GNN) approach is introduced in this work which enables mesh-based three-dimensional super-resolution of fluid flows. In this framework, the GNN is designed to operate not on the full mesh-based field at once, but on localized meshes of elements (or cells) directly. To facilitate mesh-based GNN representations in a manner similar to spectral (or finite) element discretizations, a baseline GNN layer (termed a message passing layer, which updates local node properties) is modified to account for synchronization of coincident graph nodes, rendering compatibility with commonly used element-based mesh connectivities. Furthermore, the architecture is multiscale in nature, and is comprised of a combination of coarse-scale and fine-scale message passing layer sequences (termed processors) separated by a graph unpooling layer. The coarse-scale processor embeds a query element (alongside a set number of neighboring coarse elements) into a single latent graph representation using coarse-scale synchronized message passing over the element neighborhood, and the fine-scale processor leverages additional message passing operations on this latent graph to correct for interpolation errors. Demonstration studies are performed using hexahedral mesh-based data from Taylor–Green Vortex and backward-facing step flow simulations at Reynolds numbers of 1600 and 3200. Through analysis of both global and local errors, the results ultimately show how the GNN is able to produce accurate super-resolved fields compared to targets in both coarse-scale and multiscale model configurations. Reconstruction errors for fixed architectures were found to increase in proportion to the Reynolds number. Geometry extrapolation studies on a separate cavity flow configuration show promising cross-mesh capabilities of the super-resolution strategy.

Backward-facing step↗

hPIC2: A hardware-accelerated, hybrid particle-in-cell code for dynamic plasma-material interactions

The exascale era of high performance computing promises to bring the field of computational plasma physics ever closer to the goal of accurate multiscale modeling. Such computers will rely on hardware acceleration to offload work to dedicated components, notably general-purpose graphics processing units (GPUs). However, devices from different manufacturers require software to be written with different parallel programming models, greatly increasing the code maintenance burden of applications designed to perform on more than one such device. hPIC2 is a hybrid plasma simulation code developed with the Kokkos performance portability framework to target the architectures that will drive exascale computing for the foreseeable future. As a hybrid simulation code, hPIC2 investigates the simultaneous use of various plasma models on the same domain, at the same time. hPIC2 also optionally couples to RustBCA, which accurately models ion-material interactions using the binary collision approximation (BCA) method. In conclusion, hPIC2 therefore achieves scalable performance on a variety of computing architectures when simulating complex and diverse plasmas, particularly near plasma-material interfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Parallel transport dynamics for mixed quantum states with applications to time-dependent density functional theory

Direct simulation of the von Neumann dynamics for a general (pure or mixed) quantum state can often be expensive. One prominent example is the real-time time-dependent density functional theory (rt-TDDFT), a widely used framework for the first principle description of many-electron dynamics in chemical and materials systems. Practical rt-TDDFT calculations often avoid the direct simulation of the von Neumann equation, and solve instead a set of Schrödinger equations, of which the dynamics is equivalent to that of the von Neumann equation. However, the time step size employed by the Schrödinger dynamics is often much smaller. Here, in order to improve the time step size and the overall efficiency of the simulation, we generalize a recent work of the parallel transport (PT) dynamics for simulating pure states [An, Lin, Multiscale Model. Simul. 18, 612, 2020] to general quantum states. The PT dynamics provides the optimal gauge choice, and can employ a time step size comparable to that of the von Neumann dynamics. Going beyond the linear and near adiabatic regime in previous studies, we find that the error of the PT dynamics can be bounded by certain commutators between Hamiltonians, density matrices, and their derived quantities. Such a commutator structure is not present in the Schrödinger dynamics. We demonstrate that the parallel transport-implicit midpoint (PT-IM) method is a suitable method for simulating the PT dynamics, especially when the spectral radius of the Hamiltonian is large. The commutator structure of the error bound, and numerical results for model rt-TDDFT calculations in both linear and nonlinear regimes, confirm the advantage of the PT dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Solution of the Schrödinger equation for quasi-one-dimensional materials using helical waves

We formulate and implement a spectral method for solving the Schrödinger equation, as it applies to quasi-one-dimensional materials and structures. This allows for computation of the electronic structure of important technological materials such as nanotubes (of arbitrary chirality), nanowires, nanoribbons, chiral nanoassemblies, nanosprings and nanocoils, in an accurate, efficient and systematic manner. Our work is motivated by the observation that one of the most successful methods for carrying out electronic structure calculations of bulk/crystalline systems — the plane-wave method — is a spectral method based on eigenfunction expansion. Our scheme avoids computationally onerous approximations involving periodic supercells often employed in conventional plane-wave calculations of quasi-one-dimensional materials, and also overcomes several limitations of other discretization strategies, e.g., those based on finite differences and atomic orbitals. The basis functions in our method — called helical waves (or twisted waves) — are eigenfunctions of the Laplacian with symmetry adapted boundary conditions, and are expressible in terms of plane waves and Bessel functions in helical coordinates. We describe the setup of fast transforms to carry out discretization of the governing equations using our basis set, and the use of matrix-free iterative diagonalization to obtain the electronic eigenstates. Miscellaneous computational details, including the choice of eigensolvers, use of a preconditioning scheme, evaluation of oscillatory radial integrals and the imposition of a kinetic energy cutoff are discussed. We have implemented these strategies into a computational package called HelicES (Helical Electronic Structure). We demonstrate the utility of our method in carrying out systematic electronic structure calculations of various quasi-one-dimensional materials through numerous examples involving nanotubes, nanoribbons and nanowires. We also explore the convergence properties of our method, and assess its accuracy and computational efficiency by comparison against reference finite difference, transfer matrix method and plane-wave results. We anticipate that our method will find applications in computational nanomechanics and multiscale modeling, for carrying out transport calculations of interest to the field of semiconductor devices, and for the discovery of novel chiral phases of matter that are of relevance to the burgeoning quantum hardware industry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Microstructural heterogeneity of the buffer layer of TRISO nuclear fuel particles

Tristructural isotropic (TRISO) nuclear fuel particles contain a layered spherical shell designed to retain fission products; however, failure occurs in rare cases—commonly initiated in the porous pyrocarbon buffer layer. Achieving a comprehensive understanding of the buffer-initiated failure mechanisms requires detailed characterization of the buffer porosity and its heterogeneous distribution across multiple length scales. Here we performed FIB-SEM tomography across the buffer layer thickness (~100 µm) to produce 3D reconstructions of the buffer microstructure with 50 nm spatial resolution. We found an average overall porosity of ~14%, which does not solely account for the low density of the buffer (50% of the theoretical density). Additionally, the local porosity and its fluctuation increase from the kernel interface towards the inner pyrocarbon (IPyC) layer, which we attribute to the chemical vapor deposition process conditions during the TRISO particle fabrication. Detailed characterization of the porous microstructure—including analysis of the pore size, distribution, shape, and orientation—provides insight into the process-structure-property-performance relations of TRISO nuclear fuel particles and will inform multiscale models designed to predict the failure of TRISO particles under irradiation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Additively manufactured strain sensors for in-pile applications

Accurate, real-time monitoring of strain in fuel, cladding, and structural components of nuclear reactors is critical to better understand radiation induced phenomena during reactor tests and operations. The data provided is crucial to verify physics-based, multiscale modeling and simulation efforts, which aim to shorten the timeline for the development of new nuclear materials. Resistive strain gauges have limited performance during in-pile experiments due to the harsh operating conditions and limited physical space between fuel and cladding components. In this work, aerosol jet printing using silver nanoparticle inks was used to fabricate interdigitated electrode capacitive strain gauges on aluminum alloy 6061 tensile specimens. Here to simulate the temperatures of a traditional light water reactor, the capacitive strain gauges were tested with a mechanical test frame up to 300 °C and compared to commercially available bondable resistive strain gauges. The printed capacitive strain gauges exhibited a gauge factor of 1.0 and showed higher reproducibility and predictability of strain sensing performance than the resistive strain gauge. The results demonstrate the potential of aerosol jet printing to fabricate strain sensors with predictable performance and reduced invasiveness for high-temperature applications with confined spacing.

36 MATERIALS SCIENCE↗

Grain2mesh: A Python and cubit mesh generator from unprocessed mesoscale images

Predicting bulk behavior from microscale features constitutes a key objective in multiscale modeling research, often involving numerical models composed of finite elements that capture the diversity of constituent phases, shapes, and orientations within the material. The Grain2mesh toolbox allows the user to input unprocessed mesoscopic images for automatic segmentation, pre-processing, quality control, and numerical mesh generation. The numerical mesh generation incorporates Cubit routines to generate robust multi-phase mesh structure for use in computational mechanics solvers. The python classes developed contain detailed documentation and examples to support standard usage and case-specific alternative options.

58 GEOSCIENCES↗

Bridging Scales in Bioenergy and Catalysis: A Review of Mesoscale Modeling Applications, Methods, and Future Directions

Between the molecular and reactor scales, which are familiar to the chemical engineering community, lies an intermediate regime, here termed the “mesoscale,” where transport phenomena and reaction kinetics compete on similar time scales. Bioenergy and catalytic processes offer particularly important examples of mesoscale phenomena owing to their multiphase nature and the complex, highly variable porosity characteristic of biomass and many structured catalysts. In this review, we overview applications and methods central to mesoscale modeling as they apply to reaction engineering of biomass conversion and catalytic processing. A brief historical perspective is offered to put recent advances in context. Applications of mesoscale modeling are described, and several specific examples from biomass pyrolysis and catalytic upgrading of bioderived intermediates are highlighted. Methods including reduced order modeling, finite element and finite volume approaches, geometry construction and import, and visualization of simulation results are described; in each category, recent advances, current limitations, and areas for future development are presented. Owing to improved access to high-performance computational resources, advances in algorithm development, and sustained interest in reaction engineering to sustainably meet societal needs, we conclude that a significant upsurge in mesoscale modeling capabilities is on the horizon that will accelerate design, deployment, and optimization of new bioenergy and catalytic technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unexpected Kinetic Solvent Effects Enhance Activity and Selectivity in Biphasic Systems

Biphasic dehydration of fructose to 5-hydroxymethylfurfural (HMF) has shown unprecedented increases in productivity, but a mechanistic understanding is lacking. Herein, we couple fast experimental reaction kinetics, multiscale modeling (phase behavior, classical molecular dynamics(MD), and quantum mechanics/molecular mechanics MD), in situ sampling, and IR and 13 C-NMR spectroscopy to elucidate the complex effects of nonpolar extracting organic solvents on the kinetics of fructose dehydration. We show that these organic solvents can reach significant mutual solubility with water at reaction temperatures, enabling the partition of the sugar and catalyst into the extracting phase. In the organic-rich environment, the dehydration of fructose proceeds faster and more selectively than in water due to increased relative abundance of the reactive furanose isomer, enhanced water–catalyst–substrate interactions driven by nanophase separation, and higher product stability stemming from preferential solvation. Furthermore, we demonstrate that these solvent effects impact other critical biphasic reactions in biomass upgrading and provide qualitative principles for solvent selection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pathways to High-Performance Salt Hydrate Thermochemical Energy Storage Materials and Systems

Thermochemical materials (TCMs) based on salt hydrates are promising for thermal energy storage as they combine high energy densities with low reaction temperatures. However, their adoption is hindered by poor structural integrity and degradation under hygrothermal cycling. Storage performance is governed not only by the chemical reaction, but also by the coupled thermo-chemo-mechanical behavior that evolves with cycling. Understanding and controlling this coupling across length scales (material-to-reactor) is necessary to improve TCM stability and lifetime. In this perspective, we discuss the shortcomings of current characterization approaches and emphasize the need for measuring transport properties and structural transformations using in situ techniques that capture the dynamic evolution of these materials. We also outline opportunities for multiscale modeling frameworks that link thermodynamics and mechanics, enabling predictive evaluation of composite architectures designed for cycling stability. We conclude by identifying research questions that must be addressed to transform TCMs into viable energy storage technologies.

Composites↗

How Does Water Dissociation Work in Bipolar Membranes?

Bipolar membranes (BPMs) create counteracting spatial gradients of pH and electrostatic potential in electrochemical systems, enabling applications in pH regulation, electrocatalysis, and separations. At the polarized junction of a BPM the water dissociation (WD, 2H2O ⇌ H3O+ + OH-) reaction can be driven, but it remains poorly understood. In this Perspective, we integrate molecular insights from bulk-water autoionization and the associated field effects with continuum descriptions of BPM electrostatics and experimental WD kinetic analyses to describe possible mechanisms of voltage-driven WD. Pristine BPM junctions highlight both the limits of primarily electric-field-driven WD and the practical challenges of junction stability at extreme reverse bias. Introducing heterogeneous catalyst layers, commonly metal oxides and graphene oxides, accelerates WD by orders of magnitude through hypothesized coupled effects in which surface acid-base functionality and high-density hydroxyl sites mediate proton-transfer steps, and catalyst mobile electronic/ionic charges redistribute the junction electric potential drop to shape the local electric fields and reactive microenvironments. Kinetic analyses suggest two regimes of heterogeneous WD mechanism, including field-driven ordering of interfacial water and a Second-Wien-Effect dissociation-barrier lowering. We conclude by defining the key unknown variables (local pH, electrostatic potential, catalyst charge state and relationships among mechanisms) and outlining experimental and multiscale modeling strategies needed for predictive WD catalysis and for controlling related ion-transfer reactions.

Wu, Yifan↗

Earth and Space Science Informatics Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science

Abstract This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles (Goldman, et al., 2021b, https://doi.org/10.1029/2021EO153180 ) in Earth and Space Science Informatics (ESSI) and includes discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (Section 2) Global collaboration, cyberinfrastructure, and data sharing; (Section 3) Machine learning for multiscale modeling; (Section 4) Aerial and satellite remote sensing for advancing Earth system model development by integrating field and ancillary data. ESSI addresses data management practices, computation and analysis, and hardware and software infrastructure. Our role in ICON science therefore involves collaborative work to assess, design, implement, and promote practices and tools that enable effective data management, discovery, integration, and reuse for interdisciplinary work in Earth and space science disciplines. Networks of diverse people with expertise across Earth, space, and data science disciplines are essential for efficient and ethical exchanges of findable, accessible, interoperable, and reusable (FAIR) research products and practices. Our challenge is then to coordinate the development of standards, curation practices, and tools that enable integrating and reusing multiple data types, software, multi‐scale models, and machine learning approaches across disciplines in a way that is as open and/or FAIR as ethically possible. This is a major endeavor that could greatly increase the pace and potential of interdisciplinary scientific discovery.

58 GEOSCIENCES↗

Vertically Resolved Analysis of the Madden-Julian Oscillation Highlights the Role of Convective Transport of Moist Static Energy

We simulate the Madden-Julian oscillation (MJO) over an aquaplanet with uniform surface temperature using the multiscale modeling framework (MMF) configuration of the Energy Exascale Earth System Model (E3SM-MMF). The model produces MJO-like features that have a similar spatial structure and propagation behavior to the observed MJO. To explore the processes involved in the propagation and maintenance of these MJO-like features, we perform a vertically resolved moist static energy (MSE) analysis for the MJO (Yao et al., 2022, https://doi.org/10.1175/jas-d-20-0254.1). Unlike the column-integrated MSE analysis, our method emphasizes the local production of MSE variance and quantifies how individual physical processes amplify and propagate the MJO's characteristic vertical structure. We find that radiation, convection, and boundary layer (BL) processes all contribute to maintaining the MJO, balanced by the large-scale MSE transport. Furthermore, large-scale dynamics, convection, and BL processes all contribute to the propagation of the MJO, while radiation slows the propagation. Additionally, we perform mechanism-denial experiments to examine the role of radiation and associated feedbacks in simulating the MJO. We find that the MJO can still self-emerge and maintain its characteristic structures without radiative feedbacks. This study highlights the role of convective MSE transport in the MJO dynamics, which was overlooked in the column-integrated MSE analysis.

54 ENVIRONMENTAL SCIENCES↗

Energy Infrastructure Futures: A Multiscale Evaluation of Projected Power Plant Siting Across the Western Interconnection

The US Western Interconnection is facing unprecedented challenges in the form of less predictable peak demand, increasingly diverse generating resources, and fast-growing loads due to the onset of artificial intelligence, hyperscale computing, and electrification. Projecting where future generation may be developed is critical to maintaining a robust and resilient electric grid under this mounting uncertainty and variability. Using an integrated multisectoral, multiscale modeling framework that links a human-Earth systems model, an hourly load model, a geospatial power plant siting model, and an hourly grid operations model, we evaluate the power plant landscape evolution under eight alternative futures between 2020 and 2055. These futures represent a wide but plausible range of atmospheric conditions, emissions constraints, and economic, technological, and population growth assumptions. We find that local-level development can vary substantially both by generation type and capacity buildout across these futures. Specific regions of the Western Interconnection are projected to see large amounts of capacity development regardless of the future scenario. We additionally determine that projected power plant locations are more heavily influenced by the cost to interconnect to the electric grid than the locational energy value.

Mongird, Kendall↗

Resolving Low Cloud Feedbacks Globally With E3SM High‐Res MMF: Agreement With LES but Stronger Shortwave Effects

This study investigates low cloud feedback in a warmer climate using global simulations from the High-Resolution Multi-scale Modeling Framework (HR-MMF), which explicitly simulates small-scale eddies globally. Two 5-year simulations—one with present-day sea surface temperatures (SSTs) and a second with SSTs warmed uniformly by 4 K—reveal a positive global shortwave cloud radiative effect (SWCRE = 0.3 W/m 2 /K), comparable to estimates from CMIP models. As the climate warms, significant reductions in low cloud cover occur over stratocumulus regions. This study is the first attempt to compare HR-MMF results with predictions from idealized large-eddy simulations from the CGILS intercomparison. Despite different underlying assumptions, we find qualitative agreement in SWCRE and inversion height changes between HR-MMF and CGILS predictions. This suggests reasonable credibility for the CGILS framework in predicting cloud responses under the out-of-sample conditions found in HR-MMF. However, the HR-MMF exhibits stronger SWCRE changes than predicted by CGILS. We explore potential causes for this discrepancy, examining variations in cloud-controlling factors (CCFs) and cloud conditions. Our results show a fairly homogeneous SWCRE response, with little systematic variation tied to the variations in CCFs. This reveals a dominant role for SST forcing in modulating SWCRE.

boundary-layer clouds↗

High-throughput design of high-performance lightweight high-entropy alloys

Developing affordable and light high-temperature materials alternative to Ni-base superalloys has significantly increased the efforts in designing advanced ferritic superalloys. However, currently developed ferritic superalloys still exhibit low high-temperature strengths, which limits their usage. Here we use a CALPHAD-based high-throughput computational method to design light, strong, and low-cost high-entropy alloys for elevated-temperature applications. Through the high-throughput screening, precipitation-strengthened lightweight high-entropy alloys are discovered from thousands of initial compositions, which exhibit enhanced strengths compared to other counterparts at room and elevated temperatures. The experimental and theoretical understanding of both successful and failed cases in their strengthening mechanisms and order-disorder transitions further improves the accuracy of the thermodynamic database of the discovered alloy system. This study shows that integrating high-throughput screening, multiscale modeling, and experimental validation proves to be efficient and useful in accelerating the discovery of advanced precipitation-strengthened structural materials tuned by the high-entropy alloy concept.

36 MATERIALS SCIENCE↗

Real-time dynamics and structures of supported subnanometer catalysts via multiscale simulations

Understanding the performance of subnanometer catalysts and how catalyst treatment and exposure to spectroscopic probe molecules change the structure requires accurate structure determination under working conditions. Experiments lack simultaneous temporal and spatial resolution and could alter the structure, and similar challenges hinder first-principles calculations from answering these questions. Here, we introduce a multiscale modeling framework to follow the evolution of subnanometer clusters at experimentally relevant time scales. We demonstrate its feasibility on Pd adsorbed on CeO 2 (111) at various catalyst loadings, temperatures, and exposures to CO. We show that sintering occurs in seconds even at room temperature and is mainly driven by free energy reduction. It leads to a kinetically (far from equilibrium) frozen ensemble of quasi-two-dimensional structures that CO chemisorption and infrared experiments probe. CO adsorption makes structures flatter and smaller. High temperatures drive very rapid sintering toward larger, stable/metastable equilibrium structures, where CO induces secondary structure changes only.

36 MATERIALS SCIENCE↗