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At least 433 records · Page 24

Transferring a Molecular Foundation Model for Polymer Property Predictions

Transformer-based large language models have remarkable potential to accelerate design optimization for applications such as drug development and material discovery. Self-supervised pretraining of transformer models requires large-scale data sets, which are often sparsely populated in topical areas such as polymer science. Further, state-of-the-art approaches for polymers conduct data augmentation to generate additional samples but unavoidably incur extra computational costs. In contrast, large-scale open-source data sets are available for small molecules and provide a potential solution to data scarcity through transfer learning. In this work, we show that using transformers pretrained on small molecules and fine-tuned on polymer properties achieves comparable accuracy to those trained on augmented polymer data sets for a series of benchmark prediction tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing Sulfur Chemical and Electronic Structure with Experimental Observation and Quantitative Theoretical Prediction of Kα and Valence-to-Core Kβ X-ray Emission Spectroscopy

An extensive experimental and theoretical study of the Kα and Kβ high-resolution X-ray emission spectroscopy (XES) of sulfur-bearing systems is presented here. This study encompasses a wide range of organic and inorganic compounds, including numerous experimental spectra from both prior published work and new measurements. Employing a linear-response time-dependent density functional theory (LR-TDDFT) approach, strong quantitative agreement is found in the calculation of energy shifts of the core-to-core Kα as well as the full range of spectral features in the valence-to-core Kβ spectrum. The ability to accurately calculate the sulfur Kα energy shift supports the use of sulfur Kα XES as a bulk-sensitive tool for assessing sulfur speciation. The fine structure of the sulfur Kβ spectrum, in conjunction with the theoretical results, is shown to be sensitive to the local electronic structure including effects of symmetry, ligand type and number, and, in the case of organosulfur compounds, to the nature of the bonded organic moiety. This agreement between theory and experiment, augmented by the potential for high-access XES measurements with the latest generation of laboratory-based spectrometers, demonstrates the possibility of broad analytical use of XES for sulfur and nearby third-row elements. The effective solution of the forward problem, i.e., successful prediction of detailed spectra from known molecular structure, also suggests future use of supervised machine learning approaches to experimental inference, as has seen recent interest for interpretation of X-ray absorption near-edge structure (XANES).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent Advances toward Efficient Calculation of Higher Nuclear Derivatives in Quantum Chemistry

In this article, we provide an overview of state-of-the-art techniques that are being developed for efficient calculation of second and higher nuclear derivatives of quantum mechanical (QM) energy. Calculations of nuclear Hessians and anharmonic terms incur high costs and memory and scale poorly with system size. Three emerging classes of methods—machine learning (ML), automatic differentiation (AD), and matrix completion (MC)—have demonstrated promise in overcoming these challenges. We illustrate studies that employ unsupervised ML methods to reduce the need for multiple Hessian calculations in dynamics simulations and those that utilize supervised ML to construct approximate potential energy surfaces and estimate Hessians and anharmonic terms at reduced cost. By extension, if electronic structure operations could be written in a manner similar to functions underlying ML methods, rapid differentiation or AD routines can be employed to inexpensively calculate higher arbitrary-order derivatives. While ML approaches are typically black-box, we describe methods such as compressed sensing (CS) and MC, which explicitly leverage problem-specific mathematical properties of higher derivatives such as sparsity and low-rank, to complete higher derivative information using only a small, incomplete sample. The three classes of methods facilitate reliable predictions of observables ranging from infrared spectra to thermal conductivity and constitute a promising way forward in accurately capturing otherwise intractable higher-order responses of QM energy to nuclear perturbations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Machine Learning Analysis of Direct Dynamics Trajectory Outcomes for Thermal Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene

Experimentally, the thermal gas-phase deazetization of 2,3-diazabicyclo[2.2.1]hept-2-ene (1) results in the loss of N2 and the formation of bicyclo products 3 (exo) and 4 (endo) in a nonstatistical ratio, with preference for the exo product. Here, we report unrestricted M06-2X quasiclassical trajectories initialized from the concerted N2 ejection transition state that were able to replicate the experimental preference to form 3. We found that the 3:4 ratio results from the relative amounts of very fast (ballistic) exotype trajectories versus trajectories that lead to the 1,3-diradical intermediate 2. These quasiclassical trajectories provided a set of transition-state vibrational, velocity, momenta, and geometric features for the machine learning analysis. Additionally, a selection of popular supervised classification algorithms (e.g., random forest) provided poor prediction of trajectory outcomes based on only transition-state vibrational quanta and energy features. However, these machine learning models provided more accurate predictions using atomic velocities and atomic positions, attaining ~70% accuracy using initial conditions and between 85 and 95% accuracy at later reaction time steps. This increased accuracy allowed the feature importance analysis to reveal that, at the later-time analysis, the methylene bridge out-of-plane bending is correlated with trajectory outcomes for the formation of either the exo product or toward the diradical intermediate. Possible reasons for the struggle of machine learning algorithms to classify trajectories based on transition-state features is the heavily overlapping feature values, the finite but very large possible vibrational mode combinations, and the possibility of chaos as trajectories propagate. We examined this chaos by comparing a set of nearly identical trajectories that differed by only a very small scaling of the kinetic energies resulting from the transition-state reaction coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN

Interferometric scattering microscopy (iSCAT) is a label-free optical microscopy technique that enables imaging of individual nano-objects such as nanoparticles, viruses, and proteins. Essential to this technique is the suppression of background scattering and identification of signals from nano-objects. In the presence of substrates with high roughness, scattering heterogeneities in the background, when coupled with tiny stage movements, cause features in the background to be manifested in background-suppressed iSCAT images. Traditional computer vision algorithms detect these background features as particles, limiting the accuracy of object detection in iSCAT experiments. Here, in this paper, we present a pathway to improve particle detection in such situations using supervised machine learning via a mask region-based convolutional neural network (mask R-CNN). Using a model iSCAT experiment of 19.2 nm gold nanoparticles adsorbing to a rough layer-by-layer polyelectrolyte film, we develop a method to generate labeled datasets using experimental background images and simulated particle signals and train the mask R-CNN using limited computational resources via transfer learning. We then compare the performance of the mask R-CNN trained with and without inclusion of experimental backgrounds in the dataset against that of a traditional computer vision object detection algorithm, Haar-like feature detection, by analyzing data from the model experiment. Results demonstrate that including representative backgrounds in training datasets improved the mask R-CNN in differentiating between background and particle signals and elevated performance by markedly reducing false positives. The methodology for creating a labeled dataset with representative experimental backgrounds and simulated signals facilitates the application of machine learning in iSCAT experiments with strong background scattering and thus provides a useful workflow for future researchers to improve their image processing capabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB)

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. Here we present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.

1,3,5-triamino-2,4,6-trinitrobenzene↗

Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat

The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy of the NHR-targeting entry inhibitor enfuvirtide, no potently neutralizing NHR-directed monoclonal antibodies (mAbs) nor antisera have been identified or elicited to date. The lack of potent NHR-binding mAbs both dampens enthusiasm for vaccine development efforts at this target and presents a barrier to performing passive immunization experiments with NHR-targeting antibodies. To address this challenge, we previously developed an improved variant of the NHR-directed mAb D5, called D5_AR, which is capable of neutralizing diverse tier-2 viruses. Building on that work, here we present the 2.7Å-crystal structure of D5_AR bound to NHR mimetic peptide IQN17. We then utilize protein language models and supervised machine learning to generate small (n < 100) libraries of D5_AR variants that are subsequently screened for improved neutralization potency. We identify a variant with 5-fold improved neutralization potency, D5_FI, which is the most potent NHR-directed monoclonal antibody characterized to date and exhibits broad neutralization of tier-2 and −3 pseudoviruses as well as replicating R5 and X4 challenge strains. Additionally, our work highlights the ability of protein language models to efficiently identify improved mAb variants from relatively small libraries.

Biopolymers↗

Oil and Gas Produced Water Reuse: Opportunities, Treatment Needs, and Challenges

Advances in water treatment technologies paired with potential restrictions on oil and gas (O&G) produced water disposal could incentivize the beneficial reuse of treated produced water in the O&G industry. However, the remote nature of O&G operations limits the applicability of many of these solutions, which may be spatially inefficient, require operator supervision, or are ill-suited for the complex nature of produced water. Furthermore, the responsible, sustainable reuse of produced water as an alternative water source requires standardized analytical techniques for characterizing and determining the toxicity of treated produced water and improving our understanding of the fate and transport of various constituents. In the past decade, we made little progress in economically treating produced water for beneficial reuse outside of oilfield operations; the sole major breakthrough has been in the development of salt-tolerant fracturing chemicals that allow for reuse of produced water for fracking operations. Guided research should assist in the development of fit-for-purpose solutions to maximize the reuse of treated produced water. This is exemplified by the case studies presented here that detail currently operating treatment facilities for reclamation and reuse of produced water.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Enhanced Detection of Primary Biological Aerosol Particles Using Machine Learning and Single-Particle Measurement

Accurately identifying primary biological aerosol particles (PBAPs) using analytical techniques poses inherent challenges due to their resemblance to other atmospheric carbonaceous particles. Here, we present a study of an enhanced method for detecting PBAPs by combining single-particle measurement with advanced supervised machine learning (SML) techniques. We analyzed ambient particles from a variety of environments and lab-generated standards, focusing on chemical composition for traditional rule-based and clustering approaches and incorporating morphological features into the SML approaches, neural networks and XGBoost, for improved accuracy. This study demonstrates that SML methods outperform traditional methods in quantifying PBAPs, achieving significant improvements in precision, recall, F1-score, and accuracy, leading to an increased number of detected PBAPs by at least 19%. The adaptability of the proposed XGBoost-based SML model is showcased in comparison to traditional methods in categorizing PBAPs for blind data sets from different geographical locations. Two field case studies were investigated, over agricultural land and Amazonia rain forest, representing relatively low and high concentrations of PBAPs, respectively, where XGBoost consistently detected up to 3.5 times more PBAPs than traditional methods. Precise detection of PBAPs in the atmosphere could significantly improve the prediction of climatic impacts by them.

42 ENGINEERING↗

Revealing the Chemical Bonding in Adatom Arrays via Machine Learning of Hyperspectral Scanning Tunneling Spectroscopy Data

The adatom arrays on surfaces offer an ideal playground to explore the mechanisms of chemical bonding via changes in the local electronic tunneling spectra. While this information is readily available in hyperspectral scanning tunneling spectroscopy data, its analysis has been considerably impeded by a lack of suitable analytical tools. Here we develop a machine learning based workflow combining supervised feature identification in the spatial domain and unsupervised clustering in the energy domain to reveal the details of structure-dependent changes of the electronic structure in adatom arrays on the Co 3 Sn 2 S 2 cleaved surface. This approach, in combination with first-principles calculations, provides insight for using artificial neural networks to detect adatoms and classifies each based on their local neighborhood comprised of other adatoms. These structurally classified adatoms are further spectrally deconvolved. The unexpected inhomogeneity of electronic structures among adatoms in similar configurations is unveiled using this method, suggesting there is not a single atomic species of adatoms, but rather multiple types of adatoms on the Co 3 Sn 2 S 2 surface. This is further supported by a slight contrast difference in the images (or slight size variation) of the topography of the adatoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Online LIBS–ML Framework for Dynamic Characterization of Heterogeneous Waste-Derived Gasification Feedstocks

LIBS−ML framework for real time feedstock characterization during continuous conveyor transport Heterogeneous waste derived feedstocks (e.g., waste coal, biomass and blends) introduce rapid variability in heating value and ash chemistry that affect gasifier operation, yet conventional laboratory characterization techniques are too slow to support proactive control. To address this gap, this study reports on an online, in situ, dynamic characterization framework that couple’s laser-induced breakdown spectroscopy (LIBS) with leakage safe machine learning (ML) regression to deliver real time, decision quality predictions of gasifier relevant properties. A controlled sample matrix spanning two different waste coals, two different biomasses, and engineered blends under two particle size conditions were constructed and benchmarked using standardized laboratory analyses for proximate/ultimate properties and ash composition. LIBS spectra were acquired dynamically as material flowed on a conveyor belt, using high energy 1064 nm laser ablation and shot averaging to improve repeatability and precision. Supervised regression models (multi layer perceptron (MLP) /artificial neural network (ANN), random forest (RF), and support vector regression (SVR)) and an optimized weighted ensemble were trained on emission line feature sets using nested cross validation with Bayesian hyperparameter tuning and validated against an independent hold out set. The proposed LIBS−ML workflow achieves near laboratory predictive fidelity across parametric targets (including higher heating value (HHV), ash content, fixed carbon, sulfur, major ash forming oxides, and initial deformation temperature (IDT)), with the weighted ensemble providing a robust default predictor under dynamic measurement conditions. These results demonstrate a practical pathway for real time feedstock characterization that can enable feedforward adjustments and more resilient gasifier operation for variable quality waste derived fuels.

Biomass↗

Machine Learning Correlation of Electron Micrographs and ToF-SIMS for the Analysis of Organic Biomarkers in Mudstone

The spatial distribution of organics in geological samples can be used to determine when and how these organics were incorporated into the host rock. Mass spectrometry (MS) imaging can rapidly collect a large amount of data, but ions produced are mixed without discrimination, resulting in complex mass spectra that can be difficult to interpret. Here, we apply unsupervised and supervised machine learning (ML) to help interpret spectra from time-of-flight-secondary ion mass spectrometry (ToF-SIMS) of an organic-carbon-rich mudstone of the Middle Jurassic of England (UK). It was previously shown that the presence of sterane molecular biomarkers in this sample can be detected via ToF-SIMS (Pasterski, M. J. et al., Astrobiology 2023, 23, 936). We use unsupervised ML on scanning electron microscopy–electron dispersive spectroscopy (SEM-EDS) measurements to define compositional categories based on differences in elemental abundances. We then test the ability of four ML algorithms─k-nearest neighbors (KNN), recursive partitioning and regressive trees (RPART), eXtreme gradient boost (XGBoost), and random forest (RF)─to classify the ToF-SIM spectra using (1) the categories assigned via SEM-EDS, (2) organic and inorganic labels assigned via SEM-EDS, and (3) the presence or absence of detectable steranes in ToF-SIMS spectra. In terms of predictive accuracy and balanced accuracy, KNN was the best performing model and RPART the worst. The feature importance, or the specific features of the ToF-SIM spectra used by the models to make classifications, cannot be determined for KNN, preventing posthoc model interpretation. Nevertheless, the feature importance extracted from the other models was useful for interpreting spectra. In conclusion, we determined that some of the organic ions used to classify biomarker containing spectra may be fragment ions derived from kerogen which is abundant in this mudstone sample.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nowcasting Earthquakes: Imaging the Earthquake Cycle in California With Machine Learning

We propose a new machine learning-based method for nowcasting earthquakes to image the time-dependent earthquake cycle. The result is a timeseries that may correspond to the process of stress accumulation and release. The timeseries are constructed by using principal component analysis of regional seismicity. The patterns are found as eigenvectors of the cross-correlation matrix of a collection of seismicity timeseries in a coarse grained regional spatial grid (pattern recognition via unsupervised machine learning). The eigenvalues of this matrix represent the relative importance of the various eigenpatterns. Using the eigenvectors and eigenvalues, we compute the weighted correlation timeseries of the regional seismicity. This timeseries has the property that the weighted correlation generally decreases prior to major earthquakes in the region, and increases suddenly just after a major earthquake occurs. As in a previous paper, we find that this method produces a nowcasting timeseries that resembles the hypothesized regional stress accumulation and release process characterizing the earthquake cycle. We then address the problem of whether the timeseries contain information regarding future large earthquakes. For this, we compute a receiver operating characteristic and determine the decision thresholds for several future time periods of interest (optimization via supervised machine learning). We find that signals can be detected that can be used to characterize the information content of the timeseries. These signals may be useful in assessing present and near-future seismic hazards.

58 GEOSCIENCES↗

Earthquake Phase Association Using a Bayesian Gaussian Mixture Model

Earthquake phase association algorithms aggregate picked seismic phases from a network of seismometers into individual seismic events and play an important role in earthquake monitoring and research. Dense seismic networks and improved phase picking methods produce massive seismic phase datasets, particularly for earthquake swarms and aftershocks occurring closely in time and space, making phase association a challenging problem. Here, we present a new association method, the Gaussian Mixture Model Association (GaMMA), that combines the Gaussian mixture model with earthquake location, origin time, and magnitude estimation. We treat earthquake phase association as an unsupervised clustering problem in a probabilistic framework, where each earthquake corresponds to a cluster of P and S phases with a hyperbolic moveout of arrival times and a decay of amplitude with distance. We use the multivariate Gaussian distribution to model the collection of phase picks of an event; and the mean of the multivariate Gaussian distribution is given by the predicted arrival time and amplitude from the causative event. We carry out the pick assignment to each earthquake and determine earthquake source parameters (i.e., earthquake location, origin time, and magnitude) under the maximum likelihood criterion using the Expectation-Maximization algorithm. The GaMMA method does not require typical association steps of other algorithms, such as grid-search or supervised training. The results for both synthetic tests and for the 2019 Ridgecrest earthquake sequence show that GaMMA effectively associates phases from a temporally and spatially dense earthquake sequence while producing useful estimates of earthquake location and magnitude.

58 GEOSCIENCES↗

Deep Learning for Subgrid‐Scale Turbulence Modeling in Large‐Eddy Simulations of the Convective Atmospheric Boundary Layer

Abstract In large‐eddy simulations, subgrid‐scale (SGS) processes are parameterized as a function of filtered grid‐scale variables. First‐order, algebraic SGS models are based on the eddy‐viscosity assumption, which does not always hold for turbulence. Here we apply supervised deep neural networks (DNNs) to learn SGS stresses from a set of neighboring coarse‐grained velocity from direct numerical simulations of the convective boundary layer at friction Reynolds numbers Re τ up to 1243 without invoking the eddy‐viscosity assumption. The DNN model was found to produce higher correlation between SGS stresses compared to the Smagorinsky model and the Smagorinsky‐Bardina mixed model in the surface and mixed layers and can be applied to different grid resolutions and various stability conditions ranging from near neutral to very unstable. The DNN model can capture key statistics of turbulence in a posteriori (online) tests when applied to large‐eddy simulations of the atmospheric boundary layer.

54 ENVIRONMENTAL SCIENCES↗

PreMevE Update: Forecasting Ultra-Relativistic Electrons Inside Earth's Outer Radiation Belt

Energetic electrons inside Earth's Van Allen belts pose a major radiation threat to spaceborne electronics that often play vital roles in modern society. Ultra-relativistic electrons with energies greater than or equal to two megaelectron-volt (MeV) are of particular interest, and thus forecasting these ≥2 MeV electrons has a significant meaning to all space sectors. Here, we update the latest development of the predictive model for MeV electrons in the outer radiation belt. The new version, called PREdictive MEV Electron (PreMevE)-2E, forecasts ultra-relativistic electron flux distributions across the outer belt, with no need for in situ measurements of the trapped MeV electron population except at the geosynchronous orbit (GEO). Model inputs include precipitating electrons observed in low-Earthorbits by NOAA satellites, upstream solar wind speeds and densities from solar wind monitors, as well as ultra-relativistic electrons measured by one Los Alamos GEO satellite. We evaluated 32 supervised machine learning models that fall into four different classes of linear and neural network architectures, and successfully tested ensemble forecasting by using groups of top-performing models. All models are individually trained, validated, and tested by in situ electron data from NASA's Van Allen Probes mission. It is shown that the final ensemble model outperforms individual models at most L-shells, and this PreMevE-2E model can provide 25-h (~1-day) and 50-h (~2-day) forecasts with high mean performance efficiency and correlation values. Our results also suggest that this new model is dominated by nonlinear components at L-shells <~4 for ultra-relativistic electrons, different from the dominance of linear components for 1 MeV electrons as previously discovered.

79 ASTRONOMY AND ASTROPHYSICS↗

Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle

Abstract Nowcasting is a term originating from economics, finance, and meteorology. It refers to the process of determining the uncertain state of the economy, markets or the weather at the current time by indirect means. In this paper, we describe a simple two‐parameter data analysis that reveals hidden order in otherwise seemingly chaotic earthquake seismicity. One of these parameters relates to a mechanism of seismic quiescence arising from the physics of strain‐hardening of the crust prior to major events. We observe an earthquake cycle associated with major earthquakes in California, similar to what has long been postulated. An estimate of the earthquake hazard revealed by this state variable time series can be optimized by the use of machine learning in the form of the Receiver Operating Characteristic skill score. The ROC skill is used here as a loss function in a supervised learning mode. Our analysis is conducted in the region of 5° × 5° in latitude‐longitude centered on Los Angeles, a region which we used in previous papers to build similar time series using more involved methods (Rundle & Donnellan, 2020, https://doi.org/10.1029/2020EA001097 ; Rundle, Donnellan et al., 2021, https://doi.org/10.1029/2021EA001757 ; Rundle, Stein et al., 2021, https://doi.org/10.1088/1361-6633/abf893 ). Here we show that not only does the state variable time series have forecast skill, the associated spatial probability densities have skill as well. In addition, use of the standard ROC and Precision (PPV) metrics allow probabilities of current earthquake hazard to be defined in a simple, straightforward, and rigorous way.

58 GEOSCIENCES↗

The Role of Mesoscale Cloud Morphology in the Shortwave Cloud Feedback

A supervised neural network algorithm is used to categorize near-global satellite retrievals into three mesoscale cellular convective (MCC) cloud morphology patterns. At constant cloud amount, morphology patterns differ in brightness associated with the amount of optically thin cloud features. Environmentally driven transitions from closed MCC to other morphology patterns, typically accompanied by more optically thin cloud features, are used as a framework to quantify the morphology contribution to the optical depth component of the shortwave cloud feedback. A marine heat wave is used as an out-of-sample test of closed MCC occurrence predictions. Morphology shifts in optical depth between 65°S and 65°N under projected environmental changes (i.e., from an abrupt quadrupling of CO 2 ) assuming constant cloud cover contributes between 0.04 and 0.07 W m -2 K -1 (aggregate of 0.06) to the global mean cloud feedback.

54 ENVIRONMENTAL SCIENCES↗