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DOE OSTI2022

Main and Satellite Features in the Ni 2p XPS of NiO

The origin and assignment of the complex main and satellite XPS features of the cations in ionic compounds has been the subject of extensive theoretical studies using different methods. There is agreement that within a molecular orbital model one needs to take into account different types of configurations. Specifically, those where a core electron is removed but no other configuration changes are made and those where in addition to ionization there are also shake or charge transfer changes to the ionic configuration. However, there are strong disagreements about the assignment of XPS features to these configurations. The present work is directed toward resolving the origin of main and satellite features for the Ni 2p XPS of NiO based on ab initio molecular orbital wavefunctions for a cluster model of NiO. A major problem in earlier ab initio XPS studies of ionic compounds has been the use of a common set of orbitals that was not able to properly describe all the ionic configurations that contribute to the full XPS spectra. This is resolved in the present work by using orbitals that are optimized for averages of the occupations of the different configurations that contribute to the XPS. The approach of using State Averaged orbitals is validated through comparisons between different averages and through use of higher order excitations in the wavefunctions for the ionic states. It represents a major extension of our earlier work on the main and satellite features of the Fe 2p XPS of Fe 2 O 3 and proves the reliability and the generality of the assignments of the character and origin of the different features of the XPS obtained with orbitals optimized for State Averages. These molecular orbital methods permit the characterization of the ionic states in terms of the importance of shake excitations and of the coupling of ionization of 2p 1/2 and 2p 3/2 spin-orbit split sub shells. Further, the work lays the foundation for definitive assignments of the character of main and satellite XPS features and points to their origin in the electronic structure of the material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Using Computationally-Determined Properties for Machine Learning Prediction of Self-Diffusion Coefficients in Pure Liquids

The ability to predict transport properties of liquids quickly and accurately will greatly improve our understanding of fluid properties both in bulk and complex mixtures, as well as in confined environments. Such information could then be used in the design of materials and processes for applications ranging from energy production and storage to manufacturing processes. As a first step, we consider the use of machine learning (ML) methods to predict the diffusion properties of pure liquids. Recent results have shown that Artificial Neural Networks (ANNs) can effectively predict the diffusion of pure compounds based on the use of experimental properties as the model inputs. In the current study, a similar ANN approach is applied to modeling diffusion of pure liquids using fluid properties obtained exclusively from molecular simulations. A diverse set of 102 pure liquids is considered, ranging from small polar molecules (e.g., water) to large nonpolar molecules (e.g., octane). Self-diffusion coefficients were obtained from classical molecular dynamics (MD) simulations. Since nearly all the molecules are organic compounds, a general set of force field parameters for organic molecules was used. The MD methods are validated by comparing physical and thermodynamic properties with experiment. Computational input features for the ANN include physical properties obtained from the MD simulations as well as molecular properties from quantum calculations of individual molecules. Furthermore, fluid properties describing the local liquid structure were obtained from center of mass radial distribution functions (COM-RDFs). Feature sensitivity analysis revealed that isothermal compressibility, heat of vaporization, and the thermal expansion coefficient were the most impactful properties used as input for the ANN model to predict the MD simulated self-diffusion coefficients. The MD-based ANN successfully predicts the MD self-diffusion coefficients with only a subset (2 to 3) of the available computationally determined input features required. A separate ANN model was developed using literature experimental self-diffusion coefficients as model targets. Although this second ML model was not as successful due to a limited number of data points, a good correlation is still observed between experimental and ML predicted self-diffusion coefficients.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2019

Atmospheric Chemistry Modeling Using Machine Learning

Atmospheric chemistry models are a central tool to study the impact of chemical constituents on the environment, vegetation and human health. These models split the atmosphere in a large number of grid-boxes and consider the emission of compounds into these boxes and their subsequent transport, deposition, and chemical processing. The chemistry is represented through a series of simultaneous ordinary differential equations, one for each compound. Given the difference in life-times between the chemical compounds (milli-seconds for O1D to years for CH4) these equations are numerically stiff and solving them consists of a significant fraction of the computational burden of a chemistry model. We have investigated a machine learning approach to emulate the chemistry instead of solving the differential equations numerically. From a one-month simulation of the GEOS-Chem model we have produced a training dataset consisting of the concentration of compounds before and after the differential equations are solved, together with some key physical parameters for every grid-box and time-step. From this dataset we have trained a machine learning algorithm (regression forest) to be able to predict the concentration of the compounds after the integration step based on the concentrations and physical state at the beginning of the time step. We have then included this algorithm back into the GEOS-Chem model, bypassing the need to integrate the chemistry. This machine learning approach shows many of the characteristics of the full simulation and has the potential to be substantially faster. There are a wide range of application for such an approach - generating boundary conditions, for use in air quality forecasts, chemical data assimilation systems, etc. We discuss speed and accuracy of our approach, and highlight some potential future directions for improving it.

Keller, Christoph A.↗

NASA NTRS2021

Intercomparison of the representations of the atmospheric chemistry of pre-industrial methane and ozone in earth system and other global chemistry-transport models

An intercomparison has been set up to study the representation of the atmospheric chemistry of the pre-industrial troposphere in earth system and other global tropospheric chemistry-transport models. The intercomparison employed a constrained box model and utilised tropospheric trace gas composition data for the pre-industrial times at ninety mid-latitude surface locations. Incremental additions of four organic compounds: methane, ethane, acetone and propane, were used to perturb the constrained box model and generate responses in hydroxyl radicals and tropospheric ozone at each location and with each chemical mechanism. Although the responses agreed well across the chemical mechanisms from the selected earth system and other global tropospheric chemistry-transport models, there were differences in the detailed responses between the chemical mechanisms that could be tracked down by sensitivity analysis to differences in the representation of C1–C3 chemistry. Inter-mechanism ranges in NOx compensation points were about 0.17 ± 0.12 when expressed relative to the inter-mechanism average. Monte Carlo uncertainty analysis carried out with a single chemical mechanism put the intra-mechanism range a factor of three higher at 0.50 ± 0.12. Similar differences between inter-mechanism and intra-mechanism ranges were found for hydroxyl radical depletion but were up to a factor of six wider for ozone formation from incremental additions of organic compounds. The cause of the discrepancies between the inter- and intra-mechanism ranges was found to be the large uncertainties that are present in the laboratory determinations of the rate coefficients and product channel branching ratios of some key chemical reactions involving organic peroxy radicals and hydroperoxides. Whilst these large uncertainties are present in the laboratory determinations, there will be irreducible uncertainties in the predictions from the earth system and other chemistry-transport models of methane and tropospheric ozone trends since pre-industrial times and hence their contributions to the radiative forcing of climate change. Further definitive laboratory studies of the reaction rates and product yields of the reactions of the simple organic peroxy radicals and hydroperoxides are required to resolve and reduce current uncertainties in earth system and chemistry-transport model predictions.

atmospheric chemistry↗

DOE OSTI2022

Thermodynamics Modeling for Actinide Monocarbides and Mononitrides from First Principles

The high-temperature thermodynamical properties for the actinide monocarbides and mononitrides ThC, ThN, UC, UN, PuC, and PuN are calculated from first-principles electronic-structure theory. The electronic structure is modeled with density-functional theory (DFT) and is fully relativistic, including the spin-orbit interaction. Furthermore, the DFT is extended to account for orbital–orbital interactions, by means of a parameter-free orbital-polarization (OP) technique, that has proven to be essential for the 5f electrons in plutonium. Strong anharmonicity and the temperature dependence of the lattice vibrations are captured with the self-consistent ab initio lattice dynamics (SCAILD) method. The calculated free energies and heat capacities are compared to published results from quasi-harmonic (QH) theory, and experiments, where available. For the uranium and plutonium compounds, we make use of CALPHAD assessments to help evaluate the theory. Generally, our anharmonic relativistic approach compares well with both CALPHAD and experiments. For the thorium compounds, our theory is in good accord with QH modeling of the free energy at lower temperatures but for the heat capacity the comparison is less favorable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear Cu I Compounds

A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO 2 reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between CuI and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, K eq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Lastly, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Capturing the Relative‐Humidity‐Sensitive Gas–Particle Partitioning of Organic Aerosols in a 2D Volatility Basis Set

Abstract Aerosol water affects the physicochemical properties and mass concentration of organic aerosols (OA), but it is typically omitted by air quality, weather, and climate models. We compare two classes of simplified models to estimate the OA water uptake and gas–particle partitioning of organic compounds. One class uses a single‐hygroscopicity‐parameter (κ) approach while the other is based on the reduced‐complexity Binary Activity Thermodynamics (BAT) model. We show that a BAT‐based two‐dimensional volatility basis set (VBS) model always predicts a higher OA mass concentration at elevated relative humidity (RH), for example, ∼16% at 80% RH, than any variation of theκ‐based method considered—even when BAT‐VBS predicts a lower water uptake. The main reason being that the BAT‐VBS model captures variations in effective saturation mass concentration of organics (C*) with RH, a feature that other VBS methods lack. The BAT‐VBS framework offers an efficient, RH‐sensitive treatment for reduced‐complexity OA modeling.

Geology↗

NASA NTRS2019

Machine Learning Application to Atmospheric Chemistry Modeling

Atmospheric chemistry models are a central tool to study the impact of chemical constituents on the environment, vegetation and human health. These models split the atmosphere in a large number of grid-boxes and consider the emission of compounds into these boxes and their subsequent transport, deposition, and chemical processing. The chemistry is represented through a series of simultaneous ordinary differential equations, one for each compound. Given the difference in life-times between the chemical compounds (milli-seconds for O (sup 1) D (Deuterium) to years for CH4) these equations are numerically stiff and solving them consists of a significant fraction of the computational burden of a chemistry model. We have investigated a machine learning approach to emulate the chemistry instead of solving the differential equations numerically. From a one-month simulation of the GEOS-Chem model we have produced a training dataset consisting of the concentration of compounds before and after the differential equations are solved, together with some key physical parameters for every grid-box and time-step. From this dataset we have trained a machine learning algorithm (regression forest) to be able to predict the concentration of the compounds after the integration step based on the concentrations and physical state at the beginning of the time step. We have then included this algorithm back into the GEOS-Chem model, bypassing the need to integrate the chemistry. This machine learning approach shows many of the characteristics of the full simulation and has the potential to be substantially faster. There are a wide range of application for such an approach - generating boundary conditions, for use in air quality forecasts, chemical data assimilation systems, etc. We discuss speed and accuracy of our approach, and highlight some potential future directions for improving it.

Keller, Christoph A.↗

NASA NTRS1974

Amino acids in a Fischer Tropsch type synthesis

One postulation is described for the presence of organic compounds in meteorites which states that they were formed during the condensation of the solar nebula. A viable laboratory simulation of these conditions can be modeled after the industrial Fischer Tropsch reaction, which is known to produce organic compounds called hydrocarbons. In this simulation, a mixture of carbon monoxide, hydrogen and ammonia is heated in the presence of iron meteorite. The reaction products for amino acids, a class of organic compounds important to life, were examined. A large number of these compounds is found in meteorites and other chemical evolution experiments, but only small quantities of a few amino acids were found in the present simulation work. These results are at odds with the existing literature in which many amino acids were reported.

Brown, D. L.↗

NASA NTRS1987

Perovskite oxides: Oxygen electrocatalysis and bulk structure

Perovskite type oxides were considered for use as oxygen reduction and generation electrocatalysts in alkaline electrolytes. Perovskite stability and electrocatalytic activity are studied along with possible relationships of the latter with the bulk solid state properties. A series of compounds of the type LaFe(x)Ni1(-x)O3 was used as a model system to gain information on the possible relationships between surface catalytic activity and bulk structure. Hydrogen peroxide decomposition rate constants were measured for these compounds. Ex situ Mossbauer effect spectroscopy (MES), and magnetic susceptibility measurements were used to study the solid state properties. X ray photoelectron spectroscopy (XPS) was used to examine the surface. MES has indicated the presence of a paramagnetic to magnetically ordered phase transition for values of x between 0.4 and 0.5. A correlation was found between the values of the MES isomer shift and the catalytic activity for peroxide decomposition. Thus, the catalytic activity can be correlated to the d-electron density for the transition metal cations.

Carbonio, R. E.↗

NASA NTRS1988

Perovskite-type oxides - Oxygen electrocatalysis and bulk structure

Carbonio, R. E.↗

DOE OSTI2020

Magnetothermal properties of Tm x Dy 1- x Al 2 ( x = 0.25, 0.50 and 0.75)

Here, we describe magnetic, thermal, and magnetocaloric properties of rare earth intermetallic compounds Tm x Dy 1-x Al 2 with 0.25, 0.5 and 0.75. Using model Hamiltonian we consider contributions of the crystalline electric field anisotropy in both Tm and Dy magnetic sublattices, disorder in exchange interactions among Tm-Tm, Dy-Dy and Tm-Dy magnetic ions, and the Zeeman effect. Employing earlier reported and new experimental measurements, we first determine a single free variable – the intersublattice magnetic exchange parameter – to properly model the temperature and magnetic field dependencies of heat capacity and magnetization, and then use the modeling results to explain the emergence of an anomalous spin reorientation transition and its influence on the magnetocaloric effect in the title compounds. Theoretical results agree with experimental data reasonably well.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Direct observations of Pd–Te compound formation within noble metal inclusions in spent nuclear fuel

Not Available

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Automated AI-driven Molecular Design for Therapeutic Discovery

In recent years, artificial intelligence and machine learning (AI/ML) approaches have revolutionized the process of designing new therapeutics, enabling scientists to rapidly respond to emerging threats from various pathogens. A prime example is the SARS-CoV-2 main protease, a key target for the development of antiviral inhibitors. In this study, we employed a novel, integrated approach that combines AI-driven iterative design of inhibitor candidates, screening based on physio-chemical properties and toxicity, physics-based computational modeling of protein-inhibitor interactions, and AI-assisted analysis of Native MS biophysical assay and characterization of designed candidates. Our deep learning 3D-scaffold model, which uses an input scaffold as a starting point, generated tens of thousands of compounds while preserving the key scaffold. To optimize these candidates, we calculated a comprehensive set of 136 descriptors, including both 2D and 3D molecular features, for compounds targeting the SARS-CoV-2 Main protease (Mpro) and a neurodegenerative disease-associated protein, cyclophilin (Cyp). The generated compounds were initially filtered based on their properties and then ranked according to their predicted binding affinity using our automated modeling and ML methods. Experimental validation of the Mpro candidates showing inhibitory activity demonstrates that our workflow can expedite the therapeutic discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Modeling Volatility-Based Aerosol Phase State Predictions in the Amazon Rainforest

Organic aerosol (OA) is a complex matrix of various constituents—fresh (primary organic aerosols—POA) and aged via oxidation (secondary organic aerosols—SOA), generated from biogenic, anthropogenic, and biomass burning sources. The viscosity of OA can be critical in influencing new particle formation, reactive uptake processes that impact evaporation-growth kinetics, and the lifetime of particles in the atmosphere. We report this work utilizes a well-defined relationship between volatility and viscosity for pure compounds, which we incorporated within the Weather Research and Forecasting Model coupled to chemistry (WRF-Chem) to simulate the phase state and viscosity of bulk OA during the dry-to-wet transition season (September–October) in the Amazon rainforest during 2014. Our simulations indicate spatial and temporal heterogeneity in aerosol phase state often not captured by global-scale models. We show the strong role of water associated with organic aerosol ($w_s$) as the dominant factor that can be used to quantitatively estimate OA viscosity. Analysis of WRF-Chem simulations across the entire atmospheric column indicates a strong inverse log-linear relationship between $w_s$ and OA viscosity with a correlation coefficient approaching 1, in the background and biomass burning-influenced conditions. At high altitudes where relative humidity (RH) and temperatures are low, our simulations indicate that OA exists in a semisolid-/solid-like phase state, consistent with previous studies. OA hygroscopicity is strongly correlated (ca. –0.8) with OA viscosity at RH ca. 30–50%, but this RH range is found mostly at low OA concentrations and the middle troposphere (ca. 6–10 km altitudes) in our simulated domain. OA hygroscopicity is uncorrelated with viscosity at higher-RH (near surface) and lower-RH (upper troposphere) regimes. At the urban site near surface, where day–night differences in RH are significant, RH is found to drive the phase state. At the background forested site near surface, where day–night RH differences are small, biomass burning-influenced OA is semisolid and a significant OA associated with background conditions is liquid-like. Simulations indicate a long tail of OA viscosity frequency distributions extending in the semisolid/solid regimes over background biogenic-influenced conditions due to the role of low-volatility OA components such as monoterpene oxidation products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Bacterial volatile organic compound specialists in the phycosphere

Abstract Labile dissolved organic carbon in the surface oceans accounts for about one-fourth of carbon produced through photosynthesis and turns over on average every 3 days, fueling one of the largest engines of microbial heterotrophic production on the planet. Volatile organic compounds are poorly constrained components of dissolved organic carbon. Here, we detected 72 m/z signals, corresponding to unique volatile organic compounds, including petroleum hydrocarbons, totaling ~18.5 nM in the culture medium of a model diatom. In five cocultures with bacteria adapted to grow with this diatom, 1–59 m/z signals were depleted. Two of the most active volatile organic compound consumers, Marinobacter and Roseibium, contained more genes encoding volatile organic compound oxidation proteins, and attached to the diatom, suggesting volatile organic compound specialism. With nanoscale secondary ion mass spectrometry and stable isotope labeling, we confirmed that Marinobacter incorporated carbon from benzene, one of the depleted m/z signals detected in the co-culture. Diatom gross carbon production increased by up to 29% in the presence of volatile organic compound consumers, indicating that volatile organic compound consumption by heterotrophic bacteria in the phycosphere—a region of rapid organic carbon oxidation that surrounds phytoplankton cells—could impact global rates of gross primary production.

Environmental Sciences & Ecology↗