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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

First-principles DFT modeling of nitrobenzene adsorption on the Ag(111) surface at varying monolayer coverages

Here, the adsorption behavior of nitrobenzene on the Ag(111) surface as a function of coverage is investigated using density functional theory. Adsorption energies and optimized geometries are analyzed together with isolated intermolecular interaction calculations and electronic structure analysis, including Bader charge partitioning and projected density of states, to disentangle the roles of adsorbate–surface bonding and through-space adsorbate–adsorbate interactions. At low and intermediate coverages (θ = 1/9 and θ = 2/9), bidentate adsorption at top sites is favored due to strong adsorbate–surface interactions, with additional stabilization at θ = 2/9 arising from favorable intermolecular separations. At higher coverage (θ = 1/3), bidentate adsorption is destabilized by strong intermolecular repulsion, and monodentate adsorption becomes energetically preferred as rotational freedom allows more favorable intermolecular spacing. Charge density differences, Bader charge, and density of states analyses show that charge transfer from the Ag surface is localized primarily on the nitro group and increases with coverage and adsorption denticity, although this increase does not directly correlate with adsorption strength at high coverage due to competing intermolecular interactions. These results demonstrate that surface coverage can induce a transition in preferred adsorption denticity driven by intermolecular interactions, highlighting the importance of adsorbate packing in organic molecule adsorption at metal interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2024

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Many-Body Benchmark of Electronic Charge and Spin Densities for Li 1–x NiO 2

Accurate benchmarks are particularly important for highly correlated oxides as mean-field approximations often fail to describe the subtle balance of charge transfer and magnetism in these materials with an accuracy comparable to experimental needs. Here we present accurate diffusion Monte Carlo (DMC) results of the electronic charge and spin densities for the tunable highly correlated oxide Li 1–x NiO 2 for x = 0, 1/2, and 1. To enable quantitative comparisons, we introduce a robust density-partitioning scheme, extending Voronoi analysis to assign atomic charges from spatially noisy DMC densities. We then benchmark common approximations used in density functional theory (DFT). Comparison against DMC shows that r 2 SCAN delivers the most balanced performance across charge, spin, and radial density descriptors, nearly reproducing DMC results for LiNiO 2 and apical Ni sites in Li 0.5 NiO 2 . Hybrid functionals (PBE0, SCAN0) perform unexpectedly poorly, and PBE + U + V yields inconsistent trends between charge and spin densities. Therefore, the r 2 SCAN functional minimizes errors relative to DMC while capturing the variable valence of the Ni ion and also retaining the computational efficiency of DFT for large-scale simulations of the tunable structural and electronic phases of Li1−xNiO2. Our study highlights the importance of accurate benchmarking of the fundamental quantities involved in DFT to select appropriate DFT approximations in order to advance the predictive modeling of charge-transfer-driven phenomena in correlated electron systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A coupled discontinuous Galerkin-Finite Volume framework for solving gas dynamics over embedded geometries

Herein, we present a computational framework for solving the equations of inviscid gas dynamics using structured grids with embedded geometries. The novelty of the proposed approach is the use of high-order discontinuous Galerkin (dG) schemes and a shock-capturing Finite Volume (FV) scheme coupled via an hp adaptive mesh refinement (hp-AMR) strategy that offers high-order accurate resolution of the embedded geometries. The hp-AMR strategy is based on a multi-level block-structured domain partition in which each level is represented by block-structured Cartesian grids and the embedded geometry is represented implicitly by a level set function. The intersection of the embedded geometry with the grids produces the implicitly-defined mesh that consists of a collection of regular rectangular cells plus a relatively small number of irregular curved elements in the vicinity of the embedded boundaries. High-order quadrature rules for implicitly-defined domains enable high-order accuracy resolution of the curved elements with a cell-merging strategy to address the small-cell problem. The hp-AMR algorithm treats the system with a second-order finite volume scheme at the finest level to dynamically track the evolution of solution discontinuities while using dG schemes at coarser levels to provide high-order accuracy in smooth regions of the flow. On the dG levels, the methodology supports different orders of basis functions on different levels. The space-discretized governing equations are then advanced explicitly in time using high-order Runge-Kutta algorithms. Numerical tests are presented for two-dimensional and three-dimensional problems involving an ideal gas. The results are compared with both analytical solutions and experimental observations and demonstrate that the framework provides high-order accuracy for smooth flows and accurately captures solution discontinuities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

Abstract In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2023

Development of a molecularly informed biogeochemical framework for reactive transport modeling of subsurface carbon inventories, transformations and fluxes (Final Report)

The overall objective of the project was to combine new molecular-level characterization strategies with soil carbon flux measurements to develop and evaluate model representations of subsurface carbon cycling. We expanded on existing studies in the East River watershed, Colorado, in collaboration with the Berkeley Lab Watershed Function Scientific Focus Area (SFA), SLAC Groundwater Quality SFA, and Rocky Mountain Biological Laboratory (RMBL) to develop an elevation and vegetation gradient that is now the subject of long-term monitoring by the USGS. To achieve the overall objective, we combined field studies of soil respiration with laboratory analyses, ranging from spectroscopy to incubation studies. This combination of techniques enabled us to develop a new understanding of the drivers of high-elevation soil respiration. In the process, we developed three new modeling approaches that improve our ability to conceptualize and ultimately to represent soil respiration in numerical models. The first approach is a plot-scale transient inverse model that can be used to determine in situ CO 2 production rates from measured concentration profiles and surface fluxes. Application of this method revealed the importance of plant phenology and deep CO 2 production in moderating CO 2 fluxes to the atmosphere. The second modeling approach is a molecular-scale tool that enables spectroscopic and elemental data for carbon speciation to be transformed into functional group abundances, or the ‘SOC-fga model’. This method uniquely enables carbon speciation to be tracked within a reactive transport framework to partition carbon among different pathways and storage zones within the soil. The third modeling tool builds strongly on the previous approaches and captures the microbial processes driving heterotrophic respiration. This ‘dormancy model’ allows the native soil microbial population to respond transiently to the presence or absence of water in order to catalyze carbon respiration. This approach was also compared to the simpler and more widely used first-order model using two experimental datasets with different temporal and spatial resolutions. Our results illustrate that the simpler first order model provides a robust and efficient representation of deep (>1 meter) soil respiration, but that shallow soils, where most respiration occurs, require explicit representation of moisture-dependent activation and dormancy rates. By assessing soil organic carbon turnover at multiple scales, we see a complex array of controls emerge. Atte scale of a hillslope, spatial heterogeneity in soil respiration rates dominates and is uncorrelated with instantaneous soil moisture and plant community. At the profile scale, the balance between plant inputs and water availability is the dominant control. At the microbial to molecular scale, physiological processes associated with carbon use and carbon speciation are important controls. These scale-dependent controls emphasize the need for new modeling approaches that examine their interactions and hierarchies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Urban weather modeling using WRF: linking physical assumptions, code implementation, and observational needs

The Weather Research and Forecasting (WRF) model includes urban schemes that simulate the influence of urban surfaces on the atmosphere using parameterizations for flux, and radiative exchanges. Three core schemes – the Bulk urban parameterization, Single-Layer Urban Canopy Model (SLUCM), and Multi-Layer Urban Canopy Model (MLUCM) – represent increasing levels of complexity. Although the parameterizations within these urban schemes are described in the literature, their specific implementation remains poorly documented, thus slowing down model development efforts. This manuscript provides a roadmap to the three urban schemes in WRF version 4.5.2, presenting equations using the same symbols as in the model code, along with references to code lines, and including graphics and explanations that connect the code to its physical foundations. Our thorough review of the urban parameterizations implemented in WRF version 4.5.2 highlighted a handful of parameters that may introduce discontinuities in simulations: (i) in the SLUCM, a 1 mm h −1 rain rate threshold is employed to switch between two minimum moisture availability parameterizations, thus impacting latent heat flux calculations; (ii) in the SLUCM a threshold is used to partition shortwave radiation into direct and diffuse components; (iii) in all three urban schemes, the bulk Richardson number is employed to select the similarity function, which influences the vertical distribution of heat and momentum. We also identified a highly simplified treatment of the radiative balance on roof surfaces. The implications of these simplifications can be assessed through targeted observations across relevant conditions, including varying precipitation rates, cloud cover, and transitions between stability regimes. Furthermore, the widespread application of the Monin-Obukhov similarity theory in these urban schemes warrants model evaluation under highly stable and unstable conditions and in heterogeneous urban settings with variable land cover and building heights on scales finer than model resolution. To address these challenges, we offer guidance on observational strategies, emphasizing the need for multi-parametric measurements to capture potential compensating biases and multi-height measurements that align with the levels where quantities are diagnostic and prognosed in the model (i.e., the lowest atmospheric level of the WRF model). Finally, our inspection of the code revealed implementation bugs that have now been corrected in WRF versions 4.6.0 and 4.6.1. Sensitivity tests over the Atlanta urban area show that these corrections affect surface temperatures, underscoring the importance of performing rigorous documentation and verification of the implementation of parameterizations in model code.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Alloy Partitioning Effect on Strength and Toughness of κ-Carbide Strengthened Steels

Alloy partitioning during heat treatment in a lightweight precipitation hardened steel was investigated using transmission electron microscopy and atom probe tomography. The mechanical properties are discussed as a function of the effect of solution treatment temperature and aging time, giving rise to variations in chemical modulation. A wrought lightweight steel alloy with a nominal composition of Fe-30Mn-9Al-1Si-1C-0.5Mo (wt. %) was solution-treated between 1173–1273 K and aged at 773 K. Lower solution treatment temperatures retained a finer grain size and accelerated age hardening response that also produced an improved work hardening behavior with a tensile strength of -1460 MPa at 0.4 true strain. Atom probe tomography indicated these conditions also had reduced modulation in the Si and Al content due to the reduced aging time preventing silicon from diffusing out of the κ-carbide into the austenite. This work provides the framework for heat-treating lightweight, age hardenable steels with high strength and improved energy absorption.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Pore-Space-Partition-Enabled Exceptional Ethane Uptake and Ethane-Selective Ethane–Ethylene Separation

A modell material for C 2 H 6 /C 2 H 4 separation would simultaneously have the highest C 2 H 6 uptake capacity and the highest C 2 H 6 /C 2 H 4 selectivity. But such material is elusive. A benchmark material for ethane-selective C 2 H 6 /C 2 H 4 separation is peroxo-functionalized MOF-74-Fe that exhibits the best known separation performance due to its high C 2 H 6 /C 2 H 4 selectivity (4.4), although its C 2 H 6 uptake capacity is moderate (74.3 cm 3 /g). Here, we report a family of pore-space-partitioned crystalline porous materials (CPMs) with exceptional C 2 H 6 uptake capacity and C 2 H 6 /C 2 H 4 separation potential (i.e., C 2 H 4 recovered from the mixture) despite their moderate C 2 H 6 /C 2 H 4 selectivity (up to 1.75). The ethane uptake capacity as high as 166.8 cm 3 /g at 1 atm and 298 K, more than twice that of peroxo-MOF-74-Fe, was previously achieved even though the isosteric heat of adsorption (21.9–30.4 kJ/mol) for these CPMs is as low as about one-third of that for peroxo-MOF-74-Fe (66.8 kJ/mol). While the overall C 2 H 6 /C 2 H 4 separation potentials have not yet surpassed peroxo-MOF-74-Fe, these robust CPMs exhibit outstanding properties including high thermal stability (up to 450 °C) and aqueous stability, low regeneration energy, and a high degree of chemical and geometrical tunability within the same isoreticular framework.

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

Golden ratio in venation patterns of dragonfly wings

Abstract The vein pattern in insect wings allows this lightweight structure to carry multiple biological functions. Here, an investigation of the angular distribution of the vein struts in dragonfly wings revealed that the golden angle or golden ratio dominates the venation patterns. We find that the golden angle dominates the intervein angles in regions where thin veins and membranes demand strength reinforcement. A golden ratio partition method has thus been developed that explains a set of preferred intervein angles in distorted polygon-shaped venation cells throughout the venation pattern in dragonfly wings. These observations provide new evidence that the wing structure is spatially optimized, by the golden rule in nature, for supporting biomechanical functions of dragonfly wings.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A multi-center quadrature scheme for the molecular continuum

We report a common way to evaluate electronic integrals for polyatomic molecules is to use Becke’s partitioning scheme (Becke and Chem, 1988) in conjunction with overlapping grids centered at each atomic site. The Becke scheme was designed for integrands that fall off rapidly at large distances, such as those approximating bound electronic states. When applied to states in the electronic continuum, however, Becke scheme exhibits slow convergence and it is highly redundant. Here, we present a modified version of Becke scheme that is applicable to functions of the electronic continuum, such as those involved in molecular photoionization and electron–molecule scattering, and which ensures convergence and efficiency comparable to those realized in the calculation of bound states. In this modified scheme, the atomic weights already present in Becke’s partition are smoothly switched off within a range of few bond lengths from their respective nuclei, and complemented by an asymptotically unitary weight. The atomic integrals are evaluated on small spherical grids, centered on each atom, with size commensurate to the support of the corresponding atomic weight. The residual integral of the interstitial and long-range region is evaluated with a central master grid. The accuracy of the method is demonstrated by evaluating integrals involving integrands containing Gaussian Type Orbitals and Yukawa potentials, on the atomic sites, as well as spherical Bessel functions centered on the master grid. These functions are representative of those encountered in realistic electron-scattering and photoionization calculations in polyatomic molecules.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Adiabatic quantum decoherence in many non-interacting subsystems induced by the coupling with a common boson bath

Highlights: • System–environment quantum correlation: a main solid state NMR decoherence channel. • Non-separable system–environment model yields realistic spin decoherence rates. • New open quantum system approach explains irreversible decay of refocused NMR echoes. • Adiabatic quantum decoherence is inherently irreversible and eigen-selective. This work addresses adiabatic quantum decoherence of many-body spin systems coupled with a boson field in the framework of open quantum systems theory. We generalize the traditional spin-boson model by considering a system–environment interaction Hamiltonian that represents a partition of non-interacting subsystems and highlights the collective correlation that appears exclusively due to the coupling with a common environment. Remarkably, this simple, exactly solvable model encompasses relevant aspects of a many-body open quantum system and features the subtle quantum effects that arise when the size scales up to a macroscopic level. We derive an analytical expression for the time dependence of the density matrix elements (in the preferred basis) without assuming coarse-graining. The resulting decoherence function is eigen-selective and is a complex exponential whose exponent has a real part that introduces a decay similar to that in the spin-boson model. On the contrary, the imaginary part depends on the quantum numbers and geometry of the whole partition and does not reflect the system temperature. Motivated by decoherence in solid-state NMR, and in search of realistic numerical estimations, we apply the theoretical results to a partition of dipole-coupled spin pairs in contact with a common phonon bath, using typical parameters of hydrated salts. The proposal allows estimating the decoherence time scale in terms of the system physical constants: sound velocity and eigenvalue distribution width. As a significant novelty, the decoherence function phase depends on the eigenvalue distribution throughout the sample. It plays the leading role, overshadowing the mechanism associated with the bath thermal state. Finally, we apply the formalism to describe decoherence in the “magic echo” NMR reversal experiment. We find that the system–environment correlation explains the origin of irreversibility, and both the decoherence rate value and its dependence on the dipolar frequency, are remarkably similar to the experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Degradation and fate of 2,4-dinitroanisole (DNAN) and its intermediates treated with Mg/Cu bimetal: Surface examination with XAS, DFT, and LDI-MS

In this article, a novel Mg-based bimetal reagent (Mg/Cu) was used as an enhanced reductive system to degrade insensitive munition 2,4-dinitroanisole (DNAN), a contaminant found in energetic-laden waste. Degradation of DNAN was significantly impacted by dissolved oxygen and studied in anoxic and oxic bimetal systems (i.e., purging with N 2 , air, or O 2 gas). Degradation occurred through sequential nitroreduction: first one nitro group was reduced (ortho or para) to form short-lived intermediates 2-amino-4-nitroanisole or 4-amino-2-nitroanisole (2-ANAN or 4-ANAN), and then subsequent reduction of the other nitro group formed 2,4-diaminoanisole (DAAN). The nitro-amino intermediates demonstrated regioselective reduction in the ortho position to 2-ANAN; Regioselectivity was also impacted by the anoxic/oxic environment. Under O 2 -purging DNAN degradation rate was slightly enhanced, but most notably O 2 significantly accelerated DAAN generation. DAAN also further degraded only in the oxygenated Mg/Cu system. Adsorption of DNAN byproducts to the reagent occurred regardless of anoxic/oxic condition, resulting in a partition of carbon mass between the adsorbed phase (27%-35%) and dissolved phase (59%-72%). Additional surface techniques were applied to investigate contaminant interaction with Cu. Density functional theory (DFT) calculations identified preferential adsorption structures for DNAN on Cu with binding through two O atoms of one or both nitro groups. X-ray absorption spectroscopy (XAS) measurements determined the oxidation state of catalytic metal Cu and formation of a Cu-O-N bond during treatment. Laser desorption ionization mass spectrometry (LDI-MS) measurements also identified intermediate 2-ANAN adsorbed to the bimetal surface.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

BARC Element Classifier (barc)

SAND2024-02120O This program enumerates and classifies all possible functional elements in several different categories within the Ballistic Asynchronous Reversible Computing (barc) model of computation. barc software is a research tool that is being used to help document the possible digital behaviors of primitive functional elements in the ABRC a.k.a. BARC model of computation. The method of operation of this software leverages elementary concepts and methods from discrete mathematics: combinatorics (permutations), partitions and equivalence classes, symmetry transformations, and the theory of finite groups. Implementation is in Python programming language. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Frank, Michael↗
DOE OSTI2020

Evaluating asynchronous Schwarz solvers on GPUs

With the commencement of the exascale computing era, we realize that the majority of the leadership supercomputers are heterogeneous and massively parallel. Even a single node can contain multiple co-processors such as GPUs and multiple CPU cores. For example, ORNL’s Summit accumulates six NVIDIA Tesla V100 GPUs and 42 IBM Power9 cores on each node. Synchronizing across compute resources of multiple nodes can be prohibitively expensive. Hence, it is necessary to develop and study asynchronous algorithms that circumvent this issue of bulk-synchronous computing. In this study, we examine the asynchronous version of the abstract Restricted Additive Schwarz method as a solver. We do not explicitly synchronize, but allow the communication between the sub-domains to be completely asynchronous, thereby removing the bulk synchronous nature of the algorithm. We accomplish this by using the one-sided Remote Memory Access (RMA) functions of the MPI standard. We study the benefits of using such an asynchronous solver over its synchronous counterpart. We also study the communication patterns governed by the partitioning and the overlap between the sub-domains on the global solver. Finally, we show that this concept can render attractive performance benefits over the synchronous counterparts even for a well-balanced problem.

Nayak, Pratik↗
DOE OSTI2021

Mass accommodation and gas–particle partitioning in secondary organic aerosols: dependence on diffusivity, volatility, particle-phase reactions, and penetration depth

Abstract. Mass accommodation is an essential process for gas–particle partitioning of organic compounds in secondary organic aerosols (SOA). The mass accommodation coefficient is commonly described as the probability of a gas molecule colliding with the surface to enter the particle phase. It is often applied, however, without specifying if and how deep a molecule has to penetrate beneath the surface to be regarded as being incorporated into the condensed phase (adsorption vs. absorption). While this aspect is usually not critical for liquid particles with rapid surface–bulk exchange, it can be important for viscous semi-solid or glassy solid particles to distinguish and resolve the kinetics of accommodation at the surface, transfer across the gas–particle interface, and further transport into the particle bulk. For this purpose, we introduce a novel parameter: an effective mass accommodation coefficient αeff that depends on penetration depth and is a function of surface accommodation coefficient, volatility, bulk diffusivity, and particle-phase reaction rate coefficient. Application of αeff in the traditional Fuchs–Sutugin approximation of mass-transport kinetics at the gas–particle interface yields SOA partitioning results that are consistent with a detailed kinetic multilayer model (kinetic multilayer model of gas–particle interactions in aerosols and clouds, KM-GAP; Shiraiwa et al., 2012) and two-film model solutions (Model for Simulating Aerosol Interactions and Chemistry, MOSAIC; Zaveri et al., 2014) but deviate substantially from earlier modeling approaches not considering the influence of penetration depth and related parameters. For highly viscous or semi-solid particles, we show that the effective mass accommodation coefficient remains similar to the surface accommodation coefficient in the case of low-volatility compounds, whereas it can decrease by several orders of magnitude in the case of semi-volatile compounds. Such effects can explain apparent inconsistencies between earlier studies deriving mass accommodation coefficients from experimental data or from molecular dynamics simulations. Our findings challenge the approach of traditional SOA models using the Fuchs–Sutugin approximation of mass transfer kinetics with a fixed mass accommodation coefficient, regardless of particle phase state and penetration depth. The effective mass accommodation coefficient introduced in this study provides an efficient new way of accounting for the influence of volatility, diffusivity, and particle-phase reactions on SOA partitioning in process models as well as in regional and global air quality models. While kinetic limitations may not be critical for partitioning into liquid SOA particles in the planetary boundary layer (PBL), the effects are likely important for amorphous semi-solid or glassy SOA in the free and upper troposphere (FT–UT) as well as in the PBL at low relative humidity and low temperature.

54 ENVIRONMENTAL SCIENCES↗