Results for “functions and mappings”

DOE OSTI2024

HHL algorithm with mapping function and enhanced sampling for model predictive control in microgrids

Here, this paper presents a refined quantum Harrow Hassidim Lloyd (HHL) algorithm for microgrid control. The first novelty of the developed method is that a mapping shift function enables the original HHL algorithm to handle general linear equations with non-singular and indefinite matrix. Second, a method of Matrix Extension for Amplifying Sampling Probabilities of Intended Solution (ME-ASPI) is proposed to design the reformulated linear algebraic equations, allowing for improved sampling efficiency of the quantum tomography in the refined HHL algorithm. Then, we applied the method to solve the model predictive control (MPC) problem in nonlinear dynamical microgrids. Specifically, with the ME-ASPI method, the refined HHL algorithm can effectively obtain the intended partial optimal control inputs for MPC. The optimization of quadratic programming problem in each time step of MPC is transformed into a linear system problem, which is addressed by the proposed quantum solver through using only partial information, with the time complexity improved from $\mathscr{O}(\mathscr{N}^{2.37286})$ classically to $\mathscr{O}(\mathscr{N}^{2} log \mathscr{N}$ x $p$ log $p)$ in quantum. Numerical examples have validated the effectiveness of the refined HHL algorithm with the proposed mapping function and the ME-ASPI method. By leveraging quantum properties, the proposed method provides a hybrid quantum–classical framework for microgrid control. This generic method can also potentially tackle many other challenges in analyzing and controlling general complex engineered systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

A functional map of HIV-host interactions in primary human T cells

Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

A cohesive zone treatment for the material point method involving problems of large deformation and damage

A new algorithm is described that permits the use of cohesive zones in the material point method for problems involving large deformation and fracture. In contrast to previous cohesive zone implementations, this method does not utilize massless surface-element particles. Instead, cohesive tractions are computed using the shape function mappings from a reference grid configuration in combination with explicitly defined particle surface normals and surface positions. These normals and relative surface positions are updated each time step according to particle deformation. The tractions are converted to cohesive forces using the nodal areas and mapped back to particles using the same reference shape function mappings. These forces are then remapped by conventional particle-to-grid interpolation as external forces using the current-configuration shape-function mappings. This allows highly compliant cohesive zones to function over jump displacements larger than a grid cell. Upon damage, these interfaces can revert to conventional multi-field contact surfaces. This approach is general and readily applies to two and three dimensions as well as being compatible with damage-field gradient partitioning offering exceptional computational flexibility. The framework for this method enables other capabilities, such as improved contact precision using explicitly defined surface normals and positions, and a method to mitigate spurious material damage at weak discontinuities between stiff brittle materials and soft or compliant materials.

Cohesive zone↗

DOE OSTI2024

Exploring the role of biotic factors in regulating the spatial variability in land surface phenology across four temperate forest sites

Here, land surface phenology (LSP), the characterization of plant phenology with satellite data, is essential for understanding the effects of climate change on ecosystem functions. Considerable LSP variation is observed within local landscapes, and the role of biotic factors in regulating such variation remains underexplored. In this study, we selected four National Ecological Observatory Network terrestrial sites with minor topographic relief to investigate how biotic factors regulate intra-site LSP variability. We utilized plant functional type (PFT) maps, functional traits, and LSP data to assess the explanatory power of biotic factors for the start and end of season (SOS and EOS) variability. Our results indicate that PFTs alone explain only 0.8–23.4% of intra-site SOS and EOS variation, whereas including functional traits significantly improves explanatory power, with cross-validation correlations ranging from 0.50 to 0.85. While functional traits exhibited diverse effects on SOS and EOS across different sites, traits related to competitive ability and productivity were important for explaining both SOS and EOS variation at these sites. These findings reveal that plants exhibit diverse phenological responses to comparable environmental conditions, and functional traits significantly contribute to intra-site LSP variability, highlighting the importance of intrinsic biotic properties in regulating plant phenology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

HarDWR - Harmonized Water Rights Records

For a detailed description of the database of which this record is only one part, please see the HarDWR meta-record. Here we present a new dataset of western U.S. water rights records. This dataset provides consistent unique identifiers for each spatial unit of water management across the domain, unique identifiers for each water right record, and a consistent categorization scheme that puts each water right record into one of 7 broad use categories. These data were instrumental in conducting a study of the multi-sector dynamics of intersectoral water allocation changes through water markets (Grogan et al., in review). Specifically, the data were formatted for use as input to a process-based hydrologic model, WBM, with a water rights module (Grogan et al., in review). While this specific study motivated the development of the database presented here, U.S. west water management is a rich area of study (e.g., Anderson and Woosly, 2005; Tidwell, 2014; Null and Prudencio, 2016; Carney et al, 2021) so releasing this database publicly with documentation and usage notes will enable other researchers to do further work on water management in the U.S. west. The raw downloaded data for each state is described in Lisk et al. (in review), as well as here. The dataset is a collection of objects stored within an RDate file, stateWaterRightsHarmonized.RData. Each object either describes how one should interact with the other objects, or contains the harmonized water rights data. Here is each object described in detail: states: A character vector containing the state names for those states in which data was collected for. More importantly, the index of the state name is also the index in which that state's data can be found in the various following list objects. For example, if California is the third index in this object, the data for California will also be in the third index for each accompanying list. rightsByState_ground: A list of data frames with the cleaned ground water rights collected from each state. The column headers for each data frame are: waterRightID - The unique identifying ID of the water right, the same identifier as its state uses. basinNum - The alpha-numeric identifier of the WMA the record belongs to. priorityDate - The priority date associated with the right. allocatedFlow - The maximum flow of the allocation in cubic feet per second (ft3s-1). source - Whether the right is for surface water or groundwater. origWaterUse - The original stated water use from the state. waterUse - The water use category under the unified use categories established here. rightsByState_surface: A list of the cleaned surface water rights collected from each state. See rightsByState_ground for more details on how the data is formatted. fullRightsRecs: A list of the combined groundwater and surface water records for each state. Essentially, these lists are the merging of rightsByState_ground and rightsByState_surface by state. See rightsByState_ground for more details on how the data is formatted. projProj: The spatial projection used for map creation in the beginning of the project. Specifically, the World Geodetic System (WGS84) as a coordinate reference system (CRS) string in PROJ.4 format. wmaStateLabel: The name and/or abbreviation for what each state legally calls their WMAs. h2oUseByState: A list of spatial polygon data frames which contain the area(s) in which each water right is claimed to be used. It should be noted that not all water right records have a listed area(s) of use in this object. Currently, only Idaho and Washington provided valid data to be included in this object. h2oDivByState: A list of spatial points data frames which identifies the location of the Point of Diversion for the state's water rights. It should be noted that not all water right records have a listed Point of Diversion in this object. spatialWMAByState: A list of spatial polygon data frames which contain the spatial WMA boundaries for each state. The only data contained within the table are identifiers for each polygon. It is worth reiterating that Arizona is the only state in which the surface and groundwater WMA boundaries are not the same. wmaIDByState: A list which contains the unique ID values of the WMAs for each state. plottingDim: A character vector used to inform mapping functions for internal map making. Each state is classified as either "tall" or "wide", to maximize space on a typical 8x11 page.

Economics↗

DOE OSTI2024

HarDWR - Harmonized Water Rights Records

For a detailed description of the database of which this record is only one part, please see the HarDWR meta-record. Here we present a new dataset of western U.S. water rights records. This dataset provides consistent unique identifiers for each spatial unit of water management across the domain, unique identifiers for each water right record, and a consistent categorization scheme that puts each water right record into one of 7 broad use categories. These data were instrumental in conducting a study of the multi-sector dynamics of intersectoral water allocation changes through water markets (Grogan et al., in review). Specifically, the data were formatted for use as input to a process-based hydrologic model, WBM, with a water rights module (Grogan et al., in review). While this specific study motivated the development of the database presented here, U.S. west water management is a rich area of study (e.g., Anderson and Woosly, 2005; Tidwell, 2014; Null and Prudencio, 2016; Carney et al, 2021) so releasing this database publicly with documentation and usage notes will enable other researchers to do further work on water management in the U.S. west. The raw downloaded data for each state is described in Lisk et al. (in review), as well as here. The dataset is a series of various files organized by state sub-directories. The first two characters of each file name is the abbreviation for the state the in which the file contains data for. After the abbreviation is the text which describes the contents of the file. Here is each file type described in detail: XXFullHarmonizedRights.csv: A file of the combined groundwater and surface water records for each state. Essentially, this file is the merging of XXGroundwaterHarmonizedRights.csv and XXSurfaceWaterHarmonizedRights.csv by state. The column headers for each of this type of file are: state - The name of the state the data comes from. FIPS - The two-digit numeric state ID code. waterRightID - The unique identifying ID of the water right, the same identifier as its state uses. priorityDate - The priority date associated with the right. origWaterUse - The original stated water use(s) from the state. waterUse - The water use category under the unified use categories established here. source - Whether the right is for surface water or groundwater. basinNum - The alpha-numeric identifier of the WMA the record belongs to. CFS - The maximum flow of the allocation in cubic feet per second (ft3s-1). Arizona is unique among the states, as its surface and groundwater resources are managed with two different sets of boundaries. So, for Arizona, the basinNum column is missing and instead there are two columns: surBasinNum - The alpha-numeric identifier of the surface water WMA the record belongs to. grdBasinNum - The alpha-numeric identifier of the groundwater WMA the record belongs to. XXStatePOD.shp: A shapefile which identifies the location of the Points of Diversion for the state's water rights. It should be noted that not all water right records in XXFullHarmonizedRights.csv have coordinates, and therefore may be missing from this file. XXStatePOU.shp: A shapefile which contains the area(s) in which each water right is claimed to be used. Currently, only Idaho and Washington provided valid data to include within this file. XXGroundwaterHarmonizedRights.csv: A file which contains only harmonized groundwater rights collected from each state. See XXFullHarmonizedRights.csv for more details on how the data is formatted. XXSurfaceWaterHarmonizedRights.csv: A file which contains only harmonized surface water rights collected from each state. See XXFullHarmonizedRights.csv for more details on how the data is formatted. Additionally, one file, stateWMALabels.csv, is not stored within a sub-directory. While we have referred to the spatial boundaries that each state uses to manage its water resources as WMAs, this term is not shared across all states. This file lists the proper name for each boundary set, by state. For those whom may be interested in exploring our code more in depth, we are also making available an internal data file for convenience. The file is in .RData format and contains everything described above as well as some minor additional objects used within the code calculating the cumulative curves. For completeness, here is a detailed description of the various objects which can be found within the .RData file: states: A character vector containing the state names for those states in which data was collected for. More importantly, the index of the state name is also the index in which that state's data can be found in the various following list objects. For example, if California is the third index in this object, the data for California will also be in the third index for each accompanying list. rightsByState_ground: A list of data frames with the cleaned ground water rights collected from each state. This object holds the the data that is exported to created the xxGroundwaterHarmonizedRights.csv files. rightsByState_surface: A list of data frames with the cleaned surface water rights collected from each state. This object holds the the data that is exported to created the xxSurfaceWaterHarmonizedRights.csv files. fullRightsRecs: A list of the combined groundwater and surface water records for each state. This object holds the the data that is exported to created the xxFullHarmonizedRights.csv files. projProj: The spatial projection used for map creation in the beginning of the project. Specifically, the World Geodetic System (WGS84) as a coordinate reference system (CRS) string in PROJ.4 format. wmaStateLabel: The name and/or abbreviation for what each state legally calls their WMAs. h2oUseByState: A list of spatial polygon data frames which contain the area(s) in which each water right is claimed to be used. It should be noted that not all water right records have a listed area(s) of use in this object. Currently, only Idaho and Washington provided valid data to be included in this object. h2oDivByState: A list of spatial points data frames which identifies the location of the Point of Diversion for the state's water rights. It should be noted that not all water right records have a listed Point of Diversion in this object. spatialWMAByState: A list of spatial polygon data frames which contain the spatial WMA boundaries for each state. The only data contained within the table are identifiers for each polygon. It is worth reiterating that Arizona is the only state in which the surface and groundwater WMA boundaries are not the same. wmaIDByState: A list which contains the unique ID values of the WMAs for each state. plottingDim: A character vector used to inform mapping functions for internal map making. Each state is classified as either "tall" or "wide", to maximize space on a typical 8x11 page. The code related to the creation of this dataset can be viewed within HarDWR GitHub Repository/dataHarmonization.

Economics↗

DOE OSTI2020

Symbiotic niche mapping reveals functional specialization by two ectomycorrhizal fungi that expands the host plant niche

Mutualisms are ubiquitous in natural systems, but less is known about how these positive interactions influence species distributions compared with antagonistic interactions, such as competition and predation. The niche concept is one useful approach for thinking about factors that shape species ranges, which we apply here towards understanding how the nature of plant-mycorrhizal symbioses change across large environmental gradients. We used a continuous niche mapping approach to examine how two ectomycorrhizal fungi (Thelephora terrestris, Suillus pungens) impact pine seedling growth across a two-dimensional soil nitrogen (N) and phosphorus (P) gradient. We found that ectomycorrhizal fungi improved plant growth most in nutrient addition treatments with highly imbalanced N:P ratios, demonstrating that mycorrhizal benefits depend on interactions between niche axes. Nevertheless, T. terrestris (highN:lowP) and S. pungens (lowN:highP) benefited plants most at opposite ends of the resource ratio spectrum, consistent with niche partitioning and functional specialization. While ectomycorrhizal fungi are often thought of as being most beneficial for nitrogen uptake, our results suggest that members of the Thelephoraceae may specialize in improving plant P uptake. Ectomycorrhizal colonization by a single fungus increased plant niche volume (calculated as convex hull volumes of plant growth response surfaces across N and P gradients) compared to non-mycorrhizal control plants and shows the overall positive effects of mutualisms on plant niche volume. Despite plant host benefits in S. pungens and T. terrestris single species treatments, the presence of both fungi together decreased plant niche volume. The lack of functional complementarity, despite functional specialization, indicates that in some environments, either fungal competition or the cost of maintaining a suboptimal mycorrhizal partner can limit the benefits of a higher quality partner. The niche mapping approach we present has the potential to answer fundamental questions about the dimensions of functional diversity in ectomycorrhizal fungi and the distributions of mycorrhizal symbioses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

UAS remote sensing (DJI Phantom 4 RTK platform): RGB orthomosaic, digital surface and canopy height models, plant functional type map, Seward Peninsula, Alaska, 2019

Airborne remote sensing data collected using a DJI Phantom 4 RTK unoccupied aerial system (UAS) ? operated by the University of Maine Wheatland Geospatial Lab (https://wheatlandlab.org/). This package includes data from 17 flights flown over the NGEE-Arctic Council, Kougarok, Kougarok Mile80, Teller, and Teller Mile32 sites in July 2019. The Phantom 4 RTK is a drone platform that collects very high spatial resolution optical red/green/blue (RGB) imagery. Derived image products include point cloud, ortho-mosaiced RGB, a digital surface model (DSM) using the structure from motion (SfM) technique, and a canopy height model (CHM). Unprocessed and processed data products (1,000+ files) are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *hdr,), ENVI image file (*.dat), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning

The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence–function relationships in many phage–bacterial systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Regression models using shapes of functions as predictors

Functional variables are often used as predictors in regression problems. A commonly used parametric approach, called scalar-on-function regression, uses the $\mathbb L^2$ inner product to map functional predictors into scalar responses. This method can perform poorly when predictor functions contain undesired phase variability, causing phases to have disproportionately large influence on the response variable. One past solution has been to perform phase–amplitude separation (as a pre-processing step) and then use only the amplitudes in the regression model. In this paper, we propose a more integrated approach, termed elastic functional regression model (EFRM), where phase-separation is performed inside the regression model, rather than as a pre-processing step. This approach generalizes the notion of phase in functional data, and is based on the norm-preserving time warping of predictors. Due to its invariance properties, this representation provides robustness to predictor phase variability and results in improved predictions of the response variable over traditional models. We demonstrate this framework using a number of datasets involving gait signals, NMR data, and stock market prices.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Calibration of parallel bond parameters in bonded particle models via physics-informed adaptive moment optimisation

This study proposes an automated calibration procedure for bond parameters in bonded discrete element modelling. By exploring the underlying physical correlations between microscopic parameters of bonds and macroscopic strength parameters of the continuum to be modelled, the microscopic shear strength and tensile strength are identified as independent variables for calibration purpose. Then a physics-informed iterative scheme is proposed to automatically approximate the bond parameters by viewing the micro-macro relation as an implicitly defined mathematical mapping function. As a result of highly non-convex features of this implicit mapping, the adaptive moment estimation (Adam), which is especially suitable for problems with noisy gradients, is adopted as the basic iterative scheme, in conjunction with other numerical techniques to approximately evaluate the partial derivatives involved. The whole procedure offers a simple and effective framework for bond parameter calibration. Finally, a numerical example of SiC ceramic is provided for validation. By compared with some existing calibration methods, the proposed method shows significant advantages in terms of calibration efficiency and accuracy.

42 ENGINEERING↗

DOE OSTI2024

Maps of plant functional type (PFT), PFT fractional cover, and uncertainty derived from AVIRIS-NG data, 2019, Seward Peninsula

Remote sensing maps of plant functional type (PFT), PFT fractional cover (fCover), and fCover uncertainty maps derived from NASA’s Airborne Visible / Infrared Imaging Spectrometer – Next Generation (AVIRIS-NG). The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA’s Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE’s Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for flights over Teller, Kougarok, and Council watersheds created using eight AVIRIS-NG imagery collected in July, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as GIS *.kml files. Detailed description of the methods for each map are provided in Yang et al., (2023). These datasets are provided in support of Yang et al., (In revision) “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Inversion of Time-Lapse Seismic Reservoir Monitoring Data Using CycleGAN: A Deep Learning-Based Approach for Estimating Dynamic Reservoir Property Changes

Carbon capture and storage is being pursued globally as a geoengineering measure for reducing the emission of anthropogenic CO 2 the atmosphere. Comprehensive monitoring, verification, and accounting programs must be established for demonstrating the safe storage of injected CO 2 . One of the most commonly deployed monitoring techniques is time-lapse seismic reservoir monitoring (also known as 4-D seismic), which involves comparing 3-D seismic survey data taken at the same study site but over different times. Analyses of 4-D seismic data volumes can help improve the quality of storage reservoir characterization, track the movement of injected CO 2 plume, and identify potential CO 2 spillover/leakage from the storage reservoirblue. However, the derivation of high-resolution CO 2 saturation maps from 4-D seismic data is a highly nonlinear and ill-posed inverse problem, often requiring significant computational effort. In this research, we apply a physics-based deep learning method to facilitate the solution of both the forward and inverse problems in seismic inversion while honoring physical constraints. A cycle generative adversarial neural network (CycleGAN) model is trained to learn the bidirectional functional mappings between the reservoir dynamic property changes and seismic attribute changes, such that both forward and inverse solutions can be obtained efficiently from the trained model. We show that our CycleGAN-based approach not only improves the reliability of 4-D seismic inversion but also expedites the quantitative interpretation. Our deep learning-based workflow is generic and can be readily used for reservoir characterization and reservoir model updates involving the use of 4-D seismic data.

58 GEOSCIENCES↗

DOE OSTI2021

The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa

Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Prediction and uncertainty quantification of shale well performance using multifidelity Monte Carlo

Uncertainty quantification is an integral component of reservoir management, especially considering the inherent uncertainty in subsurface systems. While a standard practice to estimate the uncertainty, Monte Carlo (MC) simulation is computationally intense when the sampling population comprises high-fidelity simulations. Alternatively, the Multi-fidelity Monte Carlo (MFMC) simulation overcomes this computational intensity by integrating low- and high-fidelity simulations. Our goal is to minimize the number of expensive high-fidelity simulations while maintaining accuracy and using numerous fast and cheap low-fidelity simulations to efficiently sample to input parameter space of interest. We selected gas production from unconventional wells to demonstrate the potential speedups and accuracy of the MFMC approach. The model fidelity usually determines the trade-off between accuracy and efficiency. While the high-fidelity model is more accurate, the low-fidelity model is more efficient. Our high-fidelity simulation includes reservoir simulations of a hydraulically fractured well. On the other hand, our low-fidelity model comprises the parallel-plate flow model. We used differential programming to efficiently solve the 1D flow model, where automatic differentiation is used to efficiently compute the gradients. We matched the production profile of high-fidelity simulations with our low-fidelity simulations. Then, we used a support vector regression to map the high- and low-fidelity input parameters. The mapping function is essential to tune the low-dimensional parameter space of the low-fidelity model to the high-dimensional parameter space of the high-fidelity model. We found that we can use a combination of 9 high fidelity and 10,000 low fidelity simulations to efficiently and accurately simulate pressure management. This method is at least two orders of magnitude faster than only using high-fidelity simulations. Finally, from a broader perspective, MFMC could efficiently estimate the uncertainty of various systems and models, integrating low- and high-fidelity models.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2024

A deep learning-based workflow for fast prediction of 3D state variables in geological carbon storage: A dimension reduction approach

Deep learning (DL) models are extensively used as surrogate models for high-fidelity simulations of multiphase fluid flow in porous media at large scales, enabling fast forecasts of the spatial–temporal evolution of three-dimensional (3D) state variables in geological carbon storage (GCS). However, training these models in high-dimensional space remains computationally demanding and prone to overfitting because of limited training data. This paper presents a novel workflow to address these challenges by integrating dimension reduction (DR) methods. Here, the proposed workflow employed pre-trained DR models to extract the latent variables of geological models and state variables and utilized the multi-layer perceptron (MLP) for constructing mapping functions between the input and output variables in latent spaces. Subsequently, the pre-trained reconstruction models converted the MLP-predicted latent state variables to their original high-dimensional form. Furthermore, we proposed a novel strategy for the DR and reconstruction of 3D saturation fields to account for the unique data characteristics of sparsity, nonuniformity, and discontinuity. The proposed strategy applied PCA and inverse PCA for 2D average saturation fields and developed a DL-based 3D reconstruction model, leveraging three 2D average saturation fields as input to produce a 3D saturation field as output. The pre-training of DR and reconstruction models and training of MLP models were conducted on 84 Gulf of Mexico (GoM) simulations and evaluated on 12 testing simulations. Each simulation contained 720 monthly time steps, with the first 360 months as the injection period and the rest as the post-injection period. The proposed workflow, incorporating DR and DL models, accurately predicts the normalized 3D pressure fields, achieving mean square error (MSE) of 2.92 × 10 -7 compared to the ground truth obtained from a full-physics simulator. Furthermore, the proposed strategy outperformed PCA and convolutional autoencoder (CAE) models on 3D saturation fields, resulting in minor workflow prediction errors with an MSE of 2.93 × 10 -5 . The results suggest the proposed workflow provides sufficient predictive fidelity across temporal and spatial scales, and enables a speedup of 160 times compared to the full-physics simulator, facilitating improved decision-making and risk assessment for large-scale GCS management in real-time scenarios.

3D reconstruction model↗

DOE OSTI2020

Dissolution of a cylindrical disk in Hele-Shaw flow: a conformal-mapping approach

Here we apply conformal mapping to find the evolving shapes of a dissolving cylinder in a potential flow. Similar equations can be used to describe melting in a flowing liquid phase. Results are compared with microfluidic experiments and numerical simulations. Shapes predicted by conformal mapping agree almost perfectly with experimental observations, after a modest (20 %) rescaling of the time. Finite-volume simulations show that the differences with experiment are connected to the underlying assumptions of the analytical model: potential flow and diffusion-limited dissolution. Approximate solutions of the equations describing the evolution of the shape of the undissolved solid can be derived from a Laurent expansion of the mapping function from the unit circle. Asymptotic expressions for the evolution of the area of the disk and the shift in its centre of mass have been derived at low and high Péclet number. Analytic approximations to the leading-order Laurent coefficients provide additional insight into the mechanisms underlying pore-scale dissolution.

58 GEOSCIENCES↗

DOE OSTI2021

Trap-Assisted Dopant Compensation Prevents Shunting in Poly-Si Passivating Interdigitated Back Contact Silicon Solar Cells

Using a trap-assisted compensation model, we explain why polycrystalline Si (poly-Si) passivating contacts are able to achieve low leakage current between the doped fingers of interdigitated back contact (IBC) monocrystalline Si solar cells despite mixing of boron and phosphorus dopants in the isolation region. The fill factor of IBC solar cells is strongly affected by the electrical isolation region between n- and p-type fingers, as this region is critical in minimizing shunting losses. During fabrication of monocrystalline Si solar cells with poly-Si passivating contacts, the intrinsic poly-Si isolation region inevitably gets contaminated with both p- and n-type dopants. Using dopant profiles measured with time-of-flight secondary ion mass spectrometry and scanning probe measurements of the isolation region, we demonstrate that despite the dopant spreading during cell processing, a well-compensated region between the doped fingers exists that prevents shunting. The trap-assisted dopant compensation mechanism significantly widens the compensated region to tens of microns, where the residual dopant densities are below the trap density. This enables a high-resistivity region, resulting in low shunt current. Using one-dimensional (1-D) finite element diode simulations, we identify the design parameters and experimental conditions under which a sufficiently resistive region can form. Furthermore, our measurements of 2-D local resistivity and work function maps across the isolation region using scanning spreading resistance microscopy and Kelvin probe force microscopy demonstrate the existence of a highly resistive, wide compensated region and confirm our proposed compensation mechanism. For our structures, this region is ~25 µm in width within a ~150 µm wide finger isolation region with nearly 3 orders of magnitude higher resistivity than the regions dominated by a single type of dopant.

14 SOLAR ENERGY↗