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At least 379 records · Page 21

From Qualitative to Quantitative AOP: A Case Study of Neurodegeneration

Adverse outcome pathways (AOPs) include a sequence of events that connect a molecular-level initiating event with an adverse outcome at the cellular level for human health endpoints, or at the population level for ecological endpoints. When there is enough quantitative understanding of the relationships between key events in an AOP, a mathematical model may be developed to connect key events in a quantitative AOP (qAOP). Ideally, a qAOP will reduce the time and resources spent for chemical toxicity testing and risk assessment and enable the extrapolation of data collected at the molecular-level by in vitro assays, for example, to predict whether an adverse outcome may occur. Here, we review AOPs in the AOPWiki, an AOP repository, to determine best practices that would facilitate conversion from AOP to qAOP. Then, focusing on a particular case study, acetylcholinesterase inhibition leading to neurodegeneration, we describe specific methods and challenges. Examples of challenges include the availability and collection of quantitative data amenable to model development, the lack of studies that measure multiple key events, and model accessibility or transferability across platforms. We conclude with recommendations for improving key event and key event relationship descriptions in the AOPWiki that facilitate the transition of qualitative AOPs to qAOPs.

Sinitsyn, Dennis↗

Stiff neural ordinary differential equations

Neural Ordinary Differential Equations (ODEs) are a promising approach to learn dynamical models from time-series data in science and engineering applications. This work aims at learning neural ODEs for stiff systems, which are usually raised from chemical kinetic modeling in chemical and biological systems. We first show the challenges of learning neural ODEs in the classical stiff ODE systems of Robertson’s problem and propose techniques to mitigate the challenges associated with scale separations in stiff systems. We then present successful demonstrations in stiff systems of Robertson’s problem and an air pollution problem. The demonstrations show that the usage of deep networks with rectified activations, proper scaling of the network outputs as well as loss functions, and stabilized gradient calculations are the key techniques enabling the learning of stiff neural ODEs. The success of learning stiff neural ODEs opens up possibilities of using neural ODEs in applications with widely varying time-scales, such as chemical dynamics in energy conversion, environmental engineering, and life sciences.

97 MATHEMATICS AND COMPUTING↗

A data-driven method to estimate the antiproton background in the Mu2e experiment

The Mu2e experiment at Fermilab will search for the Charged Lepton Flavour Violating (CLFV) process of coherent, neutrinoless µ− → e − conversion in the field of an aluminum nucleus. The expected signal is a monochromatic electron with the energy of 104.97 MeV, slightly below the muon rest mass. Observation of a CLFV process would provide unambiguous evidence for Beyond the Standard Model (BSM) physics. Mu2e is sensitive to a wide range of BSM models and has the capability to distinguish between them, guiding us towards the most accurate models. The key features of the Mu2e experiment are: (1) a high intensity pulsed negative muon beam with about 1010 stopped µ −/s, and (2) a sophisticated superconducting solenoid system with a gradient magnetic field to form and guide the intense muon beam to the target. The Mu2e physics data taking is expected to begin in 2027. For Run I, the expected 5σ discovery sensitivity is Rµe = 1.2 × 10−15, with a total expected background of 0.11 ± 0.03 events. In the absence of a signal, the expected upper limit is Rµe < 6.2 × 10−16 at 90% CL. The success of this experiment hinges on the accurate estimation of the background from various SM processes that could provide signal-like electrons. One of the background processes is antiprotons annihilating in the stopping target to produce signal like electrons through π0 → γγ decays followed by γ conversions, and π− → µ−ν¯ decays followed by µ− decay. It is a relatively small background with large uncertainty (100%) due to the lack of antiproton production cross section information for the Mu2e proton beam energy of 8 GeV. We have developed a novel methodology to estimate the antiproton background in-situ. This forms the main theme of the thesis. We observed that at Mu2e energies, antiproton annihilation in the stopping target is the only source of events with multiple, simultaneous particle trajectories. From Geant4 simulations, only about 0.2% of the simulated antiproton annihilation events have a signal-like electron. Meanwhile, ∼ 5% of events have multiple reconstructible particle tracks per event. Therefore, we have devised a methodology to reconstruct the multi-track events and estimate the antiproton background by exploiting the large ratio of the production rates of the two final states.

Chithirasreemadam, Namitha [Pisa U.] (ORCID:000000↗

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications

Here, we present an update and revision to our 2010 review on the topic of proton- coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XHn in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H 2 ), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H 2 ) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comment on Improved CO 2 Hydrogenation on Ni–ZnO/MCM-41 Catalysts with Cooperative Ni and ZnO Sites

A recent publication from Murthy et al.1 describes experiments in which they proposed the hypothesis that a bifunctional catalyst consisting of adlineated,2 nanometer-sized domains of Ni and ZnO, confined within the pores of MCM-41, hydrogenates carbon dioxide adsorbed on the ZnO using hydrogen atoms produced by the Ni-catalyzed dissociation of H2. The reanalysis of their data presented below suggests that the reaction rates they employed to test their hypothesis, when properly normalized, show little to no effect of bifunctionality. This closer inspection of their data raises the possibility that the observed effects may instead arise from experimental artifacts (e.g., different levels of conversion, finite rates of mass transport) or morphological correlations that were not considered by the authors.

36 MATERIALS SCIENCE↗

Perovskite- and Dye-Sensitized Solar-Cell Device Databases Auto-generated Using ChemDataExtractor

The number of scientific publications reporting cutting-edge third-generation photovoltaic devices is increasing rapidly, owing to the pressing need to develop renewable-energy technologies that address the climate-change crisis. Consequently, the field could benefit from a central repository where photovoltaic-performance metrics, such as the power-conversion efficiency (η) are recorded. We present two automatically generated databases that contain photovoltaic properties and device material data for dye-sensitized solar cells (DSCs) and perovskite solar cells (PSCs), totalling 660,881 data entries representing 57,678 photovoltaic devices. The databases were generated by applying the text-mining toolkit ChemDataExtractor on a corpus of 25,720 articles. A multi-faceted evaluation, incorporating manual and automatic methods, was applied to ensure that the data contained therein were of the highest quality, with precision metrics ranging from 73.1% to 95.8%. The DSC database contains 475,045 entries representing 41,680 devices, and the PSC database contains 185,836 entries representing 15,818 devices. The databases are available in MongoDB and JSON formats, which can be queried in Python, R, Java and MATLAB for data-driven photovoltaic materials discovery.

14 SOLAR ENERGY↗

Collaborative Research: Explosive reconnection in relativistic magnetically-dominated plasmas (Final Report)

Magnetic fields can be the dominant component of astrophysical plasmas, so that the magnetic energy density might exceed even the rest-mass energy density of matter. In this extreme (and largely unexplored) regime the magnetic field controls the overall plasma evolution, dissipation, and acceleration of non-thermal particles. This plasma regime, applicable to a variety of astrophysical sources - magnetars, pulsars and pulsar wind nebulae (PWNe), jets of Active Galactic Nuclei (AGNs) and Gamma-Ray Bursters (GRBs) - is dramatically different from laboratory plasmas, the magnetospheres of planets, and the interplanetary plasma. Relativistic astrophysical sources then provide an unique opportunity to study the fundamental plasma physics of magnetically-dominated plasmas; a novel and fast-evolving field of theoretical research which, by investigating energy conversion and particle energization processes in plasmas, is of vital importance to the Fusion Energy Sciences DoE program. Data coming from astrophysical high-energy missions, especially the Crab Nebula flares recently observed by the Fermi and AGILE satellites, suggest that the acceleration of non-thermal particles to the highest energies occurs in magnetic reconnection events - a major change of paradigm in high-energy astrophysics. Most importantly, observations demand that particle acceleration should proceed extremely fast (with accelerating electric field of the order of the magnetic field) and on macroscopic scales (much larger, e.g., than the microscopic plasma skin depth). We are conducting studies of the microphysics of magnetically-dominated plasmas focussing in particular on the highly dynamic regime of explosive reconnection and associated particle acceleration in relativistic plasmas. We are studying the stability and explosive plasma dynamics, particle acceleration and radiation production in a number of idealized plasma configurations that approximate relevant astrophysical sources (like the magnetic ABC structures and interacting flux tubes, as well as generalizations of analytical models of X-point collapse to relativistic plasmas). The well-studied case of the Crab Nebula is taken as a prototypical example for the application of the model. We are combining analytical studies of explosive magnetic dynamics and dissipation in relativistic plasmas with particle-in-cell (PIC) simulations and fluid simulations. The theoretical model, fluid and particle-in-cell simulations are cross-checked for agreement and convergence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Conversion of METL Diagnostic Flowmeters to Permanent Magnet Based Electromagnetic Flowmeters

The Mechanisms Engineering Test Loop (METL) uses three flowmeters to monitor sodium circulation through the main loop, the Cold Trap leg, and the Plugging Meter leg. When constructed, the Cold Trap flowmeter (CTFM) and Plugging Meter flowmeter (PMFM) were equipped with permanent magnets and Hall Sensors. By October of 2019, during normal operations, both the CTFM and PMFM failed, producing either erroneous or zero signals. Repairs to the flowmeters were attempted in January of 2020 but failed to resolve the issues. Therefore, starting in March of 2021, a plan was developed to convert the installed flowmeters to more robust permanent magnet based electromagnetic flowmeters (EMFMs). The Cold Trap EMFM (CT EMFM) and Plugging Meter EMFM (PM EMFM) were fully installed by August of 2021. Initial testing and commissioning were completed in November of 2021. Finally, the first calibration runs were finished in March of 2022. This report discusses the design, conversion, and calibration of the as-built CTFM and PMFM to robust permanent magnet based EMFMs. During the design phase, theoretical models were used to estimate the signal output and required magnet sizes. Then, the CTFM and PMFM were disassembled and converted to EMFMs. After commissioning, the CT EMFM and PM EMFM were calibrated using a ‘Time Transfer Procedure’ carried out with METL Expansion Vessels and Test Vessel Two. The accuracy of the calibration was estimated through an uncertainty analysis. Finally, the report describes some lessons learned for future flowmeter conversions and follow-up work. In total, both METL EMFM’s met the desired performance targets. Testing data showed that the METL EMFMs provide a output signal of roughly 2 mV at 1 GPM and 250 °C. During calibration, flowrates between 0.7 GPM and 2.4 GPM were achieved. In this flow range, calibration coefficients of 0.485 and 0.935 were measured as with errors ranging from 15-5% and 16-5% for the CT EMFM and PM EMFM, respectively. Above 1.5 GPM, the error was assumed to be about 5% for both METL EMFMs. Several points will be considered for future follow-up work on the METL EMFM’s. First, the signal noise issues in the PM EMFM will be addressed. It is likely the source of the noise is due to some stray EMF from a heater. Secondly, the NdFeB magnets will be replaced with a grade that has a Curie temperature above 80 °C. For example, a few grades of NeFeB magnets have Curie temperatures which exceed 150 °C and some SmCo magnets have Curie temperatures as high as 500 °C. Third, more calibration runs will be completed in the range of 0.5-2.5 GPM. This will further improve the accuracy of the calibration coefficient. Fourth, calibration runs will be completed up to 5 GPM. This requires a larger pressure relief valve to be installed on the Expansion Vessel and Test Vessel 2, as well as a revised calibration procedure. Lastly, calibration runs will be completed to account for cold spots in the system, which reduced the inlet temperature of the METL EMFMs. Overall, these points will improve the calibration coefficients derived in this work and also improve the performance of the METL EMFMs.

42 ENGINEERING↗

Developing a Prototype Methodology to Rank CO2-EOR Wells and Assess Their Reuse Potential for Geologic Carbon Sequestration

This study presents a prototype methodology for evaluating the reuse potential of Class II CO₂-enhanced oil recovery (CO₂-EOR) wells as Class VI wells for geologic carbon sequestration. The approach focuses on assessing wellbore construction materials—casing, cement, tubing, and packers—based on U.S. Environmental Protection Agency (EPA) Class VI well conversion guidelines. Utilizing Python scripts and JSON representations, the methodology automates checks on digitized Texas Railroad Commission (TRRC) data to rank wells based on regulatory and integrity criteria. Key factors include casing integrity, cementing techniques, tubing compatibility, and packer selection. Due to limitations in digitized data, manual verification is required for certain sections. Future enhancements include incorporating non-digitized data via web scraping and machine learning. This research provides a practical framework for well owners and regulators, supporting informed decision-making for sustainable CO₂ storage.

carbon sequestration↗

A Data-Driven Framework for Predicting the Sorting and Screening Performance of an Integrated Biomass Feedstock Preprocessing System

The characteristics of mechanically sorted and screened lignocellulosic biomass, such as the mass contents of corn stover anatomical fractions (leaves, husks, stalks, cobs, etc.), can be used to calculate the intermediate feedstock quality attributes “yield” and “purity” that indicate the conversion efficiency of biocrude. No prior study has investigated the correlations from the characteristics of raw biomass and preprocessing unit operation parameters to those intermediate feedstock quality attributes. This work presents a data-driven framework for assessing and predicting the intermediate feedstock quality attributes in an integrated biomass feedstock preprocessing system. Our study used corn stover as a typical type of herbaceous biomass because of its abundance in the U.S. It began with data acquisition of moisture content, particle size distribution, and anatomical fractions of the materials after each unit operation in the system. The objective of this preprocessing system is to minimize husks and leaves and maximizing cobs and stalks by mechanically separating the materials into three streams via disc screen and air separator. Prototype neural network models were then developed to evaluate the feasibility of predicting process outcomes based on measurable parameters. It is found that incorporating physical constraints into these prediction models significantly enhances the accuracy of the predicted yield and purity against the ground truth data. The experimental data and model predictions indicate that decreasing throughput increases purity, while higher throughput results in lower purity. Finally, an optimization problem was introduced to search optimal combinations of feed material properties and preprocessing unit operation parameters, as the intermediate feedstock quality attributes – yield and purity, appeared to be competing factors. The study also suggests the continual need to improve the data-driven framework’s predictability by incorporating more accurate physical models to describe the dynamics in the preprocessing units such as the air separator.

09 - BIOMASS FUELS↗

Deep learning of electrochemical CO 2 conversion literature reveals research trends and directions

Large-scale and openly available material science databases are mainly composed of computer simulation results rather than experimental data. Some examples include the Materials Project, Open Quantum Materials Database, and Open Catalyst 2022. Unfortunately, building large-scale experimental databases remains challenging due to the difficulties in consolidating locally distributed datasets. In this work, focusing on the catalysis literature of CO 2 reduction reactions (CO 2 RRs), we present a machine learning (ML)-based protocol for selecting highly relevant papers and extracting important experimental data. First, we report a document embedding method (Doc2Vec) for collecting papers of greatest relevance to the specific target domain, which yielded 3154 CO 2 RR-related papers from six publishers. Next, we developed named entity recognition (NER) models to extract twelve entities related to material names (catalyst, electrolyte, etc.) and catalytic performance (Faradaic efficiency, current density, etc.). Further, among several tested models, the MatBERT-based approach achieved the highest accuracy, with an average F1-score of 90.4% and an F1-score of 95.2% in a boundary relaxation evaluation scheme. The accurate and accelerated NER-based data extraction from a large volume of catalysis literature enables temporal trend analyses of the CO 2 RR catalysts, products, and performances, revealing the potentially effective material space in CO 2 RRs. While this work demonstrates the effectiveness of our ML-based text mining methods for specifically CO 2 RR literature, the methods and approach are applicable to and may be used to accelerate the development of other catalytic chemical reactions.

36 MATERIALS SCIENCE↗

Data from Response Surface Methodology Guided Adsorption and Recovery of Free Fatty Acids from Oil Using Resin

The presence of free fatty acids interferes with the conversion of plant oils to biodiesel. Four strong and weak base resins were evaluated for the removal of free fatty acids (FFA) from oil. Amberlite FPA 51 showed the highest adsorption capacity of FFA. A resin concentration above 3% could enable a higher percentage FFA adsorption. The adsorption process fitted a pseudo-first-order kinetic model and achieved equilibrium in approximately 8 h. A full factorial design was used to optimize the resin and FFA concentrations at a fixed temperature (40° C). A ratio of resin to fatty acid concentrations above 1.875 was sufficient for 70% adsorption and the amount adsorbed continued to increase with further added resin. A two-step washing of resin using hexane and ethanol recovered approximately 67.55% ± 4.05% of the initially added fatty acid. The resin that was used was regenerated with 5% NaOH and re-used for a minimum of three consecutive cycles. However, the adsorption capacity diminished to 75% of the initial cycle in cycles 2 and 3. Thus, the work presents a resin-based process for deacidification of oil to reduce fatty acid content of oil for biodiesel production.

Conversion↗

Synthesis of motif and symmetry for accelerated learning, discovery, and design of electronic structures for energy conversion applications (Final Technical Report)

The overall goal of the projects is to develop a framework to incorporate structure motifs and crystal/orbital symmetries into the data-driven materials discovery infrastructure. The PI proposed to develop structure-motif- and symmetry-based graph convolutional networks for effective learning and efficient predictions of electronic structures and related properties. Fundamental understanding of the roles of structure motif and symmetry will establish new hypothesis and design rules, which will be combined with high-throughput computations based on density functional theory to discover novel light absorbers, transparent conductors, as well as 2D light emitting materials and heterojunctions for optoelectronics.

36 MATERIALS SCIENCE↗

UBW (USLCI-Brightway2) [SWR-25-169]

Life cycle inventory (LCI) data are critical for robust life cycle assessment (LCA), yet many widely used datasets such as the U.S. Life Cycle Inventory (USLCI) are not natively compatible with advanced modeling frameworks like Brightway2. This work presents an automated pipeline to transform USLCI data into a fully functional Brightway2 project. The workflow performs systematic data cleaning, resolves duplicate process and exchange identifiers, and applies allocation to multi-output processes. Technosphere and biosphere flows are harmonized through unit conversions and a bridge mapping to the biosphere3 database, with comprehensive logging of missing flows and cutoff issues. The resulting Brightway2 database is validated using matrix diagnostics to ensure consistency of the technosphere, and is benchmarked via life cycle impact assessment (LCIA) methods such as ReCiPe and IPCC GWP. Outputs include reproducible CSV exports of corrected processes, elementary flows, characterization factors, and LCIA results, alongside backup utilities for project sharing. This pipeline lowers barriers for integrating USLCI data into open-source LCA workflows, enabling reproducible, validated LCA inventories within the Brightway 2 framework.

Ghosh, Tapajyoti [National Laboratory of the Rocki↗

Kinetics Modeling and Reactor Design Study of Glucose-to-Terpenes Cell-Free Conversion

Cell-free systems offer many advantages over traditional biological conversion by eliminating biological growth constraints. It also offers easy manipulation and finetuning of the reaction conditions for each individual enzyme. The conversion of cellulosic glucose to Limonene, a terpene, is a promising pathway for producing fuels and chemicals. Recent advances in developing cell-free systems focuses on bench scale optimization of terpene yield and to demonstrate its feasibility towards commercialization [1,2]. There is significant knowledge gap regarding reaction kinetics of these cell-free systems to further study how it will perform at larger scale. We present here, our studies on reaction kinetics and reactor design implications of cell-free glucose to Limonene conversion to facilitate the further development and commercialization of this process. We developed a novel kinetic model based on the metabolic-network structure of the cell-free system with multi-substrate reversible Michaelis-Menten rate law. To estimate kinetic parameters for this system of rate equations, we employed Bayesian optimization to perform global search with the assistance of gaussian processes to balance exploration and exploitation. The model parameters estimated showed good results compared with experimental data. The estimated parameters were used to perform sensitivity analysis. We found that Hexokinase is one of the most critical enzymes that affect the conversion of the glucose. We also observed that abundance of co-factors is also critical to the conversion of glucose to limonene. We investigated packed bed reactors with enzymes immobilized on the surface of particles to convert glucose stream into Limonene for larger scale production. The reactor design such as particle size, enzyme loading, and flow rate are found to be critical for improving yields. [1] Dudley, Q.M., Nash, C.J. and Jewett, M.C., 2019. Synthetic Biology, 4(1), p.ysz003. [2] Korman, T.P., Opgenorth, P.H. and Bowie, J.U., 2017. Nature communications, 8(1), p.15526.

09 BIOMASS FUELS↗

Combustion machine learning: Principles, progress and prospects

Progress in combustion science and engineering has led to the generation of large amounts of data from large-scale simulations, high-resolution experiments, and sensors. This corpus of data offers enormous opportunities for extracting new knowledge and insights—if harnessed effectively. Machine learning (ML) techniques have demonstrated remarkable success in data analytics, thus offering a new paradigm for data-intense analyses and scientific investigations through combustion machine learning (CombML). While data-driven methods are utilized in various combustion areas, recent advances in algorithmic developments, the accessibility of open-source software libraries, the availability of computational resources, and the abundance of data have together rendered ML techniques ubiquitous in scientific analysis and engineering. This article examines ML techniques for applications in combustion science and engineering. Starting with a review of sources of data, data-driven techniques, and concepts, we examine supervised, unsupervised, and semi-supervised ML methods. Various combustion examples are considered to illustrate and to evaluate these methods. Next, we review past and recent applications of ML approaches to problems in combustion, spanning fundamental combustion investigations, propulsion and energy-conversion systems, and fire and explosion hazards. Challenges unique to CombML are discussed and further opportunities are identified, focusing on interpretability, uncertainty quantification, robustness, consistency, creation and curation of benchmark data, and the augmentation of ML methods with prior combustion-domain knowledge.

33 ADVANCED PROPULSION SYSTEMS↗

Event-to-Video Conversion for Overhead Object Detection

Collecting overhead imagery using an event camera is desirable due to the energy efficiency of the image sensor compared to standard cameras. However, event cameras complicate downstream image processing, especially for complex tasks such as object detection. In this paper, we investigate the viability of event streams for overhead object detection. We demonstrate that across a number of standard modeling approaches, there is a significant gap in performance between dense event representations and corresponding RGB frames. We establish that this gap is, in part, due to a lack of overlap between the event representations and the pre-training data that the object detectors were initially trained on through a number of experiments. Then, apply an off-the-shelf event-to-video conversion tool that converts event streams into gray-scale video to close this gap. We demonstrate that this approach results in a large performance increase, outperforming even event-specific object detection techniques on our overhead target task. These results suggest that better aligning event representations with existing large pre-trained models may result in greater short-term performance gains compared to end-to-end event-specific architectural improvements.

machine learning (ML), computer vision, Neuromorph↗