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At least 649 records · Page 36

Predicting Hugoniot equation of state in erythritol with ab initio and reactive molecular dynamics

Erythritol has been proposed as an inert surrogate for developing theoretical and computational models to study aging in energetic materials. In this work, we present a comparison of mechanical and shock properties of erythritol computed using the ReaxFF reactive force field and from ab initio calculations employing density functional theory (DFT). We screened eight different ReaxFF parameterizations, of which the CHO parameters developed for hydrocarbon oxidation provide the most accurate predictions of mechanical properties and the crystal structure of erythritol. Further validation of the applicability of this ReaxFF parameterization for modeling erythritol is demonstrated by comparing predictions of the elastic constants, crystal structure, vibrational density of states, and Hugoniot curves against DFT calculations. The ReaxFF predictions are in close agreement with the DFT simulations for the elastic constants and shock Hugoniot when the crystal is loaded along its c axis but show as much as 30% disagreement in the elastic constants in the ab plane and 12% difference in shock pressures when shocked along the a or b crystal axes. Last, we compare thermomechanical properties predicted from classical molecular dynamics with those calculated using the quasi-harmonic approximation and show that quantum mechanical effects produce large discrepancies in the computed values of heat capacity and thermal expansion coefficients compared with classical assumptions. Combining classical molecular dynamics predictions of mechanical behavior with phonon-based calculations of thermal behaviors, we show that predicted shock-induced temperatures for pressures up to 6.5 GPa do not exceed the pressure-dependent melting point of erythritol.

Hu, Jing↗

Equilibrium reconstruction of DIII-D plasmas using predictive modeling of the pressure profile

New workflows have been developed for predictive modeling of magnetohydrodynamic (MHD) equilibrium in tokamak plasmas. The goal of this work is to predict the MHD equilibrium in tokamak discharges without having measurements of the kinetic profiles. The workflows include a cold start tool, which constructs all the profiles and power flows needed by transport codes; a Grad–Shafranov equilibrium solver; and various codes for the sources and sinks. For validation purposes, a database of DIII-D tokamak discharges has been constructed that is comprised of scans in the plasma current, toroidal magnetic field, and triangularity. Initial efforts focused on developing a workflow utilizing an empirically derived pressure model tuned to DIII-D discharges with monotonic safety factor profiles. This workflow shows good agreement with experimental kinetic equilibrium calculations, but is limited in that it is a single fluid (equal ion and electron temperatures) model and lacks H-mode pedestal predictions. The best agreement with the H-mode database is obtained using a theory-based workflow utilizing pressure profile predictions from a coupled TGLF turbulent transport and EPED pedestal models together with external magnetics and Motional Stark Effect (MSE) data to construct the equilibrium. Here, we obtain an average root mean square error of 5.1% in the safety factor profile when comparing the predicted and experimental kinetic equilibrium. We also find good agreement with the plasma stored energy, internal inductance, and pressure profiles. Including MSE data in the theory-based workflow results in noticeably improved agreement with the q-profiles in high triangularity discharges in comparison with the results obtained with magnetic data only. The predictive equilibrium workflow is expected to have wide applications in experimental planning, between-shot analysis, and reactor studies.

Kinsey, J. E. (ORCID:0000000193347473)↗

A machine learning framework for elastic constants predictions in multi-principal element alloys

On the one hand, multi-principal element alloys (MPEAs) have created a paradigm shift in alloy design due to large compositional space, whereas on the other, they have presented enormous computational challenges for theory-based materials design, especially density functional theory (DFT), which is inherently computationally expensive even for traditional dilute alloys. In this paper, we present a machine learning framework, namely PREDICT (PRedict properties from Existing Database In Complex alloys Territory), that opens a pathway to predict elastic constants in large compositional space with little computational expense. The framework only relies on the DFT database of binary alloys and predicts Voigt–Reuss–Hill Young’s modulus, shear modulus, bulk modulus, elastic constants, and Poisson’s ratio in MPEAs. We show that the key descriptors of elastic constants are the A–B bond length and cohesive energy. The framework can predict elastic constants in hypothetical compositions as long as the constituent elements are present in the database, thereby enabling property exploration in multi-compositional systems. We illustrate predictions in a FCC Ni-Cu-Au-Pd-Pt system.

Linton, Nathan (ORCID:0000000315485613)↗

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗

Optimization of simulated high-field side lower hybrid current drive coupling using machine learning predictions of scrape-off layer density

Lower hybrid current drive (LHCD) is a potential source of non-inductive off-axis current drive (CD) for tokamaks. Although LHCD has been successfully deployed on a number of tokamaks, it is highly sensitive to the scrape-off layer (SOL) conditions local to the LHCD launcher. Large gaps between the launcher and plasma core, SOL turbulence, or edge density perturbations due to edge-localized modes can hamper CD or cause large reflected power. These coupling issues in part motivated the installation of an LHCD launcher on the high-field side (HFS) of DIII-D. On the HFS, the SOL is less turbulent and more controllable compared to the low-field side. This quiescence may result in more predictable edge conditions and thus a more predictable CD. Here, in this work, HFS SOL reflectometry measurements are predicted from global plasma parameters using machine learning models. The SOL predictions coupled with the full-wave simulation of the LHCD launcher allow for the prediction of reflected power, directivity, and arcing risk before the discharge. Launcher performance is then optimized using multi-objective Bayesian optimization, finding the shot parameters that result in an optimal SOL density that maximizes CD while minimizing the risk of arcing. The predictions and optimizations of LHCD performance are then accelerated using a surrogate model of the full-wave LHCD simulation.

Bayesian optimization↗

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗

TEM Approaches for Microstructure-Informed Prediction of Mechanical Properties in Structural Alloys

Predicting the mechanical performance of structural alloys from their evolving microstructure remains a major challenge in materials science, particularly for nuclear structural materials, where irradiation-induced defects span multiple types and length scales and interact through complex mechanisms. The dispersed barrier hardening (DBH) [1] and Friedel–Kroupa–Hirsch (FKH) [2,3] models have been widely used to evaluate the hardening contributions of individual obstacles and to estimate tensile strength from quantified microstructures; however, when multiple size-dependent obstacles coexist and evolve, predicting temperature-dependent tensile strength becomes significantly more complex, and a fully consistent hardening model is still lacking. Transmission electron microscopy (TEM) plays a central role in refining hardening models and enabling predictive assessments of tensile strength evolution by providing quantitative characterization of dislocations, irradiation-induced defects (e.g., dislocation loops and cavities), precipitates, and grain structure (Fig. 1.). These experimentally measured defect densities are incorporated into physically based hardening models with size- and shape- dependent obstacle strengths [4], using root-sum-square superposition for obstacles of comparable strength and linear superposition for dissimilar ones [5]. In addition, recent advances in TEM [6-8], including high-resolution imaging, 4D-STEM strain mapping, EDS/EELS elemental analysis, and flash-polishing-based TEM specimen preparation and extraction-replica methods (Fig. 2), further improve the accuracy of microstructural quantification. By comparison with prior studies as well as our own results, we show that when TEM-derived microstructural information is carefully integrated with physically grounded hardening models, yield strength (or irradiation-induced hardening) measured at room temperature can be predicted with good quantitative agreement across multiple alloy classes. In-situ TEM combined with high-temperature mechanical testing represents an important next step for refining hardening models by directly probing dislocation–obstacle interactions across varying irradiation doses and temperatures [9]. Because the barrier strength factor (α) depends on both temperature and obstacle size, it should not be treated as a constant fitting parameter; rather, it must be explicitly evaluated to achieve physically meaningful predictions of mechanical behaviour at operating temperatures. This presentation therefore discusses why all strengthening contributions (e.g., Peierls stress, solid-solution strengthening, voids, bubbles, dislocation loops, dislocation lines, and grain boundaries) must be considered collectively, why appropriate superposition methods are essential when obstacles possess different barrier strength factors, how hardness measurements can be meaningfully related to tensile properties, and how TEM-derived microstructural information can be systematically incorporated into hardening models. More broadly, it outlines a pathway toward microstructure-informed prediction of mechanical properties and supports the goal of establishing science-based tools for evaluating structural materials in extreme environments [10].

Lin, Yan-Ru [ORNL] (ORCID:0000000339991473)↗

Accurate machine-learning predictions of coercivity in high-performance permanent magnets

Increased demand for high-performance permanent magnets in the electric vehicle and wind-turbine industries has prompted the search for cost-effective alternatives. Discovering magnetic materials with the desired intrinsic and extrinsic permanent magnet properties presents a significant challenge to researchers because of issues with the global supply of rare-earth elements, material stability, and a low maximum magnetic energy product BH max . While first-principles density functional theory (DFT) predicts materials’ magnetic moments, magnetocrystalline anisotropy constants, and exchange interactions, it cannot compute extrinsic properties such as coercivity (H c ). Although it is possible to calculate H c theoretically with micromagnetic simulations, the predicted value is larger than the experiment by almost an order of magnitude due to the Brown paradox. To circumvent these issues, we employ machine-learning (ML) methods on an extensive database obtained from experiments, DFT calculations, and micromagnetic modeling. The use of a large experimental dataset enables realistic H c predictions for materials such as Ce-doped Nd 2 ⁢Fe 14 ⁢B, comparing favorably against micromagnetically simulated coercivities. Remarkably, our ML model accurately identifies uniaxial magneto-crystalline anisotropy as the primary contributor to H c . With DFT calculations, we predict the Nd-site-dependent magnetic anisotropy behavior in Nd 2 ⁢Fe 14 ⁢B, confirming that Nd 4⁢g sites mainly contribute to uniaxial magnetocrystalline anisotropy, and also calculate the Curie temperature (T c ). Finally, both calculated results are in good agreement with the experiments. The coupled experimental dataset and ML modeling with DFT input predict H c with far greater accuracy and speed than was previously possible using micromagnetic modeling. Further, we reverse engineer the grain-boundary and intergrain exchange coupling with micromagnetic simulations by employing the ML predictions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

First-principles predictions of temperature-dependent infrared dielectric function of polar materials by including four-phonon scattering and phonon frequency shift

Recently, first-principles calculations based on density functional theory have been widely used to predict the temperature-dependent infrared spectrum of polar materials, but the calculations are usually limited to the harmonic frequency (0 K) and three-phonon scattering damping for the zone-center infrared-active optical phonon modes, and fail to predict the high-temperature infrared optical properties of materials such as sapphire (α–Al 2 O 3 ), GaAs, TiO 2 , etc., due to the neglect of high-order phonon scattering damping and phonon frequency shift. In this work, we implemented first-principles calculations to predict the temperature-dependent infrared dielectric function of polar materials by including four-phonon scattering and phonon frequency shift. The temperature-dependent phonon damping by including three- and four-phonon scattering as well as the phonon frequency shift by including cubic and quartic anharmonicity and the thermal expansion effect are calculated based on anharmonic lattice dynamics method. The infrared dielectric function of α–Al 2 O 3 is parameterized, and then the temperature-dependent infrared optical reflectance is determined. We find that our predictions agree better with the experimental data than the previous density functional theory-based methods. Lastly, this work will help to effectively predict the thermal radiative properties of polar materials at elevated temperature, which is generally difficult to measure, and will enable predictive design of new materials for radiative applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗

Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic experiments, and with accelerators like GPUs and TPUs making inference using large models rapid, genome-level structure prediction becomes an obvious aim. Leadership-class computing resources can be used to perform genome-scale protein structure prediction using state-of-the-art deep learning models, providing a wealth of new data for systems biology applications. Here we describe our efforts to efficiently deploy the AlphaFold v.2 program, for full-proteome structure prediction, at scale on the Oak Ridge Leadership Computing Facility's resources, including the Summit supercomputer. We performed inference to produce the predicted structures for 40,526 protein sequences, corresponding to four prokaryotic proteomes and one plant proteome, using under 4,400 total Summit node hours, equivalent to using the majority of the supercomputer for a little over one hour. We also designed an optimized structure refinement that reduced the time for the relaxation stage of the AlphaFold pipeline by over 10X for longer sequences. We demonstrate the types of analyses that can be performed on proteome-scale collections of sequences, including a search for novel quaternary structures and implications for functional annotation.

Gao, Mu↗

Three-Stage Adjusted Regression Forecasting for Software Defect Prediction

In this paper, a three-stage adjusted regression forecasting model is proposed to forecast the local regression model [6]. This is a growth curve approximation model that predicts the parameters for a future linear model based on a sliding window of previous linear models. The three stages of the model are as follows: • Initial fit: train regression models on a sliding window of the date and record model coefficients. • Prediction: fit new regression models to the coefficient lists and predict the value of the next coefficient. • Error correction: correct coefficient prediction error using the residual of the last point of the coefficient list and moving average. The resulting model from the multi-stage process is a forecast of the local regression model that represents the future window of data and is referred to as the predicted line. Results suggest the three-stage model demonstrates better prediction capability compared to existing solutions.

Pritchard, Shadow↗

Prediction of DIII-D Pedestal Structure From Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. Here, an experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (n e ) and electron temperature (T e ) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (I p ), toroidal magnetic field (B Φ ), neutral beam heating power (P NBI ) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sensitivity of Thermal Predictions to Uncertain Surface Tension Data in Laser Additive Manufacturing

To understand the process-microstructure relationships in additive manufacturing (AM), it is necessary to predict the solidification characteristics in the melt pool. This study investigates the influence of Marangoni driven fluid flow on the predicted melt pool geometry and solidification conditions using a continuum finite volume model. A calibrated laser absorptivity was determined by comparing the model predictions (neglecting fluid flow) against melt pool dimensions obtained from single laser melt experiments on a nickel super alloy 625 (IN625) plate. Using this calibrated efficiency, predicted melt pool geometries agree well with experiments across a range of process conditions. When fluid mechanics is considered, a surface tension gradient recommended for IN625 tends to overpredict the influence of convective heat transfer, but the use of an intermediate value reported from experimental measurements of a similar nickel super alloy produces excellent experimental agreement. Despite its significant effect on the melt pool geometry predictions, fluid flow was found to have a small effect on the predicted solidification conditions compared to processing conditions. We find that this result suggests that under certain circumstances, a model only considering conductive heat transfer is sufficient for approximating process-microstructure relationships in laser AM. Extending the model to multiple laser passes further showed that fluid flow also has a small effect on the solidification conditions compared to the transient variations in the process. Furthermore, limitations of the current model and areas of improvement, including uncertainties associated with the phenomenological model inputs are discussed.

36 MATERIALS SCIENCE↗

MACHINE LEARNING-ENABLED PREDICTION OF TRANSIENT INJECTION MAP IN AUTOMOTIVE INJECTORS WITH UNCERTAINTY QUANTIFICATION

Accurate prediction of injection profiles is a critical aspect of linking injector operation with engine performance and emissions. However, highly resolved injector simulations can take one to two weeks of wall-clock time, which is incompatible with engine design cycles with desired turnaround times of less than a day. Hence, it is important to reduce the time-to-solution of the internal flow simulations by several orders of magnitude to make it compatible with engine simulations. This work demonstrates a data-driven approach for tackling the computational overhead of injector simulations, whereby the transient injection profiles are emulated for a side-oriented, single-hole diesel injector using a Bayesian machine-learning framework. First, an interpretable Bayesian learning strategy was employed to understand the effect of design parameters on the total void fraction field. Then, autoencoders are utilized for efficient dimensionality reduction of the flowfields. Gaussian process models are finally used to predict the spatiotemporal void fraction field at the injector exit for unknown operating conditions. The Gaussian process models produce principled uncertainty estimates associated with the emulated flowfields, which provide the engine designer with valuable information of where the data-driven predictions can be trusted in the design space. The Bayesian flowfield predictions are compared with the corresponding predictions from a deep neural network, which has been transfer-learned from static needle simulations from a previous work by the authors. The emulation framework can predict the void fraction field at the exit of the orifice within a few seconds, thus achieving a speed-up factor of up to 38 x 10(6) over the traditional simulation-based approach of generating transient injection maps.

machine learning↗

Efficient Probabilistic Prediction and Uncertainty Quantification of Tropical Cyclone–Driven Storm Tides and Inundation

Abstract This study proposes and assesses a methodology to obtain high-quality probabilistic predictions and uncertainty information of near-landfall tropical cyclone–driven (TC-driven) storm tide and inundation with limited time and resources. Forecasts of TC track, intensity, and size are perturbed according to quasi-random Korobov sequences of historical forecast errors with assumed Gaussian and uniform statistical distributions. These perturbations are run in an ensemble of hydrodynamic storm tide model simulations. The resulting set of maximum water surface elevations are dimensionality reduced using Karhunen–Loève expansions and then used as a training set to develop a polynomial chaos (PC) surrogate model from which global sensitivities and probabilistic predictions can be extracted. The maximum water surface elevation is extrapolated over dry points incorporating energy head loss with distance to properly train the surrogate for predicting inundation. We find that the surrogate constructed with third-order PCs using elastic net penalized regression with leave-one-out cross validation provides the most robust fit across training and test sets. Probabilistic predictions of maximum water surface elevation and inundation area by the surrogate model at 48-h lead time for three past U.S. landfalling hurricanes (Irma in 2017, Florence in 2018, and Laura in 2020) are found to be reliable when compared to best track hindcast simulation results, even when trained with as few as 19 samples. The maximum water surface elevation is most sensitive to perpendicular track-offset errors for all three storms. Laura is also highly sensitive to storm size and has the least reliable prediction. Significance Statement The purpose of this study is to develop and evaluate a methodology that can be used to provide high-quality probabilistic predictions of hurricane-induced storm tide and inundation with limited time and resources. This is important for emergency management purposes during or after the landfall of hurricanes. Our results show that sampling forecast errors using quasi-random sequences combined with machine learning techniques that fit polynomial functions to the data are well suited to this task. The polynomial functions also have the benefit of producing exact sensitivity indices of storm tide and inundation to the forecasted hurricane properties such as path, intensity, and size, which can be used for uncertainty estimation. The code implementing the presented methodology is publicly available on GitHub.

54 ENVIRONMENTAL SCIENCES↗

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

Background: G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies. Results: G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R 2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion: G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans.

59 BASIC BIOLOGICAL SCIENCES↗