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All sources NASA NTRS DOE OSTI

DOE OSTI2020

Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels

Coproduction of high-value bioproducts at biorefineries is a key factor in making biofuels more cost-competitive. One strategy for generating coproducts is to directly engineer bioenergy crops to accumulate bioproducts in planta that can be fractionated and recovered at biorefineries. Here, we develop quantitative insights into the relationship between bioproduct market value and target accumulation rates by investigating a set of industrially relevant compounds already extracted from plant sources with a wide range of market prices and applications, including <$10/kg (limonene, latex, and polyhydroxybutyrate [PHB]), $10 to $100/kg (cannabidiol), and >$100/kg (artemisinin). These compounds are used to identify a range of mass fraction thresholds required to achieve net economic benefits for biorefineries and the additional amounts needed to reach a target $2.50/gal biofuel selling price, using cellulosic ethanol production as a test case. Bioproduct market prices and recovery costs determine the accumulation threshold; we find that moderate- to high-value compounds (i.e., cannabidiol and artemisinin) offer net economic benefits at accumulation rates of just 0.01% dry weight (dwt) to 0.02 dwt%. Lower-value compounds, including limonene, latex, and PHB, require at least an order-of-magnitude greater accumulation to overcome additional extraction and recovery costs (0.3 to 1.2 dwt%). We also find that a diversified approach is critical. For example, global artemisinin demand could be met with fewer than 10 biorefineries, while global demand for latex is equivalent to nearly 180 facilities. Our results provide a roadmap for future plant metabolic engineering efforts aimed at increasing the value derived from bioenergy crops.

09 BIOMASS FUELS↗

DOE OSTI2022

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.

Cohen, Natalie R.↗

DOE OSTI2025

Data-driven emulation of modal aerosol microphysics via neural operator-based modeling

The complexity and the small characteristic scales of aerosol microphysical processes pose a big challenge for accurate and efficient Earth system simulations at regional and global scales. In this work, we construct and evaluate a surrogate model: the aerosol deep operator network (ADON), a physics-inspired dual-net architecture for emulating the aerosol microphysics parameterization suite in the version 2 of the Energy Earth System Model (E3SMv2). The current version of the surrogate model is trained on a dataset comprising 9.8 million samples obtained from a global E3SMv2 simulation with the horizontal resolution of about one degree under cloud-free conditions. Incorporating domain spatial and temporal coordinates, as well as principle components extracted from training data, the dual-net surrogate model effectively captures the intricate representations of aerosol and the relationship with atmospheric state variables, achieving an R-squared score over $$95.7\%$$ for all the lognormal aerosol modes in the extrapolated regime. The validated model provides feature importance of input variables and their impact on the predictive capacity of the surrogate model in relation to the E3SM. The computational cost of online inference time deployed on CPUs and GPUs with lower precisions highlights ADON’s efficiency and potential in robust predictive modeling for large-scale Earth system computations.

Bai, Zhe↗

DOE OSTI2020

System and methods for automated detection, reasoning and recommendations for resilient cyber systems

A method for securing an IT (information technology) system using a set of methods for knowledge extraction, event detection, risk estimation and explanation for ranking cyber-alerts which includes a method to explain the relationship (or an attack pathway) from an entity (user or host) and an event context to another entity (a high-value resource) and an event context (attack or service failure).

Choudhury, Sutanay↗

DOE OSTI2024

Dual X-ray computed tomography-aided classification of melt pool boundaries and flaws in crept additively manufactured parts

In metal additive manufacturing (AM), understanding the process-structure-performance relationships requires a combination of multi-scale characterization techniques that allows for the measurement of the melt pool shape and boundary and classifying various defects and flaws in the AM parts. Such approaches can be destructive, only 2D in nature, or have a small field of view and can be complex to co-register and analyze. Here, in this work, we present a non-destructive 3D inspection technique that employs dual-energy X-ray computed tomography (XCT) along with a model-based iterative reconstruction (MBIR) and a new segmentation algorithm. The proposed approach and algorithm are not only capable of classifying and quantifying flaws such as pores, cracks, and inclusions, but they also allow for the extraction of microstructural features such as melt pool boundaries (MPB) and melt pool regions (MPR), that can help understand process-structure-performance relationships for alloys under study. As an exemplar application, we employed the method for characterization of an additively manufactured aluminum alloy crept under tensile stress at 300 °C for 1064 h. Our results demonstrate high quality segmentation and classification of various flaws and MPB and MPR, for the first time, using 3D X-ray CT inspection. The delineated MPB and MPR in the crept samples reveal the preferential growth paths of cracks that formed during creep deformation. The technique was used for successfully quantifying the characteristics (number of defects, their density, volume fraction, etc.) of the manufacturing-induced pores and creep-induced cracks, which is necessary to better understand the creep failure mechanisms of the material.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Structural and Mechanical Analysis of Individual Mineralized Collagen Fibrils Using In Situ Transmission Electron Microscopy

Bone serves as an example of nature’s architectured material with its characteristic blend of strength and toughness, all at a lightweight design. Given the hierarchical nature of these materials, it is essential to understand the governing mechanisms and organization of their constituents across length scales for bioinspired structural design. Despite recent advances in transmission electron microscopy (TEM) that have allowed us to witness the hierarchical arrangement of bone at micro-down to the nanoscale, we are still missing the details about the structural organization and mechanical properties of the main building blocks of bone─mineralized collagen fibrils (MCFs). Here, we present a method to extract individual MCFs from nature’s model material, mineralized turkey leg tendon, using a dropcasting procedure. By isolating the MCFs onto TEM supporting grids, we visualized the arrangement of organic and mineral phases within individual MCFs at the nanoscale. Using a four-dimensional scanning transmission electron microscopy (4D-STEM) approach, the orientation of individual mineral crystals within the MCFs was examined. Furthermore, we conducted in situ tensile experiments, revealing exceptional tensile strains of at least 8%, demonstrating the intricate relationship between structural organization and the mechanical behavior of MCFs. These insights into the ultrastructure of mineralized tissue building blocks, as well as the proposed sample-extraction method compatible with in situ mechanical testing, provide a strong basis for research into nature-inspired material design.

4D-STEM↗

DOE OSTI2023

Understanding structure-processing relationships in metal additive manufacturing via featurization of microstructural images

Understanding and predicting accurate property-structure-processing relationships for additively manufactured components is important for both forward and inverse design of robust, reliable parts and assemblies. While direct mapping of process parameters to properties is sometimes plausible, it is often rendered difficult due to poor microstructural control. Exploring the direct relationship between processing conditions and microstructural features can thus provide significant physical insights and aid the overall design process. Here, in this study, we develop an automated high-throughput framework to simulate an uncertainty-aware additive manufacturing (AM) process, characterize microstructural images, and extract meaningful features/descriptors. A kinetic Monte Carlo (KMC) based model of the AM process is used to simulate microstructural evolution for a diverse set of experimentally relevant processing conditions. We perform a parametric study to explore the relationship between microstructural features and processing conditions. Our results indicate that a many-to-one mapping can exist between processing conditions and typical descriptors; therefore, multiple descriptors are thus necessary to unambiguously represent microstructural images. Our work provides crucial quantitative and qualitative in-formation that would aid in the selection of features for microstructural images. Featurized microstructures could then be utilized to build data-driven models for predictive control of microstructures and thereby properties of additively manufactured components.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Solid‐state nuclear magnetic resonance of spin‐9/2 nuclei 115 In and 209 Bi in functional inorganic complex oxides

Abstract Indium and bismuth are technologically important elements, in particular as oxides for optoelectronic applications. 115 In and 209 Bi are both I = 9/2 nuclei with high natural abundances and moderately high frequencies but large nuclear electric quadrupole moments. Leveraging the quadrupolar interaction as a measure of local symmetry and polyhedral distortions for these nuclei could provide powerful insights on a range of applied materials. However, the absence of reported nuclear magnetic resonance (NMR) parameters on these nuclei, particularly in oxides, hinders their use by the broader materials community. In this contribution, solid‐state 115 In and 209 Bi NMR of three recently discovered quaternary bismuth or indium oxides are reported, supported by density functional theory calculations, numerical simulations, diffraction and additional multinuclear ( 27 Al, 69,71 Ga, and 121 Sb) solid‐state NMR measurements. The compounds LiIn 2 SbO 6 , BiAlTeO 6 , and BiGaTeO 6 are measured without special equipment at 9.4 T, demonstrating that wideline techniques such as the QCPMG pulse sequence and frequency‐stepped acquisition can enable straightforward extraction of quadrupolar tensor information in I = 9/2 115 In and 209 Bi even in sites with large quadrupolar coupling constants. Relationships are described between the NMR observables and local site symmetry. These are amongst the first reports of the NMR parameters of 115 In, 121 Sb, and 209 Bi in oxides.

Griffith, Kent J.↗

DOE OSTI2020

Chemometric modeling of power conversion efficiency of organic dyes in dye sensitized solar cells for the future renewable energy

The present study reports chemometric modeling of power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs) using the biggest available data set till date which comprises around 1200 dyes covering 7 chemical classes. To extract the best structural features required for higher PCE, we have developed multiple partial least squares (PLS) quantitative structure-property relationship (QSPR) models for the Triphenylamine, Phenothiazine, Indoline, Porphyrin, Coumarin, Carbazole and Diphenylamine chemical classes using descriptors derived from the best subset selection method followed by selection of best five models in each dataset based on the Mean Absolute Error (MAE) values. The models were validated both internally and externally followed by the consensus predictions employing “Intelligent Consensus Predictor” tool to examine whether the quality of predictions can be improved with the “intelligent” selection of multiple PLS models. The quality of predictions for the respective external sets showed that the consensus models (CM) are better than the individual models (IM) in most of the cases. From the insights of the developed models, we concluded that attributes like a packed structure toward higher conductivity of electrons, auxiliary donor fragment of aromatic tertiary amines, number of thiophenes inducing the bathochromic shift and augmenting the absorption, presence of additional electron donors, enhancement of electron-donating abilities, number of non-aromatic conjugated C(sp 2 ) which helps as conjugation extension units to broaden the absorption and highly conjugated $π$-systems exert positive contributions to the PCE. On the contrary, features negatively contributing to PCE are the followings: fragments which lower the tendency of localized $π–π*$ transition, fragments related to larger volume and surface area of dyes along with hydrophobicity resulting in poor adhesion, fragment RC = N causing dye hydrolysis, steric hindrance for π electronic mobility, fragments enhancing polarity, etc. Finally, the identified features from the best QSPR model of the coumarin dataset was employed in designing of ten more efficient coumarin dyes (predicted %PCE ranging from 8.93 to 10.62) than the existing ones.

14 SOLAR ENERGY↗

DOE OSTI2025

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine↗

DOE OSTI2020

Robust PCA-Deep Belief Network Surrogate Model for Distribution System Topology Identification with DERs

With the expansion of distribution networks and increased penetration of distributed energy resources (DERs), it is becoming increasingly important to obtain accurate distribution network topology in real-time. In this paper, a robust principal component analysis coupled deep belief network (PCA-DBN) surrogate model is proposed for distribution system topology identification. It integrates the benefits of robust feature extraction from PCA to deal with data quality issues and filter out noise, and the strength of DBN in capturing the nonlinear relationship between voltage amplitudes and the binary states of switchable connections. This also significantly reduces the DBN training complexity without loss of accuracy. It is shown that the widely used standard deviation of voltage drop and the voltage covariance matrix features yield less accuracy as compared to that of the voltage amplitudes in presence of high penetration of DERs and ZIP loads. Comparison results with other alternatives, such as the random forest (RF), multi-output regression (MOR) and the traditional DBN methods demonstrate that the proposed method can achieve a much higher topology identification accuracy while maintaining robustness to missing data and measurement noise under various penetration levels of DERs.

deep belief network↗

DOE OSTI2020

Understanding relative metal prices and availability: Combining physical and economic perspectives

Abstract Scientists typically use physical indicators, such as average crustal abundance, and energy requirements in production, as measures of the availability of mineral resources. Economists, on the other hand, typically rely on measures such as prices, and extraction costs. This study investigates the role of crustal abundance, energy requirements, and other physical indicators in determining relative metal prices. The relationship between prices, and physical indicators is estimated statistically for a sample of 22 chemical elements over the period 1970–2013 using an economic market model. The results suggest that energy requirements in production explain 43% of observed variation in metal prices, crustal abundance 21%, and other physical indicators (toxicity, native metal status, and melting point) combine to explain 12% of the observed differences in metal prices.

Watson, Brett J.↗

DOE OSTI2026

A Nonparametric Method for the Inference of Halo Occupation Distributions

The galaxy–halo connection traces processes by which galaxies form and evolve. The halo occupation distribution (HOD) describes the relationship between galaxies and their host dark matter haloes. Measurements of the galaxy two-point correlation function (2PCF) allow us to extract information about the HODs of observed galaxy samples. Several parametric HOD models have been proposed in the literature, but the choice of parameterization restricts the space of possible HODs. To resolve this issue, we introduce a nonparametric HOD fitting method in which we train an emulator to learn the mappings among the galaxy 2PCF, physical properties used to select galaxy samples, and the HOD, all obtained from simulated past light cones constructed with the Santa Cruz semianalytic model. Implementing this emulator within a likelihood analysis framework, we derive constraints on the HOD of a galaxy sample when provided with a measurement of its 2PCF. Using the emulator to accelerate likelihood evaluations, we test the nonparametric HOD approach on a set of 2PCFs for mock galaxy samples drawn from the TNG100-1 simulation and selected above threshold values of stellar mass and star formation rate. Our framework is able to recover TNG100-1 HODs within 0.2 dex. We use the TNG100-1 mocks to tune the reported uncertainties to estimate those expected in the analysis of observations. Comparing to parametric HOD modelling routines applied to the same mock galaxy samples, our approach consistently infers the HOD with comparable or greater precision and accuracy.

Kennedy, Jacob [Rutgers Univ., Piscataway, NJ (Uni↗

DOE OSTI2024

Getting allometry right at the Oak Ridge free‐air CO 2 enrichment experiment: Old problems and new opportunities for global change experiments

Societal Impact Statement Free‐air CO 2 enrichment (FACE) experiments provide essential data on forest responses to increasing atmospheric CO 2 for evaluations of climate change impacts on humanity. Understanding and reducing the uncertainty in the experimental results is critical to ensure scientific and public confidence in the models and policy initiatives that derive therefrom. One source of uncertainty is the estimation of tree biomass using mathematical relationships between biomass and easily obtained and non‐destructive measurements (allometry). We evaluated the robustness of the allometric relationships established at the beginning of a FACE experiment and discuss the challenges and opportunities for the new generation of FACE experiments. Summary Long‐term field experiments to elucidate forest responses to rising atmospheric CO 2 concentration require allometric equations to estimate tree biomass from non‐destructive measurements of tree size. We analyzed whether the allometric equations established at the beginning of a free‐air CO 2 enrichment (FACE) experiment in a Liquidambar styraciflua plantation were still valid at the end of the 12 year experiment. Aboveground woody biomass was initially predicted by an equation that included bole diameter, taper, and height, assuming that including taper and height as predictors would accommodate changes in tree structure that might occur over time and in response to elevated CO 2 . At the conclusion of the FACE experiment, we harvested 23 trees, measured dimensions and dry mass of boles and branches, and extracted and measured the woody root mass of 10 trees. Although 10 of the harvested trees were larger than the trees used to establish the allometric relationship, measured aboveground woody biomass was well predicted by the original allometry. The initial linear equation between bole basal area and woody root biomass underestimated final root biomass by 28%, but root biomass was just 21% of total wood mass, and errors in aboveground and belowground estimates were offsetting. The allometry established at the beginning of the experiment provided valid predictions of tree biomass throughout the experiment. New allometric approaches using terrestrial laser scanning should reduce an important source of uncertainty in decade‐long forest experiments and in assessments of centuries‐long forest biomass accretion used in evaluating carbon offsets and climate mitigation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Extracting dependencies between network assets using deep learning

A network analysis tool receives network flow information and uses deep learning—machine learning that models high-level abstractions in the network flow information—to identify dependencies between network assets. Based on the identified dependencies, the network analysis tool can discover functional relationships between network assets. For example, a network analysis tool receives network flow information, identifies dependencies between multiple network assets based on evaluation of the network flow information, and outputs results of the identification of the dependencies. When evaluating the network flow information, the network analysis tool can pre-process the network flow information to produce input vectors, use deep learning to extract patterns in the input vectors, and then determine dependencies based on the extracted patterns. The network analysis tool can repeat this process so as to update an assessment of the dependencies between network assets on a near real-time basis.

Carroll, Thomas E.↗

DOE OSTI2021

Unexpected inverse correlations and cooperativity in ion-pair phase transfer

Liquid/liquid extraction is one of the most widely used separation and purification methods, where a forefront of research is the study of transport mechanisms for solute partitioning and the relationships that these have to solution structure at the phase boundary. To date, organized surface features that include protrusions, water-fingers, and molecular hinges have been reported. Many of these equilibrium studies have focused upon small-molecule transport – yet the extent to which the complexity of the solute, and the competition between different solutes, influence transport mechanisms have not been explored. Here we report molecular dynamics simulations that demonstrate that a metal salt (LiNO 3 ) can be transported via a protrusion mechanism that is remarkably similar to that reported for H 2 O by tri-butyl phosphate (TBP), a process that involves dimeric assemblies. Yet the LiNO 3 out-competes H 2 O for a bridging position between the extracting TBP dimer, which in-turn changes the preferred transport pathway of H 2 O. Examining the electrolyte concentration dependence on ion-pair transport unexpectedly reveals an inverse correlation with the extracting surfactant concentration. As [LiNO 3 ] increases, surface adsorbed TBP becomes a limiting reactant in correlation with an increased negative surface charge induced by excess interfacial NO 3 – , however the rate of transport is enhanced. Within the highly dynamic interfacial environment, we hypothesize that this unique cooperative effect may be due to perturbed surface organization that either decreases the energy of formation of transporting protrusion motifs or makes it easier for these self-assembled species to disengage from the surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Real-World Driving Features for Identifying Intelligent Driver Model Parameters

Driver behavior models play a significant role in representing different driving styles and the associated relationships with traffic patterns and vehicle energy consumption in simulation studies. The models often serve as a proxy for baseline human driving when assessing energy-saving strategies that alter vehicle velocity. Such models are especially important in connectivity-enabled energy-saving strategy research because they can easily adapt to changing driving conditions like posted speed limits or change in traffic light state. While numerous driver models exist, parametric driver models provide the flexibility required to represent variability in real-world driving through different combinations of model parameters. These model parameters must be informed by a representative set of parameter values for the driver model to adequately represent a real-world driver. It stands to reason that determining the parameter values from real-world driving data would serve the purpose of representing a real-world driver. Although the published literature is replete with techniques and consequences of using real-world driving data to determine parameter values for parametric driver models, none have explored them in the context of using shorter driving features where the parameter values may change over the course of a single trip for the same driver. In this study we consider the “intelligent driver model” (IDM) as our driver behavior model and use real-world driving data from the Transportation Secure Data Center (TSDC) maintained at the National Renewable Energy Laboratory (NREL). The TSDC includes real-world travel data from across the United States, from which NREL has created a wide range of driving routes consisting of road features such as speed limits, stop locations, and turn locations. The real-world driving data are categorized into different driving regimes and extracted into driving features. The driving features are then used to calibrate the parameter values for the IDM. The distribution of the parameters and the relationships among them are reported. The insights obtained from this study enable judicious usage of IDM or similar parametric driver models to represent baseline human driver behavior in simulations.

27 ARPA - Advanced Research Projects Agency-Energy↗

DOE OSTI2021

Real-World Driving Features for Identifying Intelligent Driver Model Parameters: Preprint

Driver behavior models play a significant role in representing different driving styles and the associated relationships with traffic patterns and vehicle energy consumption in simulation studies. The models often serve as a proxy for baseline human driving when assessing energy-saving strategies that alter vehicle velocity. Such models are especially important in connectivity-enabled energy-saving strategy research because they can easily adapt to changing driving conditions like posted speed limits or change in traffic light state. While numerous driver models exist, parametric driver models provide the flexibility required to represent variability in real-world driving through different combinations of model parameters. These model parameters must be informed by a representative set of parameter values for the driver model to adequately represent a real-world driver. It stands to reason that determining the parameter values from real-world driving data would serve the purpose of representing a real-world driver. While the published literature is replete with techniques and consequences of using real-world driving data to determine parameter values for parametric driver models, none have explored them in the context of using shorter driving features where the parameter values may change over the course of a single trip for the same driver. In this study we consider the “Intelligent Driver Model” (IDM) as the driver behavior model to explore and real-world driving data from the Transportation Secure Data Center (TSDC) maintained at the National Renewable Energy Laboratory (NREL). The TSDC includes real-world travel data from across the United States, from which NREL has created a wide range of driving routes consisting of road features such as speed limits, stop locations and turn locations. The real-world driving data are categorized into different driving regimes and extracted into driving features. The driving features are then used to calibrate the parameter values for the IDM. The distribution of the parameters and the relationships among them are reported. The insights obtained from this study enable judicious usage of IDM or similar parametric driver models to represent baseline human driver behavior in simulations.

27 ARPA - Advanced Research Projects Agency-Energy↗