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At least 1,621 records · Page 90

Deep Learning-based Parameterization of Complex 3D CO2 Saturation Data in Large-scale Geological Carbon Storage

In deep learning (DL), dimension reduction plays a pivotal role in improving training efficiency and minimizing overfitting, especially when working with complex datasets like three-dimensional (3D) saturation data. In the context of geological carbon storage (GCS), 3D saturation data introduces unique challenges due to its sparse nature and sharp transitions at plume boundaries, known as shock fronts. To tackle these challenges, we developed a novel DL framework that combines dimension reduction with advanced 3D reconstruction techniques. Our approach utilizes latent variables derived from 2D average saturation fields to efficiently capture the essential features of high-dimensional data while reducing the number of variables. This enhances both the robustness and accuracy of DL models, making the framework more practical for real-world applications. By offering a tailored solution for modeling complex 3D saturation dynamics, this framework holds significant potential for environmental monitoring, energy storage, and other geological applications.

Wang, Hongsheng [University of Texas at Austin]↗

Multiscale Nuclear-Electronic Orbital Quantum Dynamics in Complex Environments

Many renewable energy conversion processes rely on the movement of protons as well as electrons through either electrocatalysis or photoexcitation. The simulation of such processes requires a quantum mechanical description of coupled nuclear-electronic dynamics in a solvent or heterogeneous chemical environment. The overall objective of this project is the development of theoretical and computational capabilities for simulating nuclear-electronic quantum dynamics in complex environments and the creation of high-performance, open-source software. This multiscale framework will enable simulations of the real-time dynamics of nonequilibrium excited state proton-coupled electron transfer, quantum decoherence, vibronic energy transfer, and ultrafast radiolysis, as well as their associated time-resolved multidimensional spectroscopies. An important outcome of this project will be a sustainable, reusable, and interoperable open-source software ecosystem. This software will be designed for emerging exascale and future national leadership computers. Another key outcome will be a multiscale quantum dynamics method and software enabling simulations of nonequilibrium nuclear-electronic quantum dynamics in complex environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Low‐dimensional manifold learning for uncertainty quantification in complex multi‐scale stochastic systems

Broadly speaking, the goals of the project are to develop techniques to use manifold learning to develop reduced‐order and surrogate models for "hyper‐reduction" of very high‐dimensional complex multi‐scale systems. This is being achieved by employing a newly proposed form of manifold projection and learning that leverages recent advancements in computational geometry and data‐driven modeling. In particular, we are applying a manifold projection technique to project the solutions of very high‐dimensional systems onto the so‐called Grassmannmanifold, a Reimannian manifold comprised of orthonormal matrices. We then apply data‐driven machine learning techniques to classify the solutions on the manifold (e.g. clustering techniques) according to their proximity on the manifold and leverage a further nonlinear dimension reduction to organize the structured data on the manifold. Finally, we are developing novel techniques that enable us to directly interpolate the hyper‐reduced data such that we can predict the solution of the complex, high‐ dimensional system without need to call the full expensive computational model. Given their adherence to the underlying structure of the solution of the physical system, it is expected that these approximate solutions will be sufficiently constrained so as to (approximately) adhere to physical principles.

97 MATHEMATICS AND COMPUTING↗

Mini-cell: Compact all optical gas monitoring sensor for persistent surveillance of complex system

Persistent surveillance of complex systems by embedded sensing is the new paradigm of aging awareness and monitoring. In any complex system with a long-term lifespan plan, the persistent surveillance of critical parameters warrants the reliability and safety/security of the system by the continuous monitoring of the state of health and aging conditions. Therefore, embedded sensors of physical, chemical, and structural features/traits are critical for uncovering occurrences of undesired/unexpected events. Gas sensing can provide early detection of a broad range of problems such as decomposing components, corrosion, failures, and leaks. For the application of interest, the sensors must be: 1/highly selective and sensitive for a broad range of gas molecules, 2/compact, 3/minimally invasive, 4/rugged for vibration and thermal excursions, and 5/ environmentally inert.

47 OTHER INSTRUMENTATION↗

Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems (Final Report for AEOLUS)

The AEOLUS Center is dedicated to developing a unified optimization-under-uncertainty framework for: (1) learning predictive models from data; and (2) optimizing experiments, processes, and designs governed by these models, all driven by complex, uncertain energy systems. AEOLUS addresses the critical need for principled, rigorous, scalable, and structure-exploiting capabilities for exploring parameter and decision spaces of complex forward simulation models. This report summarizes the key highlights of our research during the period of performance.

97 MATHEMATICS AND COMPUTING↗

Uinta Basin CarbonSAFE II: Storage Complex Feasibility (Final Report)

The primary objective of this CarbonSAFE Phase II project was to establish the technical and commercial feasibility of a commercial-scale CO 2 geological storage complex for Deseret Power Electric Cooperative Bonanza Power Plant and other CO 2 sources in the northeast Uinta Basin, Utah, with the goal to securely store at least 50 million metric tons of captured CO 2 and accelerate CO 2 capture, utilization, and storage (CCUS) deployment. The project team established high-potential technical and commercial feasibility for a storage site within the east Uinta Basin (Utah), in the Cretaceous sandstones (Frontier, Dakota, and Buckhorn), Entrada Sandstone, Nugget Sandstone, and/or Weber Sandstone southwest of the Bonanza coal-fired power plant. This project collected and analyzed state-of-the-art data to characterize the storage complex consistent with Environmental Protection Agency (EPA) permitting standards. The team conducted extensive analog studies, outcrop mapping, and data sampling, which largely contributed to understanding the subsurface lithology and facies. Existing data were obtained and assessed from Utah Division of Oil, Gas, and Mining (DOGM), Utah Geological Survey (UGS), Colorado Geological Survey (CGS), U.S. Geological Survey (USGS), and EPA. These data were analyzed using state-of-the-art CCUS technologies for Societal Considerations, Site Characterization, Modeling and Simulations, Risk Assessment, Management and Monitoring, potential Underground Injection Control (UIC) Class VI Well Permitting, and Technical/Economic Feasibility. Through these high-resolution data collection and feasibility studies, this project was expected to provide a reference for initiating Underground Injection Control (UIC) and other commercial-scale geological storage permitting processes in the Western United States, ultimately contributing to the nation's decarbonization goals through low-risk, cost-effective commercial-scale carbon capture, utilization, and storage (CCUS) projects.

42 ENGINEERING↗

AI-Ready Control System for the Fermilab Accelerator Complex

Reliable, high-intensity operation of the Fermilab Accelerator Complex is critical to the success of the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment. We describe the requirements and infrastructure necessary to support routine use of artificial intelligence and machine learning (AI/ML) in the accelerator control system. Three capabilities are identified: a machine learning operations (MLOps) framework standardizing the lifecycle of AI/ML automation from data management through deployment and monitoring; a data quality framework defining and enforcing standards required to build trustworthy AI/ML applications; and workflow integration with large language models to assist physicists, engineers, and operators with information retrieval, code development, and routine analysis. Use cases spanning beam diagnostics, beam control, and support system automation illustrate the technical requirements across the complex.

43 PARTICLE ACCELERATORS↗

Final Technical Report: Transport of Complex Mixtures in Ion-Containing Polymer Membranes

Permselective ion-containing membranes are an integral component for many applications from water treatment, fuel cells, and solar fuels devices where the selective transport of molecules and ions is desired. In solar fuels devices, ion-containing polymer membranes are responsible for permitting selective transport of ions between electrodes to maintain overall charge neutrality yet limit transport of reaction products produced at the electrodes. While the transport of single solutes through such membranes has been fairly well described, binary and multicomponent transport is poorly understood due to the myriad of interactions that occur in these systems (i.e. between co-permeants and between permeants and the membrane). Solar fuels devices are just one example of an application where understanding the transport of multiple simultaneous species is critically important to improving device performance as product crossover leads to reductions in overall device performance. The objectives of this research was to improve our understanding of the complex array of factors that influence transport behavior of multiple solutes within ion-containing polymer membranes. This experimental project addressed the lack of fundamental understanding of multicomponent transport behavior by synthesizing ion exchange membranes with varied incorporation of comonomers (ionic and neutral moieties) to investigate fundamental relationships between membrane structure, membrane physiochemical properties, and transport behavior of solutes and complex solute mixtures through dense, hydrated membranes.

25 ENERGY STORAGE↗

Energy Transfer in Lanthanide Luminescent Complexes

The primary objective of this project was to investigate the mechanisms of energy transfer in lanthanide luminescent complexes, focusing on elucidating the role of ligand-to-metal charge transfer processes and the efficiency of sensitization mechanisms. Specifically, this work aimed to determine the mechanistic details of energy transfer pathways in systems incorporating lanthanide ions such as terbium and europium, with a focus on advancing the application of these complexes in molecular imaging and photonic technologies.

Raymond, Kenneth [University of California, Berkel↗

SAND - System for on-Axis Neutrino Detection - in the DUNE Near Detector Complex

The DUNE experiment aims to precisely measure the long baseline neutrino oscillation parameters. The DUNE Far Detector consists of four liquid argon time-projection chambers (total LAr mass of 17 kton for each cryostat), that will be installed at the Sanford Underground Research Facility (SURF) in South Dakota, 1300 km from the proton beam target. The Near Detector complex, located at Fermilab, is fundamental for limiting the systematic uncertainties, due to the neutrino/antineutrino flux and to the cross-section. It comprises three complementary detectors: ND-Lar, ND-Gar and SAND (System for on-Axis Neutrino Detection). ND-Lar and ND-Gar can move off-axis, while SAND is the only detector permanently on-axis, whose primary goal is to monitor the beam and to measure the flux. In this talk, the SAND design and the expected performances will be described together with its role within the Near Detector complex for the DUNE physics program.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

Soil moisture and porosity regulate microbial metabolism by influencing factors such as redox conditions, substrate availability, and soil connectivity. However, the inherent biological, chemical, and physical heterogeneity of soil complicates laboratory investigations into microbial phenotypes that mediate community metabolism. This difficulty arises from challenges in accurately representing the soil environment and in establishing a tractable microbial community that limits confounding variables. To address these challenges in our investigation of community metabolism, we use a reduced-complexity microbial consortium grown in a soil analog using a glass-bead matrix amended with chitin. Long-read and short-read metagenomes, metatranscriptomes, metaproteomes, and metabolomes were analyzed to test the effects of soil structure and moisture on chitin degradation. Our soil structure analog system greatly altered microbial expression profiles compared to the liquid-only incubations, emphasizing the importance of incorporating environmental parameters, like pores and surfaces, for understanding microbial phenotypes relevant to soil ecosystems. These changes were mainly driven by differences in overall expression of chitin-degrading Streptomyces species and stress-tolerant Ensifer. Our findings suggest that the success of Ensifer in a structured environment is likely related to its ability to repurpose carbon via the glyoxylate shunt while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits like motility, stress resistance, and biofilm formation that underlie the degradation of chitin across our treatments and inform how they may ultimately alter carbon use efficiency. Together our results demonstrate that community functions like decomposition are sensitive to environmental conditions and more complex than the multi-enzyme pathways involved in depolymerization.

Rodriguez-Ramos, Josue A↗

Alkali Metal Cation Effects for Rapid C–H Activation by Iron(0) Complexes

C–H oxidative addition is a key reaction in organometallic catalysis, motivating efforts to accelerate it. Here, we examine an anionic beta-diketiminate-supported iron(0) species that was previously observed to activate C-H bonds with Na(15-crown-5), but not with K(18-crown-6) or Rb(18-crown-6). Though crown ethers are usually seen as beneficial due to their ability to solubilize alkali metal cations, we observe that removing the crown ether leads to rapid and complete oxidative addition of the C-H bond even by K, Rb, and Cs. The products are iron(II) phenyl hydride complexes that exist as dimers bridged by the alkali metals. Neutron crystallography of the cesium complex verifies the presence and location of the bridging hydrides. It is likely that the crown-free alkali metal cations have greater Lewis acidity that enables them to facilitate oxidative addition of the C-H bond. This system gives insight on how to control the rate and favorability of C-H activation through manipulation of the countercation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Editorial: Resolving atmospheric flow in complex environments: recent experiments in terrain and forest canopies

The characterization of atmospheric flows in complex environments, which may include steep terrain slopes and heterogeneous vegetation and/or forest cover, is a long-standing challenge in boundary-layer meteorology. Atmospheric observations are complicated by the presence of transient, terrain-induced flow features, forest-canopy-atmosphere interactions, and atmospheric stability effects, not to mention the logistical hurdles involved with instrument deployment, data analysis, and quality control. Furthermore, challenges in atmospheric modeling arise due to numerical errors associated with complex terrain flows, as well as reliance on simplified parameterizations for unresolved processes such as turbulent mixing and land-surface or forest-canopy-atmosphere interactions. These modeling challenges are exacerbated in the so-called “gray zone,” wherein features of interest have length scales that are similar to the model grid spacing, or when the principal flow layer is smaller than the grid spacing (e.g., slope flows).

54 ENVIRONMENTAL SCIENCES↗

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

59 BASIC BIOLOGICAL SCIENCES↗

Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication

All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.

59 BASIC BIOLOGICAL SCIENCES↗

Multimodal parameter spaces of a complex multi-channel neuron model

One of the most common types of models that helps us to understand neuron behavior is based on the Hodgkin–Huxley ion channel formulation (HH model). A major challenge with inferring parameters in HH models is non-uniqueness: many different sets of ion channel parameter values produce similar outputs for the same input stimulus. Such phenomena result in an objective function that exhibits multiple modes (i.e., multiple local minima). This non-uniqueness of local optimality poses challenges for parameter estimation with many algorithmic optimization techniques. HH models additionally have severe non-linearities resulting in further challenges for inferring parameters in an algorithmic fashion. To address these challenges with a tractable method in high-dimensional parameter spaces, we propose using a particular Markov chain Monte Carlo (MCMC) algorithm, which has the advantage of inferring parameters in a Bayesian framework. The Bayesian approach is designed to be suitable for multimodal solutions to inverse problems. We introduce and demonstrate the method using a three-channel HH model. We then focus on the inference of nine parameters in an eight-channel HH model, which we analyze in detail. We explore how the MCMC algorithm can uncover complex relationships between inferred parameters using five injected current levels. The MCMC method provides as a result a nine-dimensional posterior distribution, which we analyze visually with solution maps or landscapes of the possible parameter sets. The visualized solution maps show new complex structures of the multimodal posteriors, and they allow for selection of locally and globally optimal value sets, and they visually expose parameter sensitivities and regions of higher model robustness. We envision these solution maps as enabling experimentalists to improve the design of future experiments, increase scientific productivity and improve on model structure and ideation when the MCMC algorithm is applied to experimental data.

97 MATHEMATICS AND COMPUTING↗

Sustainable production of extracellular polymeric substances and iron or copper complex from glutinous rice processing wastewater

Essential trace minerals play vital roles in maintaining human and animal health. However, an overdose of the existing inorganic trace minerals is prone to induce detrimental effects that outweigh positive benefits. In this study, an extracellular polymeric substances (EPS)-producing bacterium, identified as Bacillus licheniformis CCTCC M2020298, was isolated from marine using glutinous rice processing wastewater as enrichment medium. The EPS yield of Bacillus licheniformis CCTCC M2020298 could reach 8.62 g/L by using glutinous rice-processing wastewater containing medium. Furthermore, the potential of the EPS as a carrier for synthesizing EPS-iron (Fe) and EPS-copper (Cu) complex was explored. The results showed that the optimum condition for the synthesis EPS-Fe were the reaction temperature 70°C, pH 8.5–9.0 and mass ratio of EPS to trisodium citrate 2:1. The iron content of EPS-Fe reached 77.4 mg/g. Under the same condition, the copper content of EPS-Cu reached 90.7 mg/g. The elemental composition, functional groups and valence state of the mineral elements of EPS-Fe and EPS-Cu were well characterized. The EPS-Fe and EPS-Cu exhibited antioxidant activity in scavenging ·OH, DPPH and ·O 2− free radicals, thereby leading to reduced oxidative stress and apoptosis levels in human colonic epithelial cells in vitro . They also inhibited the proliferation of mouse hepatocellular carcinoma H22 and the growth of intestinal pathogens in vitro . This study provided an effective avenue for EPS production from glutinous rice processing wastewater and proved the potential of EPS-Fe and EPS-Cu complexes as a new-type comprehensive essential trace mineral supplement.

Chen, Zhen↗

Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors

Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure–activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC 50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.

59 BASIC BIOLOGICAL SCIENCES↗