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DOE OSTI2019

Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography

We have developed a deep learning algorithm for chemical shift prediction for atoms in molecular crystals that utilizes an atom-centered Gaussian density model for the 3D data representation of a molecule. We define multiple channels that describe different spatial resolutions for each atom type that utilizes cropping, pooling, and concatenation to create a multiresolution 3D-DenseNet architecture (MR-3D-DenseNet). Because the training and testing time scale linearly with the number of samples, the MR-3D-DenseNet can exploit data augmentation that takes into account the property of rotational invariance of the chemical shifts, thereby also increasing the size of the training data set by an order of magnitude without additional cost. We obtain very good agreement for 13 C, 15 N, and 17 O chemical shifts when compared to ab initio quantum chemistry methods, with the highest accuracy found for 1 H chemical shifts that is comparable to the error between the ab initio results and experimental measurements. Principal component analysis (PCA) is used to both understand these greatly improved predictions for 1 H , as well as indicating that chemical shift prediction for 13 C, 15 N, and 17 O, which have far fewer training environments than the 1 H atom type, will improve once more unique training samples are made available to exploit the deep network architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Virtual Excited State Reference for the Discovery of Electronic Materials Database: An Open-Access Resource for Ground and Excited State Properties of Organic Molecules

This letter announces the Virtual Excited State Reference for the Discovery of Electronic Materials Database (VERDE materials DB), the first database to include downloadable excited-state structures (S 0 , S 1 , T 1 ) and photophysical properties. Furthermore, VERDE materials DB is searchable, open-access via www.verdedb.org , and focused on light-responsive π-conjugated organic molecules with applications in green chemistry, organic solar cells, and organic redox flow batteries. It includes results of our active and past virtual screening studies; to date, more than 13 000 density functional theory (DFT) calculations have been performed on 1 500 molecules to obtain frontier molecular orbitals and photophysical properties, including excitation energies, dipole moments, and redox potentials. To improve community access, we have made VERDE materials DB available via an integration with the Materials Data Facility. We are leveraging VERDE materials DB to train machine learning algorithms to identify new materials and structure–property relationships between molecular ground- and excited-states. We present a case-study involving photoaffinity labels, including predictions of new diazirine-based photoaffinity labels anticipated to have high photostabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Machine-Learning Identification of the Sensing Descriptors Relevant in Molecular Interactions with Metal Nanoparticle-Decorated Nanotube Field-Effect Transistors

We report that carbon nanotube-based field-effect transistors (NTFETs) are ideal sensor devices as they provide rich information regarding carbon nanotube interactions with target analytes and have potential for miniaturization in diverse applications in medical, safety, environmental, and energy sectors. Herein, we investigate chemical detection with cross-sensitive NTFETs sensor arrays comprised of metal nanoparticle-decorated single-walled carbon nanotubes (SWCNTs). By combining analysis of NTFET device characteristics with supervised machine-learning algorithms, we have successfully discriminated among five selected purine compounds, adenine, guanine, xanthine, uric acid, and caffeine. Interactions of purine compounds with metal nanoparticle-decorated SWCNTs were corroborated by density functional theory calculations. Furthermore, by testing a variety of prepared as well as commercial solutions with and without caffeine, our approach accurately discerns the presence of caffeine in 95% of the samples with 48 features using a linear discriminant analysis and in 93.4% of the samples with only 11 features when using a support vector machine analysis. Lastly, we also performed recursive feature elimination and identified three NTFET parameters, transconductance, threshold voltage, and minimum conductance, as the most crucial features to analyte prediction accuracy.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Correlating Protein Dynamics and Catalytic Activity of a Model Hydrogenase Using Paramagnetic and Biological Nuclear Magnetic Resonance Spectroscopy

Rational catalyst design remains a significant challenge, with electronic structure, steric, and electrostatic effects known to contribute to activity. Recently, dynamics has been recognized as another factor that impacts catalysis, though identifying and predicting these effects has remained out of reach. Nickel-substituted rubredoxin (NiRd), a protein-based mimic of a hydrogenase enzyme, serves as a model catalytic system in which dynamics can be systematically investigated with respect to activity. While over 30 secondary-sphere mutants of NiRd have been shown to be catalytically active, no significant correlation was observed between the rates and catalytic overpotential or electronic structure, prompting questions about the protein-derived factors that modulate activity. Here, in this work, NMR spectroscopy was used to investigate the roles of substrate accessibility, protein dynamics, and protein stability in controlling catalysis. Significant paramagnetic effects from the nickel center (S = 1) isolate the methylene proton resonances of the metal-coordinating cysteine residues. The sensitivity of resonance positions and linewidths to local environment offers an opportunity to study dynamical molecular changes around the metal center with high resolution. Machine learning algorithms were employed to identify correlations between the catalytic activity and the paramagnetic NMR spectra. These analyses revealed spectroscopic features of specific cysteine protons that report on catalytic overpotential and increased turnover rates, which are further supported by the results obtained using high-field NMR techniques. Collectively, these studies indicate the potential for multifrequency NMR techniques to resolve key contributors to catalytic activity and highlight the importance of local and outer-sphere dynamics.

Protein Engineering↗

DOE OSTI2018

Chemical Pressure-Driven Enhancement of the Hydrogen Evolving Activity of Ni 2 P from Nonmetal Surface Doping Interpreted via Machine Learning

The activity of Ni 2 P catalysts for the hydrogen evolution reaction (HER) is currently limited by strong H adsorption at the Ni 3 -hollow site. We investigate the effect of surface nonmetal doping on the HER activity of the Ni 3 P 2 termination of Ni 2 P(0001), which is stable at modest electrochemical conditions. Using density functional theory (DFT) calculations, we find that both 2p nonmetals and heavier chalcogens provide nearly thermoneutral H adsorption at moderate surface doping concentrations. We also find, however, that only chalcogen substitution for surface P is exergonic. For intermediate surface concentrations of S, the free energy of H adsorption at the Ni 3 -hollow site is -0.11 eV, which is significantly more thermoneutral than the undoped surface (-0.45 eV). We use the regularized random forest machine learning algorithm to discover the relative importance of structure and charge descriptors, extracted from the DFT calculations, in determining the HER activity of Ni 2 P(0001) under different doping concentrations. Here, we discover that the Ni–Ni bond length is the most important descriptor of HER activity, which suggests that the nonmetal dopants induce a chemical pressure-like effect on the Ni 3 -hollow site, changing its reactivity through compression and expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Soil Organic Matter Temperature Sensitivity Cannot be Directly Inferred From Spatial Gradients

Developing and testing decadal-scale predictions of soil response to climate change is difficult because there are few long-term warming experiments or other direct observations of temperature response. As a result, spatial variation in temperature is often used to characterize the influence of temperature on soil organic carbon (SOC) stocks under current and warmer temperatures. This approach assumes that the decadal-scale response of SOC to warming is similar to the relationship between temperature and SOC stocks across sites that are at quasi steady state; however, this assumption is poorly tested. We developed four variants of a Reaction-network-based model of soil organic matter and microbes using measured SOC stocks from a 4,000-km latitudinal transect. Each variant reflects different assumptions about the temperature sensitivities of microbial activity and mineral sorption. All four model variants predicted the same response of SOC to temperature at steady state, but different projections of transient warming responses. The relative importance of Q max , mean annual temperature, and net primary production, assessed using a machine-learning algorithm, changed depending on warming duration. When mineral sorption was temperature sensitive, the predicted average change in SOC after 100 years of 5 °C warming was –18% if warming decreased sorption or +9% if warming increased sorption. When microbial activity was temperature sensitive but mineral sorption was not, average site-level SOC loss was 5%. Here, we conclude that spatial climate gradients of SOC stocks are insufficient to constrain the transient response; measurements that distinguish process controls and/or observations from long-term warming experiments, especially mineral fractions, are needed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A Machine Learning Assisted Development of a Model for the Populations of Convective and Stratiform Clouds

Abstract Traditional parameterizations of the interaction between convection and the environment have relied on an assumption that the slowly varying large‐scale environment is in statistical equilibrium with a large number of small and short‐lived convective clouds. They fail to capture nonequilibrium transitions such as the diurnal cycle and the formation of mesoscale convective systems as well as observed precipitation statistics and extremes. Informed by analysis of radar observations, cloud‐permitting model simulation, theory, and machine learning, this work presents a new stochastic cloud population dynamics model for characterizing the interactions between convective and stratiform clouds, with the goal of informing the representation of these interactions in global climate models. Fifteen wet seasons of precipitating cloud observations by a C‐band radar at Darwin, Australia are fed into a machine learning algorithm to obtain transition functions that close a set of coupled equations relating large‐scale forcing, mass flux, the convective cell size distribution, and the stratiform area. Under realistic large‐scale forcing, the derived transition functions show that, on the one hand, interactions with stratiform clouds act to dampen the variability in the size and number of convective cells and therefore in the convective mass flux. On the other, for a given convective area fraction, a larger number of smaller cells is more favorable for the growth of stratiform area than a smaller number of larger cells. The combination of these two factors gives rise to solutions with a few convective cells embedded in a large stratiform area, reminiscent of mesoscale convective systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

The Illumination of Thunderclouds by Lightning: 4. Volumetric Thunderstorm Imagery

Optical instruments such as the Geostationary Lightning Mapper (GLM) detect lightning based on transient changes in cloud illumination. The horizontal location of lightning is determined from the coordinates of the pixels on the imaging array illuminated during the flash. However, the vertical position of the lightning pulses (approximated by GLM “groups”) below the cloud top cannot be routinely measured from a single space-based instrument. In our prior work, we have developed a machine learning algorithm that can infer optical source altitude for a given pulse based on how the optical energy is distributed across the group footprint and the local Advanced Baseline Imager Cloud-Top Height (CTH). In this fourth part of our thundercloud illumination study, we leverage these source altitudes to generate volumetric GLM imagery of a Colombia thunderstorm. We find that 3D versions of the current GLM meteorological imagery products (that describe thunderstorm kinematics) and thundercloud imagery products (that depict how the flashes appear from space) provide additional insights into lightning activity in the thunderstorm that are lost in the vertical integration used to generate the current 2D GLM gridded products. This new volumetric imaging capability provides a more comprehensive picture of where lightning occurs in the storm, how its physical characteristics vary across three-dimensional space, and how its optical emissions interact with surrounding the cloud medium.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

An Observationally Trained Markov Model for MJO Propagation

A Markovian stochastic model is developed for studying the propagation of the Madden-Julian Oscillation (MJO). This model represents the daily changes in real time multivariate MJO (RMM) indices as random functions of their current state and background conditions. The probability distribution function of the RMM changes is obtained using a machine learning algorithm trained to maximize MJO forecast skills using observed daily indices of RMM and different modes of variability. Skillful forecasts are obtained for lead times between 8 and 27 days. Large ensemble simulations by the stochastic model show that with monsoonal changes in the background state, MJO propagation across the Maritime Continent (MC) is most likely to be disrupted in boreal spring and summer when MJO events propagate from favorable conditions over the Indian Ocean to unfavorable ones over the MC, and predictability is higher during spring and summer when MJO activity is away from the MC region.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Machine Learning–Based Detection of Weather Fronts and Associated Extreme Precipitation in Historical and Future Climates

Extreme precipitation events, including those associated with weather fronts, have wide-ranging impacts across the world. Here we use a deep learning algorithm to identify weather fronts in high resolution Community Earth System Model (CESM) simulations over the contiguous United States (CONUS), and evaluate the results using observational and reanalysis products. We further compare results between CESM simulations using present-day and future climate forcing, to study how these features might change with climate change. We find that detected front frequencies in CESM have seasonally varying spatial patterns and responses to climate change and are found to be associated with modeled changes in large scale circulation such as the jet stream. We also associate the detected fronts with precipitation and find that total and extreme frontal precipitation mostly decreases with climate change, with some seasonal and regional differences. Here, decreases in Northern Hemisphere summer frontal precipitation are largely driven by changes in the frequency of different front types, especially cold and stationary fronts. On the other hand, Northern Hemisphere winter exhibits some regional increases in frontal precipitation that are largely driven by changes in frontal precipitation intensity. While CONUS mean and extreme precipitation generally increase during all seasons in these climate change simulations, the likelihood of frontal extreme precipitation decreases, demonstrating that extreme precipitation has seasonally varying sources and mechanisms that will continue to evolve with climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Sensitivity Analysis of Wind and Turbulence Predictions With Mesoscale‐Coupled Large Eddy Simulations Using Ensemble Machine Learning

Abstract Coupling between mesoscale models and large‐eddy simulation (LES) models is increasingly used to more realistically represent the wide range of scales of atmospheric motions affecting boundary layer winds and turbulence that need to be simulated accurately for applications such as wind energy. However, such mesoscale‐to‐microscale coupled modeling frameworks are potentially affected by a large number of uncertain closure parameters. Here, we investigate the sensitivity associated with six closure parameters related to a 1.5‐order subgrid‐scale turbulence closure for an ensemble of mesoscale‐coupled LES. The simulations are performed using the Weather Research and Forecasting model nested from horizontal resolutions of greater than a kilometer down to tens of meters. Closure parameters are varied to generate perturbed parameter ensembles for two case studies of highly sheared, convective boundary layers observed in the Columbia Basin of Oregon and Washington during the Second Wind Forecast Improvement Project. Machine learning algorithms are used to explore the sensitivity of LES predictions, considering the effects of the perturbed physical parameters alongside categorical factors such as the case study identity, measurement location, and LES resolution. For the conditions we examine, a single parameter, the eddy viscosity coefficient, is the dominant source of parametric sensitivity and its importance is comparable to the categorical factors for several of the simulation response variables we examine.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Internal Climate Variability Obscures Future Freezing Rain Changes Despite Global Warming Trend

Abstract Although numerous studies have projected changes in freezing rain under future climate conditions, the internal variability of freezing rain remains poorly quantified. Here, we introduce a framework utilizing a novel machine‐learning algorithm to diagnose freezing rain in reanalysis and climate model simulations. By employing multivariate quantile mapping, we decompose the projected freezing rain trend into contributions from changes in temperature, relative humidity, and precipitation, which helps separate the forced response from internal climate variability. Our finding reveals a notable decrease in freezing rain occurrence in most areas. Despite a substantial temperature increase, internal variability overshadows climate forcing across a large portion of the eastern United States until about 2050. This insight has implications for practitioners, suggesting that the observed freezing rain frequency climatology continues to provide a relevant baseline for decision‐making in the near term. However, longer‐term design and adaptation plans should consider the projected changes in these regions.

Zhuang, Haoyu (Richard) [Department of Atmospheric↗

DOE OSTI2020

An exponential build-up in seismic energy suggests a months-long nucleation of slow slip in Cascadia

Slow slip events result from the spontaneous weakening of the subduction megathrust and bear strong resemblance to earthquakes, only slower. This resemblance allows us to study fundamental aspects of nucleation that remain elusive for classic, fast earthquakes. We rely on machine learning algorithms to infer slow slip timing from statistics of seismic waveforms. We find that patterns in seismic power follow the 14-month slow slip cycle in Cascadia, arguing in favor of the predictability of slow slip rupture. Here, we show that seismic power exponentially increases as the slowly slipping portion of the subduction zone approaches failure, a behavior that shares a striking similarity with the increase in acoustic power observed prior to laboratory slow slip events. Our results suggest that the nucleation phase of Cascadia slow slip events may last from several weeks up to several months.

58 GEOSCIENCES↗

DOE OSTI2021

Predicting orientation-dependent plastic susceptibility from static structure in amorphous solids via deep learning

It has been a long-standing materials science challenge to establish structure-property relations in amorphous solids. Here we introduce a rotationally non-invariant local structure representation that enables different predictions for different loading orientations, which is found essential for high-fidelity prediction of the propensity for stress-driven shear transformations. This novel structure representation, when combined with convolutional neural network (CNN), a powerful deep learning algorithm, leads to unprecedented accuracy for identifying atoms with high propensity for shear transformations (i.e., plastic susceptibility), solely from the static structure in both two- and three-dimensional model glasses. The data-driven models trained on samples at one composition and a given processing history are found transferrable to glass samples with different processing histories or at different compositions in the same alloy system. Our analysis of the new structure representation also provides valuable insight into key atomic packing features that influence the local mechanical response and its anisotropy in glasses.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Filming movies of attosecond charge migration in single molecules with high harmonic spectroscopy

Electron migration in molecules is the progenitor of chemical reactions and biological functions after light-matter interaction. Following this ultrafast dynamics, however, has been an enduring endeavor. Here we demonstrate that, by using machine learning algorithm to analyze high-order harmonics generated by two-color laser pulses, we are able to retrieve the complex amplitudes and phases of harmonics of single fixed-in-space molecules. These complex dipoles enable us to construct movies of laser-driven electron migration after tunnel ionization of N 2 and CO 2 molecules at time steps of 50 attoseconds. Moreover, the angular dependence of the migration dynamics is fully resolved. By examining the movies, we observe that electron holes do not just migrate along the laser polarization direction, but may swirl around the atom centers. Our result establishes a general scheme for studying ultrafast electron dynamics in molecules, paving a way for further advance in tracing and controlling photochemical reactions by femtosecond lasers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Data-driven predictions of complex organic mixture permeation in polymer membranes

Membrane-based organic solvent separations are rapidly emerging as a promising class of technologies for enhancing the energy efficiency of existing separation and purification systems. Polymeric membranes have shown promise in the fractionation or splitting of complex mixtures of organic molecules such as crude oil. Determining the separation performance of a polymer membrane when challenged with a complex mixture has thus far occurred in an ad hoc manner, and methods to predict the performance based on mixture composition and polymer chemistry are unavailable. Here, we combine physics-informed machine learning algorithms (ML) and mass transport simulations to create an integrated predictive model for the separation of complex mixtures containing up to 400 components via any arbitrary linear polymer membrane. We experimentally demonstrate the effectiveness of the model by predicting the separation of two crude oils within 6-7% of the measurements. Integration of ML predictors of diffusion and sorption properties of molecules with transport simulators enables for the rapid screening of polymer membranes prior to physical experimentation for the separation of complex liquid mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Autonomous closed-loop mechanistic investigation of molecular electrochemistry via automation

Abstract Electrochemical research often requires stringent combinations of experimental parameters that are demanding to manually locate. Recent advances in automated instrumentation and machine-learning algorithms unlock the possibility for accelerated studies of electrochemical fundamentals via high-throughput, online decision-making. Here we report an autonomous electrochemical platform that implements an adaptive, closed-loop workflow for mechanistic investigation of molecular electrochemistry. As a proof-of-concept, this platform autonomously identifies and investigates an EC mechanism, an interfacial electron transfer ( E step) followed by a solution reaction ( C step), for cobalt tetraphenylporphyrin exposed to a library of organohalide electrophiles. The generally applicable workflow accurately discerns the EC mechanism’s presence amid negative controls and outliers, adaptively designs desired experimental conditions, and quantitatively extracts kinetic information of the C step spanning over 7 orders of magnitude, from which mechanistic insights into oxidative addition pathways are gained. This work opens opportunities for autonomous mechanistic discoveries in self-driving electrochemistry laboratories without manual intervention.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Finding predictive models for singlet fission by machine learning

Singlet fission (SF), the conversion of one singlet exciton into two triplet excitons, could significantly enhance solar cell efficiency. Molecular crystals that undergo SF are scarce. Computational exploration may accelerate the discovery of SF materials. However, many-body perturbation theory (MBPT) calculations of the excitonic properties of molecular crystals are impractical for large-scale materials screening. We use the sure-independence-screening-and-sparsifying-operator (SISSO) machine-learning algorithm to generate computationally efficient models that can predict the MBPT thermodynamic driving force for SF for a dataset of 101 polycyclic aromatic hydrocarbons (PAH101). SISSO generates models by iteratively combining physical primary features. The best models are selected by linear regression with cross-validation. The SISSO models successfully predict the SF driving force with errors below 0.2 eV. Based on the cost, accuracy, and classification performance of SISSO models, we propose a hierarchical materials screening workflow. Three potential SF candidates are found in the PAH101 set.

36 MATERIALS SCIENCE↗