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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

SASHIMI-SIDM: semi-analytical subhalo modelling for self-interacting dark matter at sub-galactic scales

We combine the semi-analytical structure formation model, SASHIMI, which predicts subhalo populations in collisionless, cold dark matter (CDM), with a parametric model that maps CDM halos to self-interacting dark matter (SIDM) halos. The resulting model, SASHIMI-SIDM, generates SIDM subhalo populations down to sub-galactic mass scales, for an arbitrary input cross section, in minutes. We show that SASHIMI-SIDM agrees with SIDM subhalo populations from high-resolution cosmological zoom-in simulations in resolved regimes. Crucially, we predict that the fraction of core-collapsed subhalos peaks at a mass scale determined by the input SIDM cross section and decreases toward higher halo masses, consistent with the predictions of gravothermal models and cosmological simulations. For the first time, we also show that the core-collapsed fraction decreases toward lower halo masses. While the dependence of the collapse time on mass and concentration implies such behaviour, our semi-analytical approach allows us to quantify and illustrate this trend clearly across the full mass spectrum of subhalos, including for subhalo masses below the resolution limit of any current cosmological SIDM simulation. As a proof of principle, we apply SASHIMI-SIDM to predict the boost to the local dark matter density and annihilation rate from core-collapsed SIDM subhalos, which can be enhanced relative to CDM by an order of magnitude for viable SIDM models. Thus, SASHIMI-SIDM provides an efficient and reliable tool for scanning SIDM parameter space and testing it with astrophysical observations. The code is publicly available at https://github.com/shinichiroando/sashimi-si.

cosmological simulations↗
NASA NTRS2003

Predicting and Managing Lighting and Visibility for Human Operations in Space

Lighting is critical to human visual performance. On earth this problem is well understood and solutions are well defined and executed. Because the sun rises and sets on average every 45 minutes during Earth orbit, humans working in space must cope with ~ extremely dynamic lighting conditions varying from very low light conditions to severe glare and contrast conditions. For critical operations, it is essential that lighting conditions be predictable and manageable. Mission planners need to detelmine whether low-light video cameras are required or whether additional luminaires, or lamps, need to be flown . Crew and flight directors need to have up to date daylight orbit time lines showing the best and worst viewing conditions for sunlight and shadowing. Where applicable and possible, lighting conditions need to be part of crew training. In addition, it is desirable to optimize the quantity and quality of light because of the potential impacts on crew safety, delivery costs, electrical power and equipment maintainability for both exterior and interior conditions. Addressing these issues, an illumination modeling system has been developed in the Space Human Factors Laboratory at ASA Johnson Space Center. The system is the integration of a physically based ray-tracing package ("Radiance"), developed at the Lawrence Berkeley Laboratories, a human factors oriented geometric modeling system developed by NASA and an extensive database of humans and their work environments. Measured and published data has been collected for exterior and interior surface reflectivity; luminaire beam spread distribution, color and intensity and video camera light sensitivity and has been associated with their corresponding geometric models. Selecting an eye-point and one or more light sources, including sun and earthshine, a ~ snapshot of the light energy reaching the surfaces or reaching the eye point is computed. This energy map is then used to extract the required information needed for useful predictions. Using a validated, comprehensive illumination model integrated with empirically derived data, predictions of lighting and viewing conditions have been successfully used for Shuttle and Space Station planning and assembly operations. It has successfully balanced the needs for adequate human performance with the utili zation of resources. Keywords: Modeling, ray tracing, luminaires, refl ectivity, luminance, illuminance.

Maida, James C.↗
DOE OSTI2023

A data-driven framework for permeability prediction of natural porous rocks via microstructural characterization and pore-scale simulation

Understanding the microstructure–property relationships of porous media is of great practical significance, based on which macroscopic physical properties can be directly derived from measurable microstructural informatics. However, establishing reliable microstructure–property mappings in an explicit manner is difficult, due to the intricacy, stochasticity, and heterogeneity of porous microstructures. In this paper, a data-driven computational framework is presented to investigate the inherent microstructure–permeability linkage for natural porous rocks, where multiple techniques are integrated together, including microscopy imaging, stochastic reconstruction, microstructural characterization, pore-scale simulation, feature selection, and data-driven modeling. A large number of 3D digital rocks with a wide porosity range are acquired from microscopy imaging and stochastic reconstruction techniques. A broad variety of morphological descriptors are used to quantitatively characterize pore microstructures from different perspectives, and they compose the raw feature pool for feature selection. Here high-fidelity lattice Boltzmann simulations are conducted to resolve fluid flow passing through porous media, from which reliable permeability references are obtained. The optimal feature set that best represents permeability is identified through a performance-oriented feature selection process, upon which a cost-effective surrogate model is rapidly fitted to approximate the microstructure-permeability mapping via data-driven modeling. This surrogate model exhibits great advantages over empirical/analytical formulas in terms of prediction accuracy and generalization capacity, which can predict reliable permeability values spanning four orders of magnitude. Besides, feature selection also greatly enhances the interpretability of the data-driven prediction model, from which new insights into the mechanism of how microstructural characteristics determine intrinsic permeability are obtained.

58 GEOSCIENCES↗
DOE OSTI2022

A deep learning-based direct forecasting of CO 2 plume migration

Accurate and timely forecasts of CO 2 plume evolution in geological reservoirs are crucial for CO 2 migration detection, leakage risk assessment, and operation decision support. Conventional forecasting usually adopts a two-step strategy, first calibrating reservoir model parameters against observations using iterative inverse modeling (or history matching) and then applying the calibrated model for predictions. This method impedes real-time forecasts due to the heavy computational demand in inverse modeling and may suffer from poor prediction accuracy because of the limited observation data. In this work, we propose a deep learning-based latent space mapping framework to forecast CO 2 plume migration directly by avoiding the inverse modeling. We first use the convolutional autoencoder to map the high-dimensional complex plume extents onto low-dimensional latent space. Next, we use neural networks to learn the relationship between the observation variables and the prediction latent variables. And then for given observation data, we infer the prediction values directly. This one-step direct forecasting is computationally efficient which requires a few number of parallelizable reservoir simulations and it can provide accurate predictions with limited observations by learning the observation-prediction relationship in the reduced dimension. Therefore, our proposed method enables an in-time forecast of dynamic CO 2 plume distributions. In this work, we demonstrate the effectiveness and accuracy of our method in predicting the CO 2 plume migration using four metrics such as plume area, centroid movement distance, and plume spreading in the primary and secondary directions. And the spatio-temporal evolution patterns of plume migration under diverse geological complexities are also accurately quantified.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗
DOE OSTI2025

Complex water networks visualized by cryogenic electron microscopy of RNA

The stability and function of biomolecules are directly influenced by their myriad interactions with water. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule: the Tetrahymena ribozyme. By using segmentation-guided water and ion modelling (SWIM), an approach combining resolvability and chemical parameters, we automatically modelled and cross-validated water molecules and Mg 2+ ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics, supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modelling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and molecular dynamics simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A machine learning approach for particle accelerator errant beam prediction using spatial phase deviation

Particle accelerators are extremely complex systems that are expected to operate on high availability. Predicting impending failures only by utilizing data collected from diagnostic equipment already on board can help operators to avoid installing expensive sensors, unscheduled downtime and associated costs. For this purpose we explore the predictive power of Machine Learning algorithms to detect faulty beams prior to the failure. In this study, we propose a Machine Learning approach to model mapping from a pair of sensors located across the accelerator. While the model is trained to represent normal operation, we evaluate the predictive performance on known faulty beam pulses. We also investigate the model performance on unseen data through k-fold cross-validation. Then we recap the analysis with a neural architecture search and hyperparameter optimization study to fine tune our initial model. In conclusion, this paper will also introduce a sustainable framework that can standardize Machine Learning workflow applied to particle accelerators.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS2009

Analytical Predictions of Thermal Stress in the Stardust PICA Heatshield Under Reentry Flight Conditions

We performed finite element analyses on a model of the Phenolic Impregnated Carbon Ablator (PICA) heatshield from the Stardust sample return capsule (SRC) to predict the thermal stresses in the PICA material during reentry. The heatshield on the Stardust SRC was a 0.83 m sphere cone, fabricated from a single piece of 5.82 cm-thick PICA. The heatshield performed successfully during Earth reentry of the SRC in January 2006. Material response analyses of the full, axisymmetric PICA heatshield were run using the Two-Dimensional Implicit Ablation, Pyrolysis, and Thermal Response Program (TITAN). Peak surface temperatures were predicted to be 3385K, while the temperature at the PICA backface remained at the estimated initial cold-soak temperature of 278K. Surface recession and temperature distribution results from TITAN, at several points in the reentry trajectory, were mapped onto an axisymmetric finite element model of the heatshield. We used the finite element model to predict the thermal stresses in the PICA from differential thermal expansion. The predicted peak compressive stress in the PICA heatshield was 1.38 MPa. Although this level of stress exceeded the chosen design limit for compressive stresses in PICA tiles for the design of the Orion crew exploration vehicle heatshield, the Stardust heatshield exhibited no obvious mechanical failures from thermal stress. The analyses of the Stardust heatshield were used to assess and adjust the level of conservatism in the finite element analyses in support of the Orion heatshield design.

Squire, Thomas↗
NASA NTRS2012

Improved Displacement Transfer Functions for Structure Deformed Shape Predictions Using Discretely Distributed Surface Strains

In the formulations of earlier Displacement Transfer Functions for structure shape predictions, the surface strain distributions, along a strain-sensing line, were represented with piecewise linear functions. To improve the shape-prediction accuracies, Improved Displacement Transfer Functions were formulated using piecewise nonlinear strain representations. Through discretization of an embedded beam (depth-wise cross section of a structure along a strain-sensing line) into multiple small domains, piecewise nonlinear functions were used to describe the surface strain distributions along the discretized embedded beam. Such piecewise approach enabled the piecewise integrations of the embedded beam curvature equations to yield slope and deflection equations in recursive forms. The resulting Improved Displacement Transfer Functions, written in summation forms, were expressed in terms of beam geometrical parameters and surface strains along the strain-sensing line. By feeding the surface strains into the Improved Displacement Transfer Functions, structural deflections could be calculated at multiple points for mapping out the overall structural deformed shapes for visual display. The shape-prediction accuracies of the Improved Displacement Transfer Functions were then examined in view of finite-element-calculated deflections using different tapered cantilever tubular beams. It was found that by using the piecewise nonlinear strain representations, the shape-prediction accuracies could be greatly improved, especially for highly-tapered cantilever tubular beams.

Ko, William L.↗
NASA NTRS2024

Soil Salinity Level Assessment and Prediction Integrating UAV-borne Hyperspectral Imaging and Machine Learning Algorithms to Combat Desertification

In response to the ongoing global food crisis, the United Nations has identified “Zero Hunger” as one of its Sustainable Development Goals. A central contributor to the crisis is the process in which agricultural lands go through desertification. Research has shown a direct correlation between soil salinity and desertification - increased salinity levels indicate a higher risk for desertification. Furthermore, researchers have explored various techniques to map soil salinity, but these methods are oftentimes inefficient and don’t address future salinity predictions. To improve desertification monitoring, soil salinity can be observed via hyperspectral imaging on unmanned aerial vehicles (UAVs) to predict the risk of agricultural desertification using artificial intelligence (AI) and machine learning (ML) techniques. A significant gap exists in past research that applies ML and imaging techniques to soil salinity: convolutional neural networks (CNNs) and regression models are rarely leveraged together, despite the efficiency and accuracy of these models. To compensate for this gap, the proposed system leverages the use of these AI and ML models to improve soil assessment and prediction techniques. This approach involves three steps - data collection, image analysis, and future prediction. Using hyperspectral cameras on UAVs to collect the data from the region, a trained CNN model will output estimated soil salinity levels at a specific time. The estimations will then be analyzed by a regression model to assess the accuracy of future soil salinity predictions. The proposed system will identify regions at risk of desertification to help farmers mitigate agricultural loss, in turn helping alleviate the food crisis.

UAV systems↗
NASA NTRSDate not supplied

TPSAS-NF1676L-13204-DND

Invasive perennial pepperweed (Lepidium latifolium) has spread rapidly throughout the western United States in the past fifteen years. Pepperweed outcompetes many native species for water and nutrients, disturbing sensitive ecosystems. The purpose of this study is to map the contemporary distribution of pepperweed throughout the wetland ecosystem of the restored South San Francisco Bay Salt Ponds and create a habitat suitability model to predict future spread. Pepperweed reflectance data were collected in-situ with the GER 1500 spectroradiometer along with presence and absence pepperweed GPS data points. A Spectral Angle Mapper (SAM) classification algorithm (Method A) was used to distinguish pepperweed spectra and map its distribution on an EO-1 Hyperion image of the study area. Similarly, a supervised classification was run on an ASTER image of the study area. A GIS multivariate habitat suitability model was created to predict areas most susceptible to pepperweed colonization. Variables incorporated into the model were tidal extent, propensity for disturbance, pond salinity, proximity to levees and channels, and terrain curvature. A Generalized Additive Model (GAM) was also used to generate a suitability map (Method B) and investigate the statistical probability that each variable contributed to predict pepperweed spread. Results from the GAM revealed distance to channels, distance to disturbance factors, extreme pond salinity and curvature as statistically significant in determining the locations of suitable pepperweed habitats

Andrew Nguyen↗
NASA NTRSDate not supplied

Marin County Wildland Fires: Examining Fuel Load and Land Cover Change to Inform Fire Prevention and Suppression Decisions in Marin County, CA

Heightened occurrence of severe wildfires in the Western United States is increasing the need to better understand regions of high potential wild fire severity and develop methodologies for identifying the best locations for fuels reduction and active wildfire suppression, especially in populated regions such as Marin County, California. Marin County, located in the San Francisco Bay Area, has had significant development in the wildland-urban interface and periods of highly wildfire-prone conditions. The NASA DEVELOP team collaborated with Fire Foundry, a Marin-based fire service work force development program, to develop new models to assist with fire management. Using data from Sentinel-2A, Planet Scope, ECOSTRESS, a county-wide LiDAR mapping effort, Landsat 7 Enhanced Thematic Mapper (ETM+), and Landsat 8 Operational Land Imager (OLI), the team developed several input data layers to three models evaluating wild fire severity. One model performed a suitability analysis with weights based on scientific literature, another utilized machine learning based on past fires in Marin and neighboring Sonoma County to predict the difference normalized burn ratio, and the third inputted data layers into the Flam Map tool, which outputs risk categories. The team compared model outputs and, using the best-fit model, performed fuzzy logic analysis to identify specific locations where a fire break could be constructed to interrupt the progress of an active fire. These tools were proven useful and will assist partners in preparing for and managing an active wildfire event.

Suhani Dalal↗
NASA NTRS1993

The importance of properties in modeling

Casting and welding of superalloys, stainless steel and titanium alloys are processes which can be improved through modeling of heat flow, fluid flow, residual stress development, and microstructural evolution. These simulations require inputs of thermophysical data, some of which involves the partially or totally liquid state. In particular, these processes involve melting, flow in the liquid, and solidification. Modeling of such processes can lead to an improved understanding of defects such as shrinkage, inclusions, cracks, incomplete filling (or penetration), macrosegregation, improper grain structure, and deviations from dimensional specifications. Effective modeling can shorten process development time and improve quality. An approach to these problems is to develop efficient models; validate through correlations with thermal, distortion, and microstructural data; run parametric studies; extract knowledge based rules; and apply to adaptive closed loop control systems. With the appropriate pre- and post-processing, such analyses can be made 'user friendly'. This would include graphical user interfaces as well as realistic images and color maps. In such form, these models can be used for sensitivity analyses, which are useful in defining appropriate sensors and in the development of control strategies. Such modeling can be done at several levels, e.g., the MARO level, modeling large scale phenomena such as heat and fluid flow or material deformation; the MICRO level, modeling the development of dendrites, grains or precipitates; or at the NANO level, modeling point defects, dislocations, stacking faults, etc. There are many computational issues associated with these simulations, e.g. computational efficiency and accuracy. In addition, there are many materials issues, not the least of which is the availability of accurate high temperature thermophysical data for complex alloys. This would include latent heat of fusion, temperature dependent heat capacity and thermal conductivity (for liquid and solid), viscosity, surface tension, thermal expansion, mechanical properties, etc. Preliminary data is frequently gathered from the literature; however, this is often not available for modern alloys. If additional data are required, measurements can be used; however, these are costly, time consuming and can be erroneous due to a lack of testing standards or impure materials. Microstructural predictors can be extracted from thermal information, e.g. cooling rate and thermal gradient; the prediction of microstructure is dependent on solidus and liquidus temperature, mushy zone permeability, the solidification curve, volume changes, phase transformations, alloying effects (such as surface tension or viscosity), mold/metal reactions, metal/environment reactions, etc. Defect maps may be needed to predict the onset of shrinkage, hot cracking or 'freckling'. Constants may be needed for stress relaxation, dendrite coarsening, vaporization, etc. Visualization was used as a tool to better comprehend complex data sets associated with the analysis of directional solidification (including crystal growth) and welding. Examples include not only isotherms, but also cooling rate, growth rate and thermal gradient. The latter two are not single valued scalars, but rather time and space dependent vector fields. Efficient models were developed for both casting and welding to predict heat flow and the relationship to dendrite and grain growth. These codes include many of the non-linear effects, e.g. radiation, which dominate these processes. The home-built FDM code(s) were designed to be useful not only to the scientist, but also to the process engineer. Special output can be requested to compare directly to experimental data. Visualization procedures were developed to visualize critical results, e.g. fusion zone width at the surface opposite that where the arc is applied ('penetration'). Both elaborate and simplified distortion analyses were carried out. It is clear that extensive mechanical property data are critical in order to accurately predict residual stress patterns. A scheme is currently being developed to integrate these modeling tools into a set of control algorithms; however, the success of this approach is critically dependent on the availability of accurate high temperature thermophysical data.

Giamei, A. F.↗
DOE OSTI2023

Using Ultrasound Image Augmentation and Ensemble Predictions to Prevent Machine-Learning Model Overfitting

Deep learning predictive models have the potential to simplify and automate medical imaging diagnostics by lowering the skill threshold for image interpretation. However, this requires predictive models that are generalized to handle subject variability as seen clinically. Here, we highlight methods to improve test accuracy of an image classifier model for shrapnel identification using tissue phantom image sets. Using a previously developed image classifier neural network—termed ShrapML—blind test accuracy was less than 70% and was variable depending on the training/test data setup, as determined by a leave one subject out (LOSO) holdout methodology. Introduction of affine transformations for image augmentation or MixUp methodologies to generate additional training sets improved model performance and overall accuracy improved to 75%. Further improvements were made by aggregating predictions across five LOSO holdouts. This was done by bagging confidences or predictions from all LOSOs or the top-3 LOSO confidence models for each image prediction. Top-3 LOSO confidence bagging performed best, with test accuracy improved to greater than 85% accuracy for two different blind tissue phantoms. This was confirmed by gradient-weighted class activation mapping to highlight that the image classifier was tracking shrapnel in the image sets. Overall, data augmentation and ensemble prediction approaches were suitable for creating more generalized predictive models for ultrasound image analysis, a critical step for real-time diagnostic deployment.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2016

Estimation of Daily PM(sub 10) Concentrations in Italy (2006-2012) Using Finely Resolved Satellite Data, Land Use Variables and Meteorology

Health effects of air pollution, especially particulate matter (PM), have been widely investigated. However, most of the studies rely on few monitors located in urban areas for short-term assessments, or land use/dispersion modelling for long-term evaluations, again mostly in cities. Recently, the availability of finely resolved satellite data provides an opportunity to estimate daily concentrations of air pollutants over wide spatio-temporal domains. Italy lacks a robust and validated high resolution spatio-temporally resolved model of particulate matter. The complex topography and the air mixture from both natural and anthropogenic sources are great challenges difficult to be addressed. We combined finely resolved data on Aerosol Optical Depth (AOD) from the Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm, ground-level PM10measurements, land-use variables and meteorological parameters into a four-stage mixed model framework to derive estimates of daily PM10concentrations at 1-km2 grid over Italy, for the years 2006-2012. We checked performance of our models by applying 10-fold cross-validation (CV) for each year. Our models displayed good fitting, with mean CV-R2=0.65 and little bias (average slope of predicted VS observed PM10=0.99). Out-of-sample predictions were more accurate in Northern Italy (Po valley) and large conurbations (e.g. Rome), for background monitoring stations, and in the winter season. Resulting concentration maps showed highest average PM10levels in specific areas (Po river valley, main industrial and metropolitan areas) with decreasing trends over time. Our daily predictions of PM10concentrations across the whole Italy will allow, for the first time, estimation of long-term and short-term effects of air pollution nationwide, even in areas lacking monitoring data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Particulate Matter/analysis↗
DOE OSTI2021

Solving the 2D SUSY Gross-Neveu-Yukawa model with conformal truncation

We use Lightcone Conformal Truncation to analyze the RG flow of the two-dimensional supersymmetric Gross-Neveu-Yukawa theory, i.e. the theory of a real scalar superfield with a $\mathbb{Z}$ 2 -symmetric cubic superpotential, aka the 2d Wess-Zumino model. The theory depends on a single dimensionless coupling $\overline{g}$, and is expected to have a critical point at a tuned value ${\overline{g}}_{\ast }$ where it flows in the IR to the Tricritical Ising Model (TIM); the theory spontaneously breaks the $\mathbb{Z}$ 2 symmetry on one side of this phase transition, and breaks SUSY on the other side. We calculate the spectrum of energies as a function of $\overline{g}$ and see the gap close as the critical point is approached, and numerically read off the critical exponent ν in TIM. Beyond the critical point, the gap remains nearly zero, in agreement with the expectation of a massless Goldstino. We also study spectral functions of local operators on both sides of the phase transition and compare to analytic predictions where possible. In particular, we use the Zamolodchikov C -function to map the entire phase diagram of the theory. Crucial to this analysis is the fact that our truncation is able to preserve supersymmetry sufficiently to avoid any additional fine tuning.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Advancing AI-Driven Analysis in X-ray Absorption Spectroscopy: Spectral Domain Mapping and Universal Models

In recent years, rapid progress has been made in developing artificial intelligence (AI) and machine learning (ML) methods for X-ray absorption spectroscopy (XAS) analysis. Compared to traditional XAS analysis methods, AI/ML approaches offer dramatic improvements in efficiency and help eliminate human bias. To advance this field, we advocate an AI-driven XAS analysis pipeline that features several interconnected key building blocks: benchmarks, workflows, databases, and AI/ML models. Specifically, we present two case studies for XAS ML. In the first study, we demonstrate the importance of reconciling the discrepancies between simulation and experiment using spectral domain mapping (SDM). Our ML model, which is trained solely on simulated spectra, predicts an incorrect oxidation state trend for Ti atoms in a combinatorial zinc titanate film. After transforming the experimental spectra into a simulation-like representation using SDM, the same model successfully recovers the correct oxidation state trend. In the second study, we explore the development of universal XAS ML models that are trained on the entire periodic table, which enables them to leverage common trends across elements. Looking ahead, we envision that an AI-driven pipeline can unlock the potential of real-time XAS analysis to accelerate scientific discovery.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗