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Liu, Yang

Publications and source records attributed to Liu, Yang.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Data-driven modeling of coarse mesh turbulence for reactor transient analysis using convolutional recurrent neural networks

Advanced nuclear reactors often exhibit complex thermal-fluid phenomena during transients. To accurately capture such phenomena, a coarse-mesh three-dimensional (3-D) modeling capability is desired for modern nuclear-system code. In the coarse-mesh 3-D modeling of advanced-reactor transients that involve flow and heat transfer, accurately predicting the turbulent viscosity is a challenging task that requires an accurate and computationally efficient model to capture the unresolved fine-scale turbulence. In this work, we propose a data-driven coarse-mesh turbulence model based on local flow features for the transient analysis of thermal mixing and stratification in a sodium-cooled fast reactor. The model has a coarse mesh setup to ensure computational efficiency, while it is trained by fine-mesh computational fluid dynamics (CFD) data to ensure accuracy. A novel neural network architecture, combining a densely connected convolutional network and a long-short-term-memory network, is developed that can efficiently learn from the spatial temporal CFD transient simulation results. The neural network model was trained and optimized on a loss-of flow transient and demonstrated high accuracy in predicting the turbulent viscosity field during the whole transient. The trained model's generalization capability was also investigated on two other transients with different inlet conditions. The study demonstrates the potential of applying the proposed data-driven approach to support the coarse-mesh multi-dimensional modeling of advanced reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancer

Redox regulation of breast cancer underlies malignant progression. Loss of the antioxidant glutathione peroxidase 2 in breast cancer cells increases reactive oxygen species, thereby activating hypoxia inducible factor-α (HIF1α) signaling. This in turn causes vascular malfunction, resulting in hypoxia and metabolic heterogeneity. HIF1α suppresses oxidative phosphorylation and stimulates glycolysis (the Warburg effect) in most of the tumor, except for one cancer subpopulation, which was capable of using both metabolic modalities. Hence, adopting a hybrid metabolic state may allow tumor cells to survive under aerobic or hypoxic conditions, a vulnerability that may be exploited for therapeutic targeting by either metabolic or redox-based strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Role of climate goals and clean-air policies on reducing future air pollution deaths in China: a modelling study

Over 3 million people still die every year from diseases caused by exposure to outdoor PM 2.5 air pollution, and more than a quarter of these premature deaths occur in China. In addition to clean air policies that target pollution emissions, climate policies aimed at reducing fossil-fuel CO 2 emissions (e.g., to avoid 1.5°C of warming) may also dramatically improve air quality and public health. Yet there has been no comprehensive accounting of public health outcomes under different energy pathways and local clean air management decisions in China. In particular, further research is needed to understand the relationships among climate and clean air polices and future health burdens in China, where an aging population will further exacerbate the impacts of air pollution. Using a China-focused integrated assessment model (GCAM-China) and a dynamic emission projection model (DPEC), we project future Chinese air quality in scenarios spanning a range of global climate targets (i.e. 1.5°0C, 2°C, NDC, unambitious, baseline, and 4.5°C) as well as national clean air actions (i.e. 2015-pollution, current-pollution, and ambitious-pollution). We then evaluate the health impacts of PM2·5 air pollution of scenario matrix using the chemical transport model WRF-CMAQ and the latest epidemiological concentration–response (C-R) functions (i.e. GBD2019). We find that, without ambitious climate mitigation (e.g., under current NDC pledges), Chinese deaths related the PM2.5 air pollution do not substantially decrease—and often grow—by mid-century, regardless of clean air policies and air quality improvements. For example, in scenarios that track China’s current NDC pledge and deploy best-available pollution control technologies, PM 2.5 -related deaths in China decrease slightly by 2030 (to 1.2 million per year) but no further by mid-century (Ambitious-pollution-NDC-goals; 1.2 million deaths in 2050) despite substantial and continuous improvements in population-weighted air quality (27.2 to 16.0 µg/m 3 from 2030 to 2050). The contrary trends of improving air quality and increasing PM 2·5 -related deaths in many of our scenarios reveals the extent to which extra efforts are needed to compensate for the established fact of increasing age of China’s population in future. Substantial decreases in China’s PM 2.5 -related deaths and age-standardized death rates (e.g., decreasing by 0.3–0.5 million deaths and 10.2–14.2 per 100,000 population age-standardized death rates per year) thus require the sort of large-scale transition in energy sources entailed by scenarios that meet international climate goals to avoid 1.5°C and 2°C of warming (Ambitious-pollution-2°C- and 1.5°C-goals).

58 GEOSCIENCES↗
DOE OSTI2022

Solving the structure of “single-atom” catalysts using machine learning – assisted XANES analysis

We show that "single-atom” catalysts (SACs) have demonstrated excellent activity and selectivity in challenging chemical transformations such as photocatalytic CO 2 reduction. For heterogeneous photocatalytic SAC systems, it is essential to obtain sufficient information of their structure at the atomic level in order to understand reaction mechanisms. In this work, a SAC was prepared by grafting a molecular cobalt catalyst on a light-absorbing carbon nitride surface. Due to the sensitivity of the X-ray absorption near edge structure (XANES) spectra to subtle variances in the Co SAC structure in reaction conditions, different machine learning (ML) methods, including principal component analysis, K-means clustering, and neural network (NN), were utilized for in situ Co XANES data analysis. As a result, we obtained quantitative structural information of the SAC nearest atomic environment thereby extending the NN-XANES approach previously demonstrated for nanoparticles and size-selective clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Replication Data for: Latent Representation Learning for Structural Characterization of Catalysts

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Butterfly-Accelerated Volume Integral Equation Solver for Broad Permittivity and Large-Scale Electromagnetic Analysis

In this work, a butterfly-accelerated volume integral equation (VIE) solver is proposed for fast and accurate electromagnetic (EM) analysis of scattering from heterogeneous objects. The proposed solver leverages the hierarchical off-diagonal butterfly (HOD-BF) scheme to construct the system matrix and obtain its approximate inverse, used as a preconditioner. Complexity analysis and numerical experiments validate the O(N log 2 N) construction cost of the HOD-BF-compressed system matrix and O(N log 1.5 N) inversion cost for the preconditioner, where N is the number of unknowns in the high-frequency EM scattering problem. For many practical scenarios, the proposed VIE solver requires less memory and computational time to construct the system matrix and obtain its approximate inverse compared to a H matrix-accelerated VIE solver. The accuracy and efficiency of the proposed solver have been demonstrated via its application to the EM analysis of large-scale canonical and real-world structures comprising of broad permittivity values and involving millions of unknowns.

42 ENGINEERING↗
DOE OSTI2021

Machine Learning Assisted Safety Modeling and Analysis of Advanced Reactors

With the advances in computational power and numerical methods, analysts can now rely on first-principle simulations to predict ultra-fine details in a variety of applications. Advances in machine learning (ML) have produced algorithms that can now learn high-level abstractions via hierarchical models. This project aims to leverage advances in ML techniques and the available high-resolution simulation data to develop a novel modeling and simulation (M\&S) methodology for reactor safety analysis. While application-agnostic ML techniques are available, complex physics constraints need to be incorporated into ML techniques to build ML-based closures for computationally efficient predictive simulations. This project intends to develop a physics-guided data-driven multi-scale methodology for M\&S of advanced reactors. The project focuses on thermal fluid (T/F) phenomena, which play major roles in advanced reactor safety. Specifically, we propose a data-driven coarse-mesh turbulence model based on local flow features for the transient analysis of thermal mixing and stratification in a sodium-cooled fast reactor (SFR). The model has a coarse-mesh setup to ensure computational efficiency, while it is trained by fine-mesh computational fluid dynamics (CFD) data with Reynolds-averaged Navier-Stokes (RANS) turbulence model to ensure accuracy. Three different neural networks are developed and tested for loss-of-flow transients in the hot pool of SFR, i.e. the densely connected convolutional neural network (DCNN), long-short-term-memory network based on proper orthogonal decomposition (POD-LSTM), and the DCNN informed by LSTM (DCNN-LSTM). The performances of these three neural networks are evaluated based on baseline models. The DCNN-LSTM model has been chosen for further hyperparameter optimization. Furthermore, based on a simplified two-dimensional case, uncertainty quantification (UQ) of the developed ML-based closure are investigated with three methods, i.e. Monte Carlo dropout, deep ensemble, and Bayesian neural network. The developed ML-based turbulent viscosity closure relation based on deep ensemble is then integrated into the system analysis module SAM and serves as a term in the conservation equations. Such a SAM-ML based procedure guarantees that the obtained results are consistent with the physical constraints of the thermal-fluid system. The SAM-ML simulation on the same loss-of-flow transient showed comparable accuracy with the CFD simulation but with a much coarser mesh setup. Last but not least, the ML-based closure improvement with the support of higher-fidelity data from large eddy simulation (LES) is discussed. As a first step towards this direction, a baseline LES simulation is performed to obtain comparable data with RANS results. Based on the early results, future investigation on further improving the ML-based closure is discussed. We believe the developed approach that combines scientific machine learning with nuclear system analysis code can benefit the advanced reactor community as more accurate safety analyses will better characterize reactor safety margins and reduce licensing efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Nickel particle–enabled width-controlled growth of bilayer molybdenum disulfide nanoribbons

Transition metal dichalcogenides exhibit a variety of electronic behaviors depending on the number of layers and width. Therefore, developing facile methods for their controllable synthesis is of central importance. We found that nickel nanoparticles promote both heterogeneous nucleation of the first layer of molybdenum disulfide and simultaneously catalyzes homoepitaxial tip growth of a second layer via a vapor-liquid-solid (VLS) mechanism, resulting in bilayer nanoribbons with width controlled by the nanoparticle diameter. Simulations further confirm the VLS growth mechanism toward nanoribbons and its orders of magnitude higher growth speed compared to the conventional noncatalytic growth of flakes. Width-dependent Coulomb blockade oscillation observed in the transfer characteristics of the nanoribbons at temperatures up to 60 K evidences the value of this proposed synthesis strategy for future nanoelectronics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Mars: new insights and unresolved questions

Mars exploration motivates the search for extraterrestrial life, the development of space technologies, and the design of human missions and habitations. Here, we seek new insights and pose unresolved questions relating to the natural history of Mars, habitability, robotic and human exploration, planetary protection, and the impacts on human society.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗