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DOE OSTI2019

UPC++ Specification v1.0, Draft 10

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

UPC++ v1.0 Specification (Revision 2019.9.0)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

UPC++ Specification v1.0, Draft 8

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

An Adaptive-Mesh-Refinement Based Computational Tool for Simulating Catalysis at Mesoscale

In this work, we present a computational tool for mesoscale applications using open-source exascale- computing compatible adaptive-mesh-refinement (AMR) library, AMReX [2]. AMReX is software library that enables development of application solvers with block-structured Cartesian AMR. Our tool has capabilities to include realistic geometry representation, chemical species transport, reactions and thermodynamics that are critical for capturing mesoscale physics. A significant achievement is the ability of our solver to automatically import electron microscopy data in the form of a stereolithography (STL) or pixelated file format (mrc, tiff) without undergoing the tedious task of unstructured mesh generation. This feature allows for rapid simulation of catalyst particles with complex morphologies using an immersed-boundary formulation. The use of AMR allows for higher resolutions at catalyst surface interfaces, which in turn provides an accurate description of surface reactions and transport. Our solver uses a hybrid distributed and shared memory parallelism (OpenMP/GPU-based) with which strong scaling up to 10,000 processors for realistic catalyst particle simulations have been demonstrated.

BIOMASS FUELS,MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Carbonation of Alkaline Earth Metal Hydroxides: Structure across Nano- to Mesoscales

The conversion of gaseous CO 2 into a solid constitution through mineralization is an active area of carbon capture, and alkaline earth metal hydroxides (M(OH) 2 , M = Ca 2+ , Mg 2+ ) are frontrunners in this area. As model systems, nanolime samples are excellent templates for the study of this reaction. Here, we have examined these under ambient pressure conditions with controlled humidity and CO 2 . Utilizing a broad range of analytical methods, we first established the purity and structures of the selected materials. We then examined the structural changes due to carbonation, using infrared spectroscopy, X-ray scattering, and neutron scattering. The resulting structural changes are resolved from nanoscale to mesoscale and from early-stage to late-stage carbonation. Ca(OH) 2 and Mg(OH) 2 are found to behave quite differently. As expected from prior work, the carbonation of Ca(OH) 2 is kinetically favored. Further, our structure studies suggest this is due to a facile reaction at the fractal interface of the particles. From early- to late-stage carbonation, there is a consistent increase in the fractal roughness. This is in contrast to Mg(OH) 2 where the same surface evolves into a smooth conformal coating. For this material the major reacting component is at the mesoscale, suggesting globular particle growth or evolving macro-porosity. Because neutron scattering is sensitive to hydrogen content, we expected a significant change as M(OH) 2 evolves to MCO 3 . Such a change is found for Ca(OH) 2 but not for Mg(OH) 2 , providing evidence for the formation of hydrated carbonates for the later material. The formation of a conformal layer along with water-rich carbonate formation is an impediment to the use of Mg(OH) 2 for carbon capture. For energy-efficient carbon capture, it would be desirable to enhance carbonation rates for Mg(OH) 2 , and one possible route would be the use of anhydrous fluids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Immobile Pore-Water Storage Enhancement and Retardation of Gas Transport in Fractured Rock

The effect of immobile pore-water on gas transport in fractured rock has implications for numerical modeling of soil vapor extraction, methane leakage, gaseous CO 2 leakage from sequestration operations, radionuclide transport from underground nuclear explosions, and nuclear waste disposal. While the ability for immobile pore-water storage to effect gas transport has been recognized in the past, the details and specific scenarios leading to enhanced, retarded, or unaffected gas transport have not been explored. In this paper, we performed numerical investigations into the enhancement and retardation of gas transport due to immobile pore-water storage in order to identify implications for gas transport applications. To do this, we developed a numerical approach to model gas transport with a single-phase flow solution coupled to the advection–dispersion equation modified to account for immobile pore-water storage. Other than the immobility of pore water, the formulation contains all other physics included in two-phase formulations (advective and diffusive gas transport in fractures and rock matrix and dissolution in immobile pore water). The assumption of immobile pore water is valid here since for many applications involving transport of soluble gases in fractured rock, the rate of aqueous transport is insignificant compared to gas transport. We verify our modeling approach with analytical solutions of: (1) 1D gas diffusion, (2) 1D gas advection, (3) barometric pumping of a fracture, and (4) gas transport with uniform fracture flow and diffusion into the matrix. We account for pore-water storage in our model by implementing a kinetic formulation of gas dissolution wherein the dissolved (aqueous) phase is considered an immobile constituent. Using this formulation, we model the effect of dissolution rate and saturation on the retardation of gas transport during pure diffusion and pure advection. We also demonstrate that although it is commonly believed that pore-water storage will always enhance gas transport in fractures during oscillatory flow (e.g., during reversing pressure gradients such as barometric pumping cycles), our simulations indicate that this may not always be the case. Our numerical investigations indicate that scenarios with lower effective diffusion coefficients ( ⪅ 10 − 5  m 2 / s ) and lower dissolution coefficients (i.e., the dissolution diffusion coefficient) ( ⪅ 10 − 11  m 2 / s ) will result in enhanced gas transport. Other combinations of gaseous diffusion and dissolution coefficients result in delayed gas transport or insignificant effect on gas transport. Based on these results, and given the fact that the free-air diffusion coefficients for many gases are slightly above 10 − 5  m 2 / s (near the boundary of enhanced/non-enhanced gas transport), tortuosity would have to be significant for gas transport enhancement to occur. Similarly, if we consider the free-water diffusion coefficient of gases (around 10 − 9  m 2 / s for many gases of interest) to be a maximum bound for the effective dissolution coefficients (i.e., the rate of diffusion into the water away from the air/water interface will limit the dissolution rate), the effective dissolution coefficient would have to be at least 2 orders of magnitude less for enhanced gas transport to occur. Otherwise, pore-water storage will delay or have negligible effect on the gas transport. The results also indicate that the assumption of instantaneous equilibrium, often invoked in numerical codes for dissolution processes (i.e., dissolution coefficient is effectively infinite), will fail to accurately capture important details of soluble gas transport. Finally, the implication of our results is that gas breakthrough times in fractured rock during oscillatory flow may be highly dependent on the effective gaseous diffusion and dissolution coefficients.

58 GEOSCIENCES↗

DOE OSTI2026

Theoretical Insights into Reaction-Induced Transformation and Tuning of Catalytic Behavior in Heterogenous Catalysis

Reaction-induced transformations in heterogenous catalysis represent diverse phenomena that challenge traditional views of static catalyst surfaces. From surface adsorbate dynamics, atomic rearrangements, to composition and phase transitions, these processes reveal the profound differences between idealized model systems under ultrahigh vacuum and the complex, evolving interfaces that govern real catalytic behaviors under reaction conditions. Here, this perspective reviews recent theoretical efforts to provide atomic-level mechanistic insights into significant reaction-induced transformations and their impact on catalytic activity and selectivity. It underscores the need for an integrated framework that combines predictive simulations with operando characterization to uncover active sites and mechanisms under realistic operating conditions. Achieving this requires accelerating existing simulations to fully capture diverse reaction-induced surface dynamics, enabling scalable and accurate modeling of catalysts as condition-dependent, dynamically evolving systems. Such approaches are critical to bridge the gap between theory and practice, offering a pathway to more impactful and predictive catalyst design.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Solidification and grain formation in alloys: a 2D application of the grand-potential-based phase-field approach

Solidification is a significant step in the forming of crystalline structures during various manufacturing and material processing techniques. Solidification characteristics and the microstructures formed during the process dictate the properties and performance of the materials. Hence, understanding how the process conditions relate to various microstructure formations is paramount. In this work, a grand-potential-based multi-phase, multi-component, multi-order-parameter phase-field model is used to demonstrate the solidification of alloys in 2D. This model has several key advantages over other multi-phase models such as it decouples the bulk energy from the interfacial energy, removes the constraints for the phase concentration variable, and prevents spurious third-phase formation at the two phase interfaces. Here, the model is implemented in a finite-element-based phase-field modeling code. The role of various modeling parameters in governing the solidification rate and the shape of the solidified structure is evaluated. It is demonstrated that the process conditions such as temperature gradient, thermal diffusion, cooling rate, etc, influence the solidification characteristics by altering the level of undercooling. Furthermore, the capability of the model to capture directional solidification and polycrystalline structure formation exhibiting various grain shapes is illustrated. In both these cases, the process conditions have been related to the growth rate and associated shape of the dendritic structure. As a result, this work serves as a stepping stone towards resolving the larger problem of understanding the process–structure–property–performance correlation in solidified materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Neutron-Friendly Li-Ion Battery Coin Cell for In Situ 3D Visualization of Li Plating

Advanced battery characterization using in situ/operando neutron imaging is critical for uncovering degradation modes such as lithium (Li) plating in Li-ion batteries (LIBs). However, conventional LIBs hinder operando neutron radiography (NR) and in situ neutron micro-computed tomography (N-μCT) for visualizing Li plating near the graphite-separator interface due to strong attenuation from hydrogen-rich components like PP–PE–PP separators, electrolyte, and Fe-based spacers. In this work, we designed and tested a neutron-friendly battery (NFB) optimized for in situ Li detection during extreme fast charging (XFC). Guided by neutron attenuation cross-sections and material transmission, the NFB enables clear visualization at the graphite–separator interface, which is typically opaque in standard LIBs. Electrochemical tests show the NFB exhibits voltage/current responses like standard cells for up to 50 XFC cycles. However, its lower reversibility and capacity are likely due to Cu-coated Al spacer degradation from delamination or corrosion. We propose titanium spacers as a more stable alternative, albeit requiring custom machining. Using this optimized cell, we achieved simultaneous neutron tomography of multiple cells, capturing in situ 3D images of dead Li accumulation, particularly near graphite edges. These heterogeneous deposits and disconnected Li clusters suggest localized current density hotspots during XFC.

25 ENERGY STORAGE↗

DOE OSTI2019

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

The calcium calmodulin-dependent protein kinase II (CaMKII) is a dodecameric holoenzyme important for encoding memory. Its activation, triggered by binding of calcium-calmodulin, persists autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phosphorylates the regulatory domain peptide of a donor kinase forming a chained dimer as the first stage of autonomous activation. Protein dynamics simulations examined the conformational changes triggered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were characterized by network centrality and community analysis. Mutual information related collective motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD conformational ensembles revealed the dynamic architecture of inactive kinase domains was co-opted in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determinants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-lobe core. The relays were organized around a hydrophobic patch between the captured peptide and a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt the allosteric network alternatively, or in addition, to altered binding affinities. Non-binding protein sectors distant from the binding sites mediated the allosteric signalling; providing possible targets for inhibitor design. Phosphorylation of the peptide modulated the dielectric of its binding pocket to strengthen the patch, non-binding sectors, domain interface and temporal correlations between parallel relays. These results provide the molecular details underlying the reported positive kinase cooperativity to enrich the discussion on how autonomous activation by phosphorylation leads to long-term behavioural effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

A Joint Modeling/Experimental Approach to Characterize Ionization and Fragmentation of SOA Molecules with CIMS

The Molecular Dynamics technique Collective variable hyperdynamics (CVHD) interfaced with density functional tight-binding at the GFN1-xTB and GFN2-xTB levels of electronic structure theory has been applied to the H + GAG positively charged peptide system to explore the fragmentation of this simple tripeptide under relatively low temperature/energy conditions. Unlike conventional chemical dynamics simulations which can only be performed up to hundreds of picoseconds when coupled with semi-empirical Hamiltonians, CVHD is able to capture the long-time dynamics of multiple proton hopping, the formation of reversible ring structures, and ester rearrangement of the H + GAG system prior to fragmentation. The CVHD method applied to H + GAG is also able to uncover alternative fragmentation pathways not considered previously such as glycine fragmentation on the N-terminal side of the charged peptide and new cyclic cationic species. These findings in the H + GAG case have implications for other peptide systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2019

Augmented Reality for Managing Nuclear Infrastructure and Operations - 19605

Emerging augmented reality tools offer great promise for helping manage nuclear infrastructure throughout its life cycle. These tools have the ability to provide operators with actionable holographic information as they work. Perhaps more excitingly these tools also feature sensors that provide the ability to document work at very high spatial resolution. These sensors include onboard cameras as well as active infrared sensors that can capture 3D geometry information on-the-fly. Coupling the visualization and sensing tools provided by augmented reality headsets with computational intelligence opens up many exciting new possibilities for managing nuclear infrastructure throughout its life cycle. In this presentation we show a number of examples of how augmented reality tools can be incorporated into the management of nuclear infrastructure. We show examples of using augmented reality as a human-machine interface for robotic control, and we show examples of augmented reality being interfaced with external sensors. Finally, we show how these sensing and visualization capabilities of augmented reality can be interfaced with intelligent algorithms to help operators perform their work in nuclear facilities. The goal of the work is to spark discussions on how emerging augmented reality tools can help enable the next generation of efficient, high-performance nuclear infrastructure. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Coupling of Nondegenerate Topological Modes in Nitrogen Core-Doped Graphene Nanoribbons

Nitrogen core-doping of graphene nanoribbons (GNRs) allows trigonal planar carbon atoms along the backbone of GNRs to be substituted by higher-valency nitrogen atoms. The excess valence electrons are injected into the π-orbital system of the GNR, thereby changing not only its electronic occupation but also its topological properties. We have observed this topological change by synthesizing dilute nitrogen core-doped armchair GNRs with a width of five atoms (N 2 -5-AGNRs). The incorporation of pairs of trigonal planar nitrogen atoms results in the emergence of topological boundary states at the interface between doped and undoped segments of the GNR. These topological boundary states are offset in energy by approximately ΔE = 300 meV relative to the topological end states at the termini of finite 5-AGNRs. Scanning tunneling microscopy (STM) and spectroscopy (STS) reveal that for finite GNRs the two types of topological states can interact through a linear combination of orbitals, resulting in a pair of asymmetric hybridized states. This behavior is captured by an effective Hamiltonian of nondegenerate diatomic molecules, where the analogous interatomic hybridization interaction strength is tuned by the distance between GNR topological modes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Detailed simulations of the first deuterium-tritium-filled double shell implosions on the National Ignition Facility

The first indirectly driven, liquid DT-filled double shell inertial confinement fusion (ICF) implosions have recently been successfully performed on the National Ignition Facility (NIF). Double shells are a class of alternative designs that use a low-Z outer shell to compress a foam cushion that accelerates a high-Z inner shell to efficiently compress a liquid DT core. Double shells are challenging to fabricate, field, and model. Important engineering features enabling double shell fabrication include a fill-tube penetrating all shells and a carefully designed and very narrow (few μm) step-joint in the ablator. Due to the higher density materials involved, high Atwood number instabilities are also important at many material interfaces. In this paper, numerical simulations of double shell implosions using the Los Alamos National Laboratory multi-physics radiation-hydrodynamics code xRAGE will be discussed. An extensive effort has been under way for several years to develop the code capabilities for ICF simulations in a common modeling framework to allow ease of simulation setup and standardization of the computational methodology. This paper will present a wide range of simulation results capturing, quantifying, and comparing the impact of all these degradation mechanisms on implosion performance. Brief comparisons with recent experimental results and suggestions for future improvements will also be discussed. Our results suggest that capsule surface roughness and the step-joint gap have the largest impact on implosion performance. Initial experimental data may suggest that the sensitivity to the step-joint gap could provide the dominant explanation for DT-filled double shell experiments that have been fielded on NIF thus far.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Polyimide dynamically compressed to decomposition pressures: Two-wave structures captured by velocimetry and modeling

We performed a series of six plate impact experiments on polyimide and modeled them using new reactant and products equations of state combined with an Arrhenius rate model. The first experiment was diagnosed with embedded electromagnetic velocity gauges through which we directly observed attenuation of the lead shock to an approximately constant state over a propagation distance of roughly 4 mm. Simulated gauge profiles were in excellent qualitative agreement with experiment and suggested a sluggish chemical reaction that did not proceed to completion. The remaining five experiments were conducted in a transmission geometry and diagnosed velocimetrically at the sample/window interface. All five of these yielded profiles with a sharp shock followed by a more gradual approach to maximum interface velocity that was “rounded” to varying degree. These profiles proved difficult to interpret unambiguously due to the convolution of the reactive wave upon first shock with reflection of the lead wave and reshock or release by the window. Comparison with thermochemical calculations strongly suggests that the point of maximum interface velocity corresponds to the equilibrium reshock or release locus. We discuss the implications of this point for the practice of impedance matching based on the reflected Hugoniot of reactive materials such as polymers. The reactant and thermochemical products equations of state are developmental SESAME tables 97710 and 97720, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Towards a predictive, physics-based friction model for the dynamics of jointed structures

Bolted connections are ubiquitous in mechanical designs and pose a significant challenge to understanding and predicting the vibration response of assembled structures. The present paper develops a physics-based rough contact model of the frictional interactions within a joint. This model sums over the probable interactions of asperities – defined as locally maximum surface features – to determine the contact forces. Here, the tangential contact forces vary smoothly between sticking and slipping and allow the model to better capture the qualitative trends of experimental amplitude dependent frequency and damping than previous studies. Furthermore, the novel model is generalized to allow for arbitrarily varying normal pressure including potential separation to better represent the interfacial dynamics. This includes developing a new, computationally tractable approximation to the analytical Mindlin partial slip solution for tangential loading of contacting spheres. Further, the results highlight the importance of accurately characterizing the as-built topology of the interface, the plastic behavior of the contacting asperities, the relevant length scale of asperities, and the eccentricity of asperities. A predictive friction coefficient based on plasticity provides a poor match to experiments, so fitting the friction coefficient is also considered. Numerical results are compared to experiments on the Brake-Reuß Beam to assess the predictive potential of the models. While blind predictions over-predict the slip limit, the current model presents a significant improvement in physics-based modeling and highlights areas for ongoing research.

42 ENGINEERING↗

DOE OSTI2020

Modeling a ring magnet in ALEGRA

We show here that Sandia's ALEGRA software can be used to model a permanent magnet in 2D and 3D, with accuracy matching that of the open-source commercial software FEMM. This is done by conducting simulations and experimental measurements for a commercial-grade N42 neodymium alloy ring magnet with a measured magnetic field strength of approximately 0.4 T in its immediate vicinity. Transient simulations using ALEGRA and static simulations using FEMM are conducted. Comparisons are made between simulations and measurements, and amongst the simulations, for sample locations in the steady-state magnetic field. The comparisons show that all models capture the data to within 7%. The FEMM and ALEGRA results agree to within approximately 2%. The most accurate solutions in ALEGRA are obtained using quadrilateral or hexahedral elements. In the case where iron shielding disks are included in the magnetized space, ALEGRA simulations are considerably more expensive because of the increased magnetic diffusion time, but FEMM and ALEGRA results are still in agreement. The magnetic field data are portable to other software interfaces using the Exodus file format.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A Generalized Transformer-Based Pulse Detection Algorithm

Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗